test_tomo_reconstruct: general.py annotate

annotate general.py @ 0:98e23dff1de2 draft default tip

planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty

author	rv43
date	Tue, 21 Mar 2023 16:22:42 +0000
parents
children

rev	line source
0 98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1 #!/usr/bin/env python3
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	2
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	3 #FIX write a function that returns a list of peak indices for a given plot
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	4 #FIX use raise_error concept on more functions to optionally raise an error
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	5
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	6 # -- coding: utf-8 --
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	7 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	8 Created on Mon Dec 6 15:36:22 2021
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	9
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	10 @author: rv43
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	11 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	12
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	13 import logging
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	14 logger=logging.getLogger(__name__)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	15
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	16 import os
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	17 import sys
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	18 import re
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	19 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	20 from yaml import safe_load, safe_dump
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	21 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	22 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	23 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	24 import h5py
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	25 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	26 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	27 import numpy as np
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	28 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	29 import matplotlib.pyplot as plt
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	30 import matplotlib.lines as mlines
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	31 from matplotlib import transforms
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	32 from matplotlib.widgets import Button
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	33 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	34 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	35
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	36 from ast import literal_eval
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	37 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	38 from asteval import Interpreter, get_ast_names
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	39 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	40 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	41 from copy import deepcopy
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	42 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	43 from sympy import diff, simplify
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	44 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	45 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	46 from time import time
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	47
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	48
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	49 def depth_list(L): return(isinstance(L, list) and max(map(depth_list, L))+1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	50 def depth_tuple(T): return(isinstance(T, tuple) and max(map(depth_tuple, T))+1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	51 def unwrap_tuple(T):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	52 if depth_tuple(T) > 1 and len(T) == 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	53 T = unwrap_tuple(*T)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	54 return(T)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	55
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	56 def illegal_value(value, name, location=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	57 if not isinstance(location, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	58 location = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	59 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	60 location = f'in {location} '
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	61 if isinstance(name, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	62 error_msg = f'Illegal value for {name} {location}({value}, {type(value)})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	63 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	64 error_msg = f'Illegal value {location}({value}, {type(value)})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	65 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	66 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	67 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	68 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	69
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	70 def illegal_combination(value1, name1, value2, name2, location=None, raise_error=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	71 log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	72 if not isinstance(location, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	73 location = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	74 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	75 location = f'in {location} '
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	76 if isinstance(name1, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	77 error_msg = f'Illegal combination for {name1} and {name2} {location}'+ \
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	78 f'({value1}, {type(value1)} and {value2}, {type(value2)})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	79 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	80 error_msg = f'Illegal combination {location}'+ \
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	81 f'({value1}, {type(value1)} and {value2}, {type(value2)})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	82 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	83 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	84 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	85 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	86
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	87 def test_ge_gt_le_lt(ge, gt, le, lt, func, location=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	88 """Check individual and mutual validity of ge, gt, le, lt qualifiers
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	89 func: is_int or is_num to test for int or numbers
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	90 Return: True upon success or False when mutually exlusive
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	91 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	92 if ge is None and gt is None and le is None and lt is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	93 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	94 if ge is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	95 if not func(ge):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	96 illegal_value(ge, 'ge', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	97 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	98 if gt is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	99 illegal_combination(ge, 'ge', gt, 'gt', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	100 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	101 elif gt is not None and not func(gt):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	102 illegal_value(gt, 'gt', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	103 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	104 if le is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	105 if not func(le):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	106 illegal_value(le, 'le', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	107 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	108 if lt is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	109 illegal_combination(le, 'le', lt, 'lt', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	110 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	111 elif lt is not None and not func(lt):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	112 illegal_value(lt, 'lt', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	113 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	114 if ge is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	115 if le is not None and ge > le:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	116 illegal_combination(ge, 'ge', le, 'le', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	117 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	118 elif lt is not None and ge >= lt:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	119 illegal_combination(ge, 'ge', lt, 'lt', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	120 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	121 elif gt is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	122 if le is not None and gt >= le:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	123 illegal_combination(gt, 'gt', le, 'le', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	124 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	125 elif lt is not None and gt >= lt:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	126 illegal_combination(gt, 'gt', lt, 'lt', location, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	127 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	128 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	129
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	130 def range_string_ge_gt_le_lt(ge=None, gt=None, le=None, lt=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	131 """Return a range string representation matching the ge, gt, le, lt qualifiers
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	132 Does not validate the inputs, do that as needed before calling
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	133 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	134 range_string = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	135 if ge is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	136 if le is None and lt is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	137 range_string += f'>= {ge}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	138 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	139 range_string += f'[{ge}, '
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	140 elif gt is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	141 if le is None and lt is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	142 range_string += f'> {gt}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	143 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	144 range_string += f'({gt}, '
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	145 if le is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	146 if ge is None and gt is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	147 range_string += f'<= {le}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	148 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	149 range_string += f'{le}]'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	150 elif lt is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	151 if ge is None and gt is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	152 range_string += f'< {lt}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	153 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	154 range_string += f'{lt})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	155 return(range_string)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	156
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	157 def is_int(v, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	158 """Value is an integer in range ge <= v <= le or gt < v < lt or some combination.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	159 Return: True if yes or False is no
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	160 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	161 return(_is_int_or_num(v, 'int', ge, gt, le, lt, raise_error, log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	162
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	163 def is_num(v, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	164 """Value is a number in range ge <= v <= le or gt < v < lt or some combination.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	165 Return: True if yes or False is no
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	166 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	167 return(_is_int_or_num(v, 'num', ge, gt, le, lt, raise_error, log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	168
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	169 def _is_int_or_num(v, type_str, ge=None, gt=None, le=None, lt=None, raise_error=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	170 log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	171 if type_str == 'int':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	172 if not isinstance(v, int):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	173 illegal_value(v, 'v', '_is_int_or_num', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	174 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	175 if not test_ge_gt_le_lt(ge, gt, le, lt, is_int, '_is_int_or_num', raise_error, log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	176 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	177 elif type_str == 'num':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	178 if not isinstance(v, (int, float)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	179 illegal_value(v, 'v', '_is_int_or_num', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	180 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	181 if not test_ge_gt_le_lt(ge, gt, le, lt, is_num, '_is_int_or_num', raise_error, log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	182 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	183 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	184 illegal_value(type_str, 'type_str', '_is_int_or_num', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	185 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	186 if ge is None and gt is None and le is None and lt is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	187 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	188 error = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	189 if ge is not None and v < ge:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	190 error = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	191 error_msg = f'Value {v} out of range: {v} !>= {ge}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	192 if not error and gt is not None and v <= gt:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	193 error = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	194 error_msg = f'Value {v} out of range: {v} !> {gt}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	195 if not error and le is not None and v > le:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	196 error = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	197 error_msg = f'Value {v} out of range: {v} !<= {le}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	198 if not error and lt is not None and v >= lt:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	199 error = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	200 error_msg = f'Value {v} out of range: {v} !< {lt}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	201 if error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	202 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	203 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	204 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	205 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	206 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	207 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	208
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	209 def is_int_pair(v, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	210 """Value is an integer pair, each in range ge <= v[i] <= le or gt < v[i] < lt or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	211 ge[i] <= v[i] <= le[i] or gt[i] < v[i] < lt[i] or some combination.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	212 Return: True if yes or False is no
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	213 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	214 return(_is_int_or_num_pair(v, 'int', ge, gt, le, lt, raise_error, log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	215
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	216 def is_num_pair(v, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	217 """Value is a number pair, each in range ge <= v[i] <= le or gt < v[i] < lt or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	218 ge[i] <= v[i] <= le[i] or gt[i] < v[i] < lt[i] or some combination.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	219 Return: True if yes or False is no
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	220 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	221 return(_is_int_or_num_pair(v, 'num', ge, gt, le, lt, raise_error, log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	222
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	223 def _is_int_or_num_pair(v, type_str, ge=None, gt=None, le=None, lt=None, raise_error=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	224 log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	225 if type_str == 'int':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	226 if not (isinstance(v, (tuple, list)) and len(v) == 2 and isinstance(v[0], int) and
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	227 isinstance(v[1], int)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	228 illegal_value(v, 'v', '_is_int_or_num_pair', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	229 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	230 func = is_int
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	231 elif type_str == 'num':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	232 if not (isinstance(v, (tuple, list)) and len(v) == 2 and isinstance(v[0], (int, float)) and
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	233 isinstance(v[1], (int, float))):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	234 illegal_value(v, 'v', '_is_int_or_num_pair', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	235 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	236 func = is_num
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	237 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	238 illegal_value(type_str, 'type_str', '_is_int_or_num_pair', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	239 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	240 if ge is None and gt is None and le is None and lt is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	241 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	242 if ge is None or func(ge, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	243 ge = 2*[ge]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	244 elif not _is_int_or_num_pair(ge, type_str, raise_error=raise_error, log=log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	245 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	246 if gt is None or func(gt, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	247 gt = 2*[gt]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	248 elif not _is_int_or_num_pair(gt, type_str, raise_error=raise_error, log=log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	249 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	250 if le is None or func(le, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	251 le = 2*[le]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	252 elif not _is_int_or_num_pair(le, type_str, raise_error=raise_error, log=log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	253 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	254 if lt is None or func(lt, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	255 lt = 2*[lt]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	256 elif not _is_int_or_num_pair(lt, type_str, raise_error=raise_error, log=log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	257 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	258 if (not func(v[0], ge[0], gt[0], le[0], lt[0], raise_error, log) or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	259 not func(v[1], ge[1], gt[1], le[1], lt[1], raise_error, log)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	260 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	261 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	262
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	263 def is_int_series(l, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	264 """Value is a tuple or list of integers, each in range ge <= l[i] <= le or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	265 gt < l[i] < lt or some combination.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	266 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	267 if not test_ge_gt_le_lt(ge, gt, le, lt, is_int, 'is_int_series', raise_error, log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	268 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	269 if not isinstance(l, (tuple, list)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	270 illegal_value(l, 'l', 'is_int_series', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	271 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	272 if any(True if not is_int(v, ge, gt, le, lt, raise_error, log) else False for v in l):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	273 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	274 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	275
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	276 def is_num_series(l, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	277 """Value is a tuple or list of numbers, each in range ge <= l[i] <= le or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	278 gt < l[i] < lt or some combination.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	279 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	280 if not test_ge_gt_le_lt(ge, gt, le, lt, is_int, 'is_int_series', raise_error, log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	281 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	282 if not isinstance(l, (tuple, list)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	283 illegal_value(l, 'l', 'is_num_series', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	284 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	285 if any(True if not is_num(v, ge, gt, le, lt, raise_error, log) else False for v in l):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	286 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	287 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	288
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	289 def is_str_series(l, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	290 """Value is a tuple or list of strings.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	291 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	292 if (not isinstance(l, (tuple, list)) or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	293 any(True if not isinstance(s, str) else False for s in l)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	294 illegal_value(l, 'l', 'is_str_series', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	295 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	296 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	297
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	298 def is_dict_series(l, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	299 """Value is a tuple or list of dictionaries.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	300 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	301 if (not isinstance(l, (tuple, list)) or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	302 any(True if not isinstance(d, dict) else False for d in l)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	303 illegal_value(l, 'l', 'is_dict_series', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	304 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	305 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	306
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	307 def is_dict_nums(l, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	308 """Value is a dictionary with single number values
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	309 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	310 if (not isinstance(l, dict) or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	311 any(True if not is_num(v, log=False) else False for v in l.values())):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	312 illegal_value(l, 'l', 'is_dict_nums', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	313 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	314 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	315
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	316 def is_dict_strings(l, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	317 """Value is a dictionary with single string values
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	318 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	319 if (not isinstance(l, dict) or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	320 any(True if not isinstance(v, str) else False for v in l.values())):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	321 illegal_value(l, 'l', 'is_dict_strings', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	322 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	323 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	324
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	325 def is_index(v, ge=0, lt=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	326 """Value is an array index in range ge <= v < lt.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	327 NOTE lt IS NOT included!
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	328 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	329 if isinstance(lt, int):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	330 if lt <= ge:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	331 illegal_combination(ge, 'ge', lt, 'lt', 'is_index', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	332 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	333 return(is_int(v, ge=ge, lt=lt, raise_error=raise_error, log=log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	334
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	335 def is_index_range(v, ge=0, le=None, lt=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	336 """Value is an array index range in range ge <= v[0] <= v[1] <= le or ge <= v[0] <= v[1] < lt.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	337 NOTE le IS included!
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	338 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	339 if not is_int_pair(v, raise_error=raise_error, log=log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	340 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	341 if not test_ge_gt_le_lt(ge, None, le, lt, is_int, 'is_index_range', raise_error, log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	342 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	343 if not ge <= v[0] <= v[1] or (le is not None and v[1] > le) or (lt is not None and v[1] >= lt):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	344 if le is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	345 error_msg = f'Value {v} out of range: !({ge} <= {v[0]} <= {v[1]} <= {le})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	346 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	347 error_msg = f'Value {v} out of range: !({ge} <= {v[0]} <= {v[1]} < {lt})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	348 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	349 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	350 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	351 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	352 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	353 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	354
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	355 def index_nearest(a, value):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	356 a = np.asarray(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	357 if a.ndim > 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	358 raise ValueError(f'Invalid array dimension for parameter a ({a.ndim}, {a})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	359 # Round up for .5
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	360 value *= 1.0+sys.float_info.epsilon
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	361 return((int)(np.argmin(np.abs(a-value))))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	362
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	363 def index_nearest_low(a, value):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	364 a = np.asarray(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	365 if a.ndim > 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	366 raise ValueError(f'Invalid array dimension for parameter a ({a.ndim}, {a})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	367 index = int(np.argmin(np.abs(a-value)))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	368 if value < a[index] and index > 0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	369 index -= 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	370 return(index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	371
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	372 def index_nearest_upp(a, value):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	373 a = np.asarray(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	374 if a.ndim > 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	375 raise ValueError(f'Invalid array dimension for parameter a ({a.ndim}, {a})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	376 index = int(np.argmin(np.abs(a-value)))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	377 if value > a[index] and index < a.size-1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	378 index += 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	379 return(index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	380
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	381 def round_to_n(x, n=1):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	382 if x == 0.0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	383 return(0)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	384 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	385 return(type(x)(round(x, n-1-int(np.floor(np.log10(abs(x)))))))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	386
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	387 def round_up_to_n(x, n=1):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	388 xr = round_to_n(x, n)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	389 if abs(x/xr) > 1.0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	390 xr += np.sign(x)10*(np.floor(np.log10(abs(x)))+1-n)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	391 return(type(x)(xr))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	392
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	393 def trunc_to_n(x, n=1):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	394 xr = round_to_n(x, n)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	395 if abs(xr/x) > 1.0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	396 xr -= np.sign(x)10*(np.floor(np.log10(abs(x)))+1-n)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	397 return(type(x)(xr))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	398
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	399 def almost_equal(a, b, sig_figs):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	400 if is_num(a) and is_num(b):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	401 return(abs(round_to_n(a-b, sig_figs)) < pow(10, -sig_figs+1))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	402 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	403 raise ValueError(f'Invalid value for a or b in almost_equal (a: {a}, {type(a)}, '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	404 f'b: {b}, {type(b)})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	405 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	406
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	407 def string_to_list(s, split_on_dash=True, remove_duplicates=True, sort=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	408 """Return a list of numbers by splitting/expanding a string on any combination of
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	409 commas, whitespaces, or dashes (when split_on_dash=True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	410 e.g: '1, 3, 5-8, 12 ' -> [1, 3, 5, 6, 7, 8, 12]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	411 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	412 if not isinstance(s, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	413 illegal_value(s, location='string_to_list')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	414 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	415 if not len(s):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	416 return([])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	417 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	418 ll = [x for x in re.split('\s+,\s+\|\s+,\|,\s+\|\s+\|,', s.strip())]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	419 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	420 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	421 if split_on_dash:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	422 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	423 l = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	424 for l1 in ll:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	425 l2 = [literal_eval(x) for x in re.split('\s+-\s+\|\s+-\|-\s+\|\s+\|-', l1)]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	426 if len(l2) == 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	427 l += l2
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	428 elif len(l2) == 2 and l2[1] > l2[0]:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	429 l += [i for i in range(l2[0], l2[1]+1)]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	430 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	431 raise ValueError
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	432 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	433 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	434 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	435 l = [literal_eval(x) for x in ll]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	436 if remove_duplicates:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	437 l = list(dict.fromkeys(l))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	438 if sort:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	439 l = sorted(l)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	440 return(l)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	441
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	442 def get_trailing_int(string):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	443 indexRegex = re.compile(r'\d+$')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	444 mo = indexRegex.search(string)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	445 if mo is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	446 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	447 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	448 return(int(mo.group()))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	449
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	450 def input_int(s=None, ge=None, gt=None, le=None, lt=None, default=None, inset=None,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	451 raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	452 return(_input_int_or_num('int', s, ge, gt, le, lt, default, inset, raise_error, log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	453
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	454 def input_num(s=None, ge=None, gt=None, le=None, lt=None, default=None, raise_error=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	455 log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	456 return(_input_int_or_num('num', s, ge, gt, le, lt, default, None, raise_error,log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	457
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	458 def _input_int_or_num(type_str, s=None, ge=None, gt=None, le=None, lt=None, default=None,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	459 inset=None, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	460 if type_str == 'int':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	461 if not test_ge_gt_le_lt(ge, gt, le, lt, is_int, '_input_int_or_num', raise_error, log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	462 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	463 elif type_str == 'num':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	464 if not test_ge_gt_le_lt(ge, gt, le, lt, is_num, '_input_int_or_num', raise_error, log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	465 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	466 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	467 illegal_value(type_str, 'type_str', '_input_int_or_num', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	468 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	469 if default is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	470 if not _is_int_or_num(default, type_str, raise_error=raise_error, log=log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	471 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	472 if ge is not None and default < ge:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	473 illegal_combination(ge, 'ge', default, 'default', '_input_int_or_num', raise_error,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	474 log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	475 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	476 if gt is not None and default <= gt:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	477 illegal_combination(gt, 'gt', default, 'default', '_input_int_or_num', raise_error,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	478 log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	479 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	480 if le is not None and default > le:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	481 illegal_combination(le, 'le', default, 'default', '_input_int_or_num', raise_error,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	482 log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	483 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	484 if lt is not None and default >= lt:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	485 illegal_combination(lt, 'lt', default, 'default', '_input_int_or_num', raise_error,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	486 log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	487 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	488 default_string = f' [{default}]'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	489 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	490 default_string = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	491 if inset is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	492 if (not isinstance(inset, (tuple, list)) or any(True if not isinstance(i, int) else
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	493 False for i in inset)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	494 illegal_value(inset, 'inset', '_input_int_or_num', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	495 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	496 v_range = f'{range_string_ge_gt_le_lt(ge, gt, le, lt)}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	497 if len(v_range):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	498 v_range = f' {v_range}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	499 if s is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	500 if type_str == 'int':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	501 print(f'Enter an integer{v_range}{default_string}: ')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	502 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	503 print(f'Enter a number{v_range}{default_string}: ')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	504 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	505 print(f'{s}{v_range}{default_string}: ')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	506 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	507 i = input()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	508 if isinstance(i, str) and not len(i):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	509 v = default
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	510 print(f'{v}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	511 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	512 v = literal_eval(i)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	513 if inset and v not in inset:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	514 raise ValueError(f'{v} not part of the set {inset}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	515 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	516 v = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	517 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	518 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	519 logger.error('Unexpected error')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	520 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	521 raise ValueError('Unexpected error')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	522 if not _is_int_or_num(v, type_str, ge, gt, le, lt):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	523 v = _input_int_or_num(type_str, s, ge, gt, le, lt, default, inset, raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	524 return(v)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	525
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	526 def input_int_list(s=None, ge=None, le=None, split_on_dash=True, remove_duplicates=True,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	527 sort=True, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	528 """Prompt the user to input a list of interger and split the entered string on any combination
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	529 of commas, whitespaces, or dashes (when split_on_dash is True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	530 e.g: '1 3,5-8 , 12 ' -> [1, 3, 5, 6, 7, 8, 12]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	531 remove_duplicates: removes duplicates if True (may also change the order)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	532 sort: sort in ascending order if True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	533 return None upon an illegal input
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	534 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	535 return(_input_int_or_num_list('int', s, ge, le, split_on_dash, remove_duplicates, sort,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	536 raise_error, log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	537
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	538 def input_num_list(s=None, ge=None, le=None, remove_duplicates=True, sort=True, raise_error=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	539 log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	540 """Prompt the user to input a list of numbers and split the entered string on any combination
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	541 of commas or whitespaces
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	542 e.g: '1.0, 3, 5.8, 12 ' -> [1.0, 3.0, 5.8, 12.0]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	543 remove_duplicates: removes duplicates if True (may also change the order)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	544 sort: sort in ascending order if True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	545 return None upon an illegal input
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	546 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	547 return(_input_int_or_num_list('num', s, ge, le, False, remove_duplicates, sort, raise_error,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	548 log))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	549
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	550 def _input_int_or_num_list(type_str, s=None, ge=None, le=None, split_on_dash=True,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	551 remove_duplicates=True, sort=True, raise_error=False, log=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	552 #FIX do we want a limit on max dimension?
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	553 if type_str == 'int':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	554 if not test_ge_gt_le_lt(ge, None, le, None, is_int, 'input_int_or_num_list', raise_error,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	555 log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	556 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	557 elif type_str == 'num':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	558 if not test_ge_gt_le_lt(ge, None, le, None, is_num, 'input_int_or_num_list', raise_error,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	559 log):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	560 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	561 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	562 illegal_value(type_str, 'type_str', '_input_int_or_num_list')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	563 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	564 v_range = f'{range_string_ge_gt_le_lt(ge=ge, le=le)}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	565 if len(v_range):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	566 v_range = f' (each value in {v_range})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	567 if s is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	568 print(f'Enter a series of integers{v_range}: ')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	569 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	570 print(f'{s}{v_range}: ')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	571 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	572 l = string_to_list(input(), split_on_dash, remove_duplicates, sort)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	573 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	574 l = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	575 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	576 print('Unexpected error')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	577 raise
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	578 if (not isinstance(l, list) or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	579 any(True if not _is_int_or_num(v, type_str, ge=ge, le=le) else False for v in l)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	580 if split_on_dash:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	581 print('Invalid input: enter a valid set of dash/comma/whitespace separated integers '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	582 'e.g. 1 3,5-8 , 12')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	583 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	584 print('Invalid input: enter a valid set of comma/whitespace separated integers '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	585 'e.g. 1 3,5 8 , 12')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	586 l = _input_int_or_num_list(type_str, s, ge, le, split_on_dash, remove_duplicates, sort,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	587 raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	588 return(l)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	589
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	590 def input_yesno(s=None, default=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	591 if default is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	592 if not isinstance(default, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	593 illegal_value(default, 'default', 'input_yesno')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	594 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	595 if default.lower() in 'yes':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	596 default = 'y'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	597 elif default.lower() in 'no':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	598 default = 'n'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	599 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	600 illegal_value(default, 'default', 'input_yesno')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	601 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	602 default_string = f' [{default}]'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	603 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	604 default_string = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	605 if s is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	606 print(f'Enter yes or no{default_string}: ')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	607 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	608 print(f'{s}{default_string}: ')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	609 i = input()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	610 if isinstance(i, str) and not len(i):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	611 i = default
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	612 print(f'{i}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	613 if i is not None and i.lower() in 'yes':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	614 v = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	615 elif i is not None and i.lower() in 'no':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	616 v = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	617 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	618 print('Invalid input, enter yes or no')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	619 v = input_yesno(s, default)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	620 return(v)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	621
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	622 def input_menu(items, default=None, header=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	623 if not isinstance(items, (tuple, list)) or any(True if not isinstance(i, str) else False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	624 for i in items):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	625 illegal_value(items, 'items', 'input_menu')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	626 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	627 if default is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	628 if not (isinstance(default, str) and default in items):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	629 logger.error(f'Invalid value for default ({default}), must be in {items}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	630 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	631 default_string = f' [{items.index(default)+1}]'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	632 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	633 default_string = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	634 if header is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	635 print(f'Choose one of the following items (1, {len(items)}){default_string}:')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	636 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	637 print(f'{header} (1, {len(items)}){default_string}:')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	638 for i, choice in enumerate(items):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	639 print(f' {i+1}: {choice}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	640 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	641 choice = input()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	642 if isinstance(choice, str) and not len(choice):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	643 choice = items.index(default)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	644 print(f'{choice+1}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	645 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	646 choice = literal_eval(choice)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	647 if isinstance(choice, int) and 1 <= choice <= len(items):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	648 choice -= 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	649 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	650 raise ValueError
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	651 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	652 choice = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	653 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	654 print('Unexpected error')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	655 raise
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	656 if choice is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	657 print(f'Invalid choice, enter a number between 1 and {len(items)}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	658 choice = input_menu(items, default)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	659 return(choice)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	660
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	661 def assert_no_duplicates_in_list_of_dicts(l: list, raise_error=False) -> list:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	662 if not isinstance(l, list):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	663 illegal_value(l, 'l', 'assert_no_duplicates_in_list_of_dicts', raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	664 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	665 if any(True if not isinstance(d, dict) else False for d in l):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	666 illegal_value(l, 'l', 'assert_no_duplicates_in_list_of_dicts', raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	667 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	668 if len(l) != len([dict(t) for t in {tuple(sorted(d.items())) for d in l}]):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	669 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	670 raise ValueError(f'Duplicate items found in {l}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	671 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	672 logger.error(f'Duplicate items found in {l}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	673 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	674 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	675 return(l)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	676
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	677 def assert_no_duplicate_key_in_list_of_dicts(l: list, key: str, raise_error=False) -> list:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	678 if not isinstance(key, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	679 illegal_value(key, 'key', 'assert_no_duplicate_key_in_list_of_dicts', raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	680 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	681 if not isinstance(l, list):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	682 illegal_value(l, 'l', 'assert_no_duplicate_key_in_list_of_dicts', raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	683 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	684 if any(True if not isinstance(d, dict) else False for d in l):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	685 illegal_value(l, 'l', 'assert_no_duplicates_in_list_of_dicts', raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	686 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	687 keys = [d.get(key, None) for d in l]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	688 if None in keys or len(set(keys)) != len(l):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	689 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	690 raise ValueError(f'Duplicate or missing key ({key}) found in {l}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	691 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	692 logger.error(f'Duplicate or missing key ({key}) found in {l}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	693 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	694 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	695 return(l)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	696
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	697 def assert_no_duplicate_attr_in_list_of_objs(l: list, attr: str, raise_error=False) -> list:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	698 if not isinstance(attr, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	699 illegal_value(attr, 'attr', 'assert_no_duplicate_attr_in_list_of_objs', raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	700 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	701 if not isinstance(l, list):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	702 illegal_value(l, 'l', 'assert_no_duplicate_key_in_list_of_objs', raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	703 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	704 attrs = [getattr(obj, attr, None) for obj in l]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	705 if None in attrs or len(set(attrs)) != len(l):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	706 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	707 raise ValueError(f'Duplicate or missing attr ({attr}) found in {l}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	708 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	709 logger.error(f'Duplicate or missing attr ({attr}) found in {l}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	710 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	711 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	712 return(l)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	713
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	714 def file_exists_and_readable(path):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	715 if not os.path.isfile(path):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	716 raise ValueError(f'{path} is not a valid file')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	717 elif not os.access(path, os.R_OK):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	718 raise ValueError(f'{path} is not accessible for reading')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	719 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	720 return(path)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	721
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	722 def create_mask(x, bounds=None, exclude_bounds=False, current_mask=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	723 # bounds is a pair of number in the same units a x
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	724 if not isinstance(x, (tuple, list, np.ndarray)) or not len(x):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	725 logger.warning(f'Invalid input array ({x}, {type(x)})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	726 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	727 if bounds is not None and not is_num_pair(bounds):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	728 logger.warning(f'Invalid bounds parameter ({bounds} {type(bounds)}, input ignored')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	729 bounds = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	730 if bounds is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	731 if exclude_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	732 mask = np.logical_or(x < min(bounds), x > max(bounds))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	733 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	734 mask = np.logical_and(x > min(bounds), x < max(bounds))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	735 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	736 mask = np.ones(len(x), dtype=bool)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	737 if current_mask is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	738 if not isinstance(current_mask, (tuple, list, np.ndarray)) or len(current_mask) != len(x):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	739 logger.warning(f'Invalid current_mask ({current_mask}, {type(current_mask)}), '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	740 'input ignored')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	741 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	742 mask = np.logical_or(mask, current_mask)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	743 if not True in mask:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	744 logger.warning('Entire data array is masked')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	745 return(mask)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	746
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	747 def eval_expr(name, expr, expr_variables, user_variables=None, max_depth=10, raise_error=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	748 log=True, **kwargs):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	749 """Evaluate an expression of expressions
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	750 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	751 if not isinstance(name, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	752 illegal_value(name, 'name', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	753 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	754 if not isinstance(expr, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	755 illegal_value(expr, 'expr', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	756 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	757 if not is_dict_strings(expr_variables, log=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	758 illegal_value(expr_variables, 'expr_variables', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	759 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	760 if user_variables is not None and not is_dict_nums(user_variables, log=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	761 illegal_value(user_variables, 'user_variables', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	762 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	763 if not is_int(max_depth, gt=1, log=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	764 illegal_value(max_depth, 'max_depth', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	765 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	766 if not isinstance(raise_error, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	767 illegal_value(raise_error, 'raise_error', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	768 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	769 if not isinstance(log, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	770 illegal_value(log, 'log', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	771 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	772 # print(f'\nEvaluate the full expression for {expr}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	773 if 'chain' in kwargs:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	774 chain = kwargs.pop('chain')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	775 if not is_str_series(chain):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	776 illegal_value(chain, 'chain', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	777 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	778 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	779 chain = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	780 if len(chain) > max_depth:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	781 error_msg = 'Exceeded maximum depth ({max_depth}) in eval_expr'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	782 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	783 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	784 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	785 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	786 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	787 if name not in chain:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	788 chain.append(name)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	789 # print(f'start: chain = {chain}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	790 if 'ast' in kwargs:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	791 ast = kwargs.pop('ast')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	792 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	793 ast = Interpreter()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	794 if user_variables is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	795 ast.symtable.update(user_variables)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	796 chain_vars = [var for var in get_ast_names(ast.parse(expr))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	797 if var in expr_variables and var not in ast.symtable]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	798 # print(f'chain_vars: {chain_vars}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	799 save_chain = chain.copy()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	800 for var in chain_vars:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	801 # print(f'\n\tname = {name}, var = {var}:\n\t\t{expr_variables[var]}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	802 # print(f'\tchain = {chain}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	803 if var in chain:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	804 error_msg = f'Circular variable {var} in eval_expr'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	805 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	806 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	807 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	808 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	809 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	810 # print(f'\tknown symbols:\n\t\t{ast.user_defined_symbols()}\n')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	811 if var in ast.user_defined_symbols():
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	812 val = ast.symtable[var]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	813 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	814 #val = eval_expr(var, expr_variables[var], expr_variables, user_variables=user_variables,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	815 val = eval_expr(var, expr_variables[var], expr_variables, max_depth=max_depth,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	816 raise_error=raise_error, log=log, chain=chain, ast=ast)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	817 if val is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	818 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	819 ast.symtable[var] = val
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	820 # print(f'\tval = {val}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	821 # print(f'\t{var} = {ast.symtable[var]}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	822 chain = save_chain.copy()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	823 # print(f'\treset loop for {var}: chain = {chain}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	824 val = ast.eval(expr)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	825 # print(f'return val for {expr} = {val}\n')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	826 return(val)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	827
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	828 def full_gradient(expr, x, expr_name=None, expr_variables=None, valid_variables=None, max_depth=10,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	829 raise_error=False, log=True, **kwargs):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	830 """Compute the full gradient dexpr/dx
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	831 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	832 if not isinstance(x, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	833 illegal_value(x, 'x', 'full_gradient', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	834 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	835 if expr_name is not None and not isinstance(expr_name, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	836 illegal_value(expr_name, 'expr_name', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	837 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	838 if expr_variables is not None and not is_dict_strings(expr_variables, log=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	839 illegal_value(expr_variables, 'expr_variables', 'full_gradient', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	840 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	841 if valid_variables is not None and not is_str_series(valid_variables, log=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	842 illegal_value(valid_variables, 'valid_variables', 'full_gradient', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	843 if not is_int(max_depth, gt=1, log=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	844 illegal_value(max_depth, 'max_depth', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	845 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	846 if not isinstance(raise_error, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	847 illegal_value(raise_error, 'raise_error', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	848 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	849 if not isinstance(log, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	850 illegal_value(log, 'log', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	851 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	852 # print(f'\nGet full gradient of {expr_name} = {expr} with respect to {x}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	853 if expr_name is not None and expr_name == x:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	854 return(1.0)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	855 if 'chain' in kwargs:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	856 chain = kwargs.pop('chain')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	857 if not is_str_series(chain):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	858 illegal_value(chain, 'chain', 'eval_expr', raise_error, log)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	859 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	860 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	861 chain = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	862 if len(chain) > max_depth:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	863 error_msg = 'Exceeded maximum depth ({max_depth}) in eval_expr'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	864 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	865 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	866 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	867 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	868 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	869 if expr_name is not None and expr_name not in chain:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	870 chain.append(expr_name)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	871 # print(f'start ({x}): chain = {chain}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	872 ast = Interpreter()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	873 if expr_variables is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	874 chain_vars = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	875 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	876 chain_vars = [var for var in get_ast_names(ast.parse(f'{expr}'))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	877 if var in expr_variables and var != x and var not in ast.symtable]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	878 # print(f'chain_vars: {chain_vars}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	879 if valid_variables is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	880 unknown_vars = [var for var in chain_vars if var not in valid_variables]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	881 if len(unknown_vars):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	882 error_msg = f'Unknown variable {unknown_vars} in {expr}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	883 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	884 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	885 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	886 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	887 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	888 dexpr_dx = diff(expr, x)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	889 # print(f'direct gradient: d({expr})/d({x}) = {dexpr_dx} ({type(dexpr_dx)})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	890 save_chain = chain.copy()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	891 for var in chain_vars:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	892 # print(f'\n\texpr_name = {expr_name}, var = {var}:\n\t\t{expr}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	893 # print(f'\tchain = {chain}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	894 if var in chain:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	895 error_msg = f'Circular variable {var} in full_gradient'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	896 if log:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	897 logger.error(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	898 if raise_error:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	899 raise ValueError(error_msg)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	900 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	901 dexpr_dvar = diff(expr, var)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	902 # print(f'\td({expr})/d({var}) = {dexpr_dvar}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	903 if dexpr_dvar:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	904 dvar_dx = full_gradient(expr_variables[var], x, expr_name=var,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	905 expr_variables=expr_variables, valid_variables=valid_variables,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	906 max_depth=max_depth, raise_error=raise_error, log=log, chain=chain)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	907 # print(f'\t\td({var})/d({x}) = {dvar_dx}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	908 if dvar_dx:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	909 dexpr_dx = f'{dexpr_dx}+({dexpr_dvar})*({dvar_dx})'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	910 # print(f'\t\t2: chain = {chain}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	911 chain = save_chain.copy()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	912 # print(f'\treset loop for {var}: chain = {chain}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	913 # print(f'full gradient: d({expr})/d({x}) = {dexpr_dx} ({type(dexpr_dx)})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	914 # print(f'reset end: chain = {chain}\n\n')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	915 return(simplify(dexpr_dx))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	916
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	917 def bounds_from_mask(mask, return_include_bounds:bool=True):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	918 bounds = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	919 for i, m in enumerate(mask):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	920 if m == return_include_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	921 if len(bounds) == 0 or type(bounds[-1]) == tuple:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	922 bounds.append(i)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	923 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	924 if len(bounds) > 0 and isinstance(bounds[-1], int):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	925 bounds[-1] = (bounds[-1], i-1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	926 if len(bounds) > 0 and isinstance(bounds[-1], int):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	927 bounds[-1] = (bounds[-1], mask.size-1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	928 return(bounds)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	929
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	930 def draw_mask_1d(ydata, xdata=None, current_index_ranges=None, current_mask=None,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	931 select_mask=True, num_index_ranges_max=None, title=None, legend=None, test_mode=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	932 #FIX make color blind friendly
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	933 def draw_selections(ax, current_include, current_exclude, selected_index_ranges):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	934 ax.clear()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	935 ax.set_title(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	936 ax.legend([legend])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	937 ax.plot(xdata, ydata, 'k')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	938 for (low, upp) in current_include:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	939 xlow = 0.5*(xdata[max(0, low-1)]+xdata[low])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	940 xupp = 0.5*(xdata[upp]+xdata[min(num_data-1, upp+1)])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	941 ax.axvspan(xlow, xupp, facecolor='green', alpha=0.5)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	942 for (low, upp) in current_exclude:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	943 xlow = 0.5*(xdata[max(0, low-1)]+xdata[low])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	944 xupp = 0.5*(xdata[upp]+xdata[min(num_data-1, upp+1)])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	945 ax.axvspan(xlow, xupp, facecolor='red', alpha=0.5)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	946 for (low, upp) in selected_index_ranges:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	947 xlow = 0.5*(xdata[max(0, low-1)]+xdata[low])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	948 xupp = 0.5*(xdata[upp]+xdata[min(num_data-1, upp+1)])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	949 ax.axvspan(xlow, xupp, facecolor=selection_color, alpha=0.5)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	950 ax.get_figure().canvas.draw()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	951
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	952 def onclick(event):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	953 if event.inaxes in [fig.axes[0]]:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	954 selected_index_ranges.append(index_nearest_upp(xdata, event.xdata))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	955
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	956 def onrelease(event):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	957 if len(selected_index_ranges) > 0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	958 if isinstance(selected_index_ranges[-1], int):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	959 if event.inaxes in [fig.axes[0]]:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	960 event.xdata = index_nearest_low(xdata, event.xdata)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	961 if selected_index_ranges[-1] <= event.xdata:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	962 selected_index_ranges[-1] = (selected_index_ranges[-1], event.xdata)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	963 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	964 selected_index_ranges[-1] = (event.xdata, selected_index_ranges[-1])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	965 draw_selections(event.inaxes, current_include, current_exclude, selected_index_ranges)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	966 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	967 selected_index_ranges.pop(-1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	968
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	969 def confirm_selection(event):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	970 plt.close()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	971
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	972 def clear_last_selection(event):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	973 if len(selected_index_ranges):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	974 selected_index_ranges.pop(-1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	975 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	976 while len(current_include):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	977 current_include.pop()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	978 while len(current_exclude):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	979 current_exclude.pop()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	980 selected_mask.fill(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	981 draw_selections(ax, current_include, current_exclude, selected_index_ranges)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	982
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	983 def update_mask(mask, selected_index_ranges, unselected_index_ranges):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	984 for (low, upp) in selected_index_ranges:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	985 selected_mask = np.logical_and(xdata >= xdata[low], xdata <= xdata[upp])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	986 mask = np.logical_or(mask, selected_mask)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	987 for (low, upp) in unselected_index_ranges:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	988 unselected_mask = np.logical_and(xdata >= xdata[low], xdata <= xdata[upp])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	989 mask[unselected_mask] = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	990 return(mask)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	991
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	992 def update_index_ranges(mask):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	993 # Update the currently included index ranges (where mask is True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	994 current_include = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	995 for i, m in enumerate(mask):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	996 if m == True:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	997 if len(current_include) == 0 or type(current_include[-1]) == tuple:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	998 current_include.append(i)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	999 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1000 if len(current_include) > 0 and isinstance(current_include[-1], int):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1001 current_include[-1] = (current_include[-1], i-1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1002 if len(current_include) > 0 and isinstance(current_include[-1], int):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1003 current_include[-1] = (current_include[-1], num_data-1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1004 return(current_include)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1005
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1006 # Check inputs
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1007 ydata = np.asarray(ydata)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1008 if ydata.ndim > 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1009 logger.warning(f'Invalid ydata dimension ({ydata.ndim})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1010 return(None, None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1011 num_data = ydata.size
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1012 if xdata is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1013 xdata = np.arange(num_data)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1014 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1015 xdata = np.asarray(xdata, dtype=np.float64)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1016 if xdata.ndim > 1 or xdata.size != num_data:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1017 logger.warning(f'Invalid xdata shape ({xdata.shape})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1018 return(None, None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1019 if not np.all(xdata[:-1] < xdata[1:]):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1020 logger.warning('Invalid xdata: must be monotonically increasing')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1021 return(None, None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1022 if current_index_ranges is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1023 if not isinstance(current_index_ranges, (tuple, list)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1024 logger.warning('Invalid current_index_ranges parameter ({current_index_ranges}, '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1025 f'{type(current_index_ranges)})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1026 return(None, None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1027 if not isinstance(select_mask, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1028 logger.warning('Invalid select_mask parameter ({select_mask}, {type(select_mask)})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1029 return(None, None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1030 if num_index_ranges_max is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1031 logger.warning('num_index_ranges_max input not yet implemented in draw_mask_1d')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1032 if title is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1033 title = 'select ranges of data'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1034 elif not isinstance(title, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1035 illegal(title, 'title')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1036 title = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1037 if legend is None and not isinstance(title, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1038 illegal(legend, 'legend')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1039 legend = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1040
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1041 if select_mask:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1042 title = f'Click and drag to {title} you wish to include'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1043 selection_color = 'green'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1044 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1045 title = f'Click and drag to {title} you wish to exclude'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1046 selection_color = 'red'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1047
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1048 # Set initial selected mask and the selected/unselected index ranges as needed
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1049 selected_index_ranges = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1050 unselected_index_ranges = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1051 selected_mask = np.full(xdata.shape, False, dtype=bool)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1052 if current_index_ranges is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1053 if current_mask is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1054 if not select_mask:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1055 selected_index_ranges = [(0, num_data-1)]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1056 selected_mask = np.full(xdata.shape, True, dtype=bool)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1057 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1058 selected_mask = np.copy(np.asarray(current_mask, dtype=bool))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1059 if current_index_ranges is not None and len(current_index_ranges):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1060 current_index_ranges = sorted([(low, upp) for (low, upp) in current_index_ranges])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1061 for (low, upp) in current_index_ranges:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1062 if low > upp or low >= num_data or upp < 0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1063 continue
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1064 if low < 0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1065 low = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1066 if upp >= num_data:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1067 upp = num_data-1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1068 selected_index_ranges.append((low, upp))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1069 selected_mask = update_mask(selected_mask, selected_index_ranges, unselected_index_ranges)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1070 if current_index_ranges is not None and current_mask is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1071 selected_mask = np.logical_and(current_mask, selected_mask)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1072 if current_mask is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1073 selected_index_ranges = update_index_ranges(selected_mask)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1074
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1075 # Set up range selections for display
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1076 current_include = selected_index_ranges
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1077 current_exclude = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1078 selected_index_ranges = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1079 if not len(current_include):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1080 if select_mask:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1081 current_exclude = [(0, num_data-1)]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1082 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1083 current_include = [(0, num_data-1)]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1084 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1085 if current_include[0][0] > 0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1086 current_exclude.append((0, current_include[0][0]-1))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1087 for i in range(1, len(current_include)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1088 current_exclude.append((current_include[i-1][1]+1, current_include[i][0]-1))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1089 if current_include[-1][1] < num_data-1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1090 current_exclude.append((current_include[-1][1]+1, num_data-1))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1091
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1092 if not test_mode:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1093
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1094 # Set up matplotlib figure
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1095 plt.close('all')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1096 fig, ax = plt.subplots()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1097 plt.subplots_adjust(bottom=0.2)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1098 draw_selections(ax, current_include, current_exclude, selected_index_ranges)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1099
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1100 # Set up event handling for click-and-drag range selection
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1101 cid_click = fig.canvas.mpl_connect('button_press_event', onclick)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1102 cid_release = fig.canvas.mpl_connect('button_release_event', onrelease)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1103
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1104 # Set up confirm / clear range selection buttons
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1105 confirm_b = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1106 clear_b = Button(plt.axes([0.59, 0.05, 0.15, 0.075]), 'Clear')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1107 cid_confirm = confirm_b.on_clicked(confirm_selection)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1108 cid_clear = clear_b.on_clicked(clear_last_selection)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1109
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1110 # Show figure
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1111 plt.show(block=True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1112
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1113 # Disconnect callbacks when figure is closed
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1114 fig.canvas.mpl_disconnect(cid_click)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1115 fig.canvas.mpl_disconnect(cid_release)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1116 confirm_b.disconnect(cid_confirm)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1117 clear_b.disconnect(cid_clear)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1118
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1119 # Swap selection depending on select_mask
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1120 if not select_mask:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1121 selected_index_ranges, unselected_index_ranges = unselected_index_ranges, \
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1122 selected_index_ranges
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1123
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1124 # Update the mask with the currently selected/unselected x-ranges
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1125 selected_mask = update_mask(selected_mask, selected_index_ranges, unselected_index_ranges)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1126
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1127 # Update the currently included index ranges (where mask is True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1128 current_include = update_index_ranges(selected_mask)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1129
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1130 return(selected_mask, current_include)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1131
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1132 def select_peaks(ydata:np.ndarray, x_values:np.ndarray=None, x_mask:np.ndarray=None,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1133 peak_x_values:np.ndarray=np.array([]), peak_x_indices:np.ndarray=np.array([]),
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1134 return_peak_x_values:bool=False, return_peak_x_indices:bool=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1135 return_peak_input_indices:bool=False, return_sorted:bool=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1136 title:str=None, xlabel:str=None, ylabel:str=None) -> list :
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1137
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1138 # Check arguments
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1139 if (len(peak_x_values) > 0 or return_peak_x_values) and not len(x_values) > 0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1140 raise RuntimeError('Cannot use peak_x_values or return_peak_x_values without x_values')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1141 if not ((len(peak_x_values) > 0) ^ (len(peak_x_indices) > 0)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1142 raise RuntimeError('Use exactly one of peak_x_values or peak_x_indices')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1143 return_format_iter = iter((return_peak_x_values, return_peak_x_indices, return_peak_input_indices))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1144 if not (any(return_format_iter) and not any(return_format_iter)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1145 raise RuntimeError('Exactly one of return_peak_x_values, return_peak_x_indices, or '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1146 'return_peak_input_indices must be True')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1147
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1148 EXCLUDE_PEAK_PROPERTIES = {'color': 'black', 'linestyle': '--','linewidth': 1,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1149 'marker': 10, 'markersize': 5, 'fillstyle': 'none'}
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1150 INCLUDE_PEAK_PROPERTIES = {'color': 'green', 'linestyle': '-', 'linewidth': 2,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1151 'marker': 10, 'markersize': 10, 'fillstyle': 'full'}
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1152 MASKED_PEAK_PROPERTIES = {'color': 'gray', 'linestyle': ':', 'linewidth': 1}
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1153
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1154 # Setup reference data & plot
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1155 x_indices = np.arange(len(ydata))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1156 if x_values is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1157 x_values = x_indices
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1158 if x_mask is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1159 x_mask = np.full(x_values.shape, True, dtype=bool)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1160 fig, ax = plt.subplots()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1161 handles = ax.plot(x_values, ydata, label='Reference data')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1162 handles.append(mlines.Line2D([], [], label='Excluded / unselected HKL', **EXCLUDE_PEAK_PROPERTIES))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1163 handles.append(mlines.Line2D([], [], label='Included / selected HKL', **INCLUDE_PEAK_PROPERTIES))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1164 handles.append(mlines.Line2D([], [], label='HKL in masked region (unselectable)', **MASKED_PEAK_PROPERTIES))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1165 ax.legend(handles=handles, loc='upper right')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1166 ax.set(title=title, xlabel=xlabel, ylabel=ylabel)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1167
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1168
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1169 # Plot vertical line at each peak
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1170 value_to_index = lambda x_value: int(np.argmin(abs(x_values - x_value)))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1171 if len(peak_x_indices) > 0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1172 peak_x_values = x_values[peak_x_indices]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1173 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1174 peak_x_indices = np.array(list(map(value_to_index, peak_x_values)))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1175 peak_vlines = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1176 for loc in peak_x_values:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1177 nearest_index = value_to_index(loc)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1178 if nearest_index in x_indices[x_mask]:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1179 peak_vline = ax.axvline(loc, **EXCLUDE_PEAK_PROPERTIES)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1180 peak_vline.set_picker(5)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1181 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1182 peak_vline = ax.axvline(loc, **MASKED_PEAK_PROPERTIES)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1183 peak_vlines.append(peak_vline)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1184
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1185 # Indicate masked regions by gray-ing out the axes facecolor
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1186 mask_exclude_bounds = bounds_from_mask(x_mask, return_include_bounds=False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1187 for (low, upp) in mask_exclude_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1188 xlow = x_values[low]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1189 xupp = x_values[upp]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1190 ax.axvspan(xlow, xupp, facecolor='gray', alpha=0.5)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1191
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1192 # Setup peak picking
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1193 selected_peak_input_indices = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1194 def onpick(event):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1195 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1196 peak_index = peak_vlines.index(event.artist)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1197 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1198 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1199 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1200 peak_vline = event.artist
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1201 if peak_index in selected_peak_input_indices:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1202 peak_vline.set(**EXCLUDE_PEAK_PROPERTIES)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1203 selected_peak_input_indices.remove(peak_index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1204 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1205 peak_vline.set(**INCLUDE_PEAK_PROPERTIES)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1206 selected_peak_input_indices.append(peak_index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1207 plt.draw()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1208 cid_pick_peak = fig.canvas.mpl_connect('pick_event', onpick)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1209
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1210 # Setup "Confirm" button
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1211 def confirm_selection(event):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1212 plt.close()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1213 plt.subplots_adjust(bottom=0.2)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1214 confirm_b = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1215 cid_confirm = confirm_b.on_clicked(confirm_selection)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1216
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1217 # Show figure for user interaction
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1218 plt.show()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1219
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1220 # Disconnect callbacks when figure is closed
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1221 fig.canvas.mpl_disconnect(cid_pick_peak)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1222 confirm_b.disconnect(cid_confirm)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1223
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1224 if return_peak_input_indices:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1225 selected_peaks = np.array(selected_peak_input_indices)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1226 if return_peak_x_values:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1227 selected_peaks = peak_x_values[selected_peak_input_indices]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1228 if return_peak_x_indices:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1229 selected_peaks = peak_x_indices[selected_peak_input_indices]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1230
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1231 if return_sorted:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1232 selected_peaks.sort()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1233
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1234 return(selected_peaks)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1235
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1236 def find_image_files(path, filetype, name=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1237 if isinstance(name, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1238 name = f'{name.strip()} '
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1239 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1240 name = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1241 # Find available index range
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1242 if filetype == 'tif':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1243 if not isinstance(path, str) or not os.path.isdir(path):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1244 illegal_value(path, 'path', 'find_image_files')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1245 return(-1, 0, [])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1246 indexRegex = re.compile(r'\d+')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1247 # At this point only tiffs
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1248 files = sorted([f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f)) and
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1249 f.endswith('.tif') and indexRegex.search(f)])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1250 num_img = len(files)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1251 if num_img < 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1252 logger.warning(f'No available {name}files')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1253 return(-1, 0, [])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1254 first_index = indexRegex.search(files[0]).group()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1255 last_index = indexRegex.search(files[-1]).group()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1256 if first_index is None or last_index is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1257 logger.error(f'Unable to find correctly indexed {name}images')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1258 return(-1, 0, [])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1259 first_index = int(first_index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1260 last_index = int(last_index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1261 if num_img != last_index-first_index+1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1262 logger.error(f'Non-consecutive set of indices for {name}images')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1263 return(-1, 0, [])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1264 paths = [os.path.join(path, f) for f in files]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1265 elif filetype == 'h5':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1266 if not isinstance(path, str) or not os.path.isfile(path):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1267 illegal_value(path, 'path', 'find_image_files')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1268 return(-1, 0, [])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1269 # At this point only h5 in alamo2 detector style
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1270 first_index = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1271 with h5py.File(path, 'r') as f:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1272 num_img = f['entry/instrument/detector/data'].shape[0]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1273 last_index = num_img-1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1274 paths = [path]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1275 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1276 illegal_value(filetype, 'filetype', 'find_image_files')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1277 return(-1, 0, [])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1278 logger.info(f'Number of available {name}images: {num_img}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1279 logger.info(f'Index range of available {name}images: [{first_index}, '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1280 f'{last_index}]')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1281
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1282 return(first_index, num_img, paths)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1283
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1284 def select_image_range(first_index, offset, num_available, num_img=None, name=None,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1285 num_required=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1286 if isinstance(name, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1287 name = f'{name.strip()} '
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1288 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1289 name = ''
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1290 # Check existing values
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1291 if not is_int(num_available, gt=0):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1292 logger.warning(f'No available {name}images')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1293 return(0, 0, 0)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1294 if num_img is not None and not is_int(num_img, ge=0):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1295 illegal_value(num_img, 'num_img', 'select_image_range')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1296 return(0, 0, 0)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1297 if is_int(first_index, ge=0) and is_int(offset, ge=0):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1298 if num_required is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1299 if input_yesno(f'\nCurrent {name}first image index/offset = {first_index}/{offset},'+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1300 'use these values (y/n)?', 'y'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1301 if num_img is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1302 if input_yesno(f'Current number of {name}images = {num_img}, '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1303 'use this value (y/n)? ', 'y'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1304 return(first_index, offset, num_img)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1305 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1306 if input_yesno(f'Number of available {name}images = {num_available}, '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1307 'use all (y/n)? ', 'y'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1308 return(first_index, offset, num_available)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1309 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1310 if input_yesno(f'\nCurrent {name}first image offset = {offset}, '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1311 f'use this values (y/n)?', 'y'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1312 return(first_index, offset, num_required)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1313
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1314 # Check range against requirements
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1315 if num_required is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1316 if num_available == 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1317 return(first_index, 0, 1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1318 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1319 if not is_int(num_required, ge=1):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1320 illegal_value(num_required, 'num_required', 'select_image_range')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1321 return(0, 0, 0)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1322 if num_available < num_required:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1323 logger.error(f'Unable to find the required {name}images ({num_available} out of '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1324 f'{num_required})')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1325 return(0, 0, 0)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1326
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1327 # Select index range
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1328 print(f'\nThe number of available {name}images is {num_available}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1329 if num_required is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1330 last_index = first_index+num_available
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1331 use_all = f'Use all ([{first_index}, {last_index}])'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1332 pick_offset = 'Pick the first image index offset and the number of images'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1333 pick_bounds = 'Pick the first and last image index'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1334 choice = input_menu([use_all, pick_offset, pick_bounds], default=pick_offset)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1335 if not choice:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1336 offset = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1337 num_img = num_available
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1338 elif choice == 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1339 offset = input_int('Enter the first index offset', ge=0, le=last_index-first_index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1340 if first_index+offset == last_index:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1341 num_img = 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1342 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1343 num_img = input_int('Enter the number of images', ge=1, le=num_available-offset)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1344 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1345 offset = input_int('Enter the first index', ge=first_index, le=last_index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1346 num_img = 1-offset+input_int('Enter the last index', ge=offset, le=last_index)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1347 offset -= first_index
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1348 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1349 use_all = f'Use ([{first_index}, {first_index+num_required-1}])'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1350 pick_offset = 'Pick the first index offset'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1351 choice = input_menu([use_all, pick_offset], pick_offset)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1352 offset = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1353 if choice == 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1354 offset = input_int('Enter the first index offset', ge=0, le=num_available-num_required)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1355 num_img = num_required
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1356
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1357 return(first_index, offset, num_img)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1358
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1359 def load_image(f, img_x_bounds=None, img_y_bounds=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1360 """Load a single image from file.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1361 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1362 if not os.path.isfile(f):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1363 logger.error(f'Unable to load {f}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1364 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1365 img_read = plt.imread(f)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1366 if not img_x_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1367 img_x_bounds = (0, img_read.shape[0])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1368 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1369 if (not isinstance(img_x_bounds, (tuple, list)) or len(img_x_bounds) != 2 or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1370 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= img_read.shape[0])):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1371 logger.error(f'inconsistent row dimension in {f}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1372 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1373 if not img_y_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1374 img_y_bounds = (0, img_read.shape[1])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1375 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1376 if (not isinstance(img_y_bounds, list) or len(img_y_bounds) != 2 or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1377 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= img_read.shape[1])):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1378 logger.error(f'inconsistent column dimension in {f}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1379 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1380 return(img_read[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1381
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1382 def load_image_stack(files, filetype, img_offset, num_img, num_img_skip=0,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1383 img_x_bounds=None, img_y_bounds=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1384 """Load a set of images and return them as a stack.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1385 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1386 logger.debug(f'img_offset = {img_offset}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1387 logger.debug(f'num_img = {num_img}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1388 logger.debug(f'num_img_skip = {num_img_skip}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1389 logger.debug(f'\nfiles:\n{files}\n')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1390 img_stack = np.array([])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1391 if filetype == 'tif':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1392 img_read_stack = []
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1393 i = 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1394 t0 = time()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1395 for f in files[img_offset:img_offset+num_img:num_img_skip+1]:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1396 if not i%20:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1397 logger.info(f' loading {i}/{num_img}: {f}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1398 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1399 logger.debug(f' loading {i}/{num_img}: {f}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1400 img_read = load_image(f, img_x_bounds, img_y_bounds)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1401 img_read_stack.append(img_read)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1402 i += num_img_skip+1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1403 img_stack = np.stack([img_read for img_read in img_read_stack])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1404 logger.info(f'... done in {time()-t0:.2f} seconds!')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1405 logger.debug(f'img_stack shape = {np.shape(img_stack)}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1406 del img_read_stack, img_read
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1407 elif filetype == 'h5':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1408 if not isinstance(files[0], str) and not os.path.isfile(files[0]):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1409 illegal_value(files[0], 'files[0]', 'load_image_stack')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1410 return(img_stack)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1411 t0 = time()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1412 logger.info(f'Loading {files[0]}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1413 with h5py.File(files[0], 'r') as f:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1414 shape = f['entry/instrument/detector/data'].shape
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1415 if len(shape) != 3:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1416 logger.error(f'inconsistent dimensions in {files[0]}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1417 if not img_x_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1418 img_x_bounds = (0, shape[1])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1419 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1420 if (not isinstance(img_x_bounds, (tuple, list)) or len(img_x_bounds) != 2 or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1421 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= shape[1])):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1422 logger.error(f'inconsistent row dimension in {files[0]} {img_x_bounds} '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1423 f'{shape[1]}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1424 if not img_y_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1425 img_y_bounds = (0, shape[2])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1426 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1427 if (not isinstance(img_y_bounds, list) or len(img_y_bounds) != 2 or
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1428 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= shape[2])):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1429 logger.error(f'inconsistent column dimension in {files[0]}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1430 img_stack = f.get('entry/instrument/detector/data')[
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1431 img_offset:img_offset+num_img:num_img_skip+1,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1432 img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1433 logger.info(f'... done in {time()-t0:.2f} seconds!')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1434 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1435 illegal_value(filetype, 'filetype', 'load_image_stack')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1436 return(img_stack)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1437
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1438 def combine_tiffs_in_h5(files, num_img, h5_filename):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1439 img_stack = load_image_stack(files, 'tif', 0, num_img)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1440 with h5py.File(h5_filename, 'w') as f:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1441 f.create_dataset('entry/instrument/detector/data', data=img_stack)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1442 del img_stack
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1443 return([h5_filename])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1444
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1445 def clear_imshow(title=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1446 plt.ioff()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1447 if title is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1448 title = 'quick imshow'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1449 elif not isinstance(title, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1450 illegal_value(title, 'title', 'clear_imshow')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1451 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1452 plt.close(fig=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1453
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1454 def clear_plot(title=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1455 plt.ioff()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1456 if title is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1457 title = 'quick plot'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1458 elif not isinstance(title, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1459 illegal_value(title, 'title', 'clear_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1460 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1461 plt.close(fig=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1462
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1463 def quick_imshow(a, title=None, path=None, name=None, save_fig=False, save_only=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1464 clear=True, extent=None, show_grid=False, grid_color='w', grid_linewidth=1,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1465 block=False, **kwargs):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1466 if title is not None and not isinstance(title, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1467 illegal_value(title, 'title', 'quick_imshow')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1468 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1469 if path is not None and not isinstance(path, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1470 illegal_value(path, 'path', 'quick_imshow')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1471 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1472 if not isinstance(save_fig, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1473 illegal_value(save_fig, 'save_fig', 'quick_imshow')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1474 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1475 if not isinstance(save_only, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1476 illegal_value(save_only, 'save_only', 'quick_imshow')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1477 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1478 if not isinstance(clear, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1479 illegal_value(clear, 'clear', 'quick_imshow')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1480 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1481 if not isinstance(block, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1482 illegal_value(block, 'block', 'quick_imshow')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1483 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1484 if not title:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1485 title='quick imshow'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1486 # else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1487 # title = re.sub(r"\s+", '_', title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1488 if name is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1489 ttitle = re.sub(r"\s+", '_', title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1490 if path is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1491 path = f'{ttitle}.png'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1492 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1493 path = f'{path}/{ttitle}.png'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1494 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1495 if path is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1496 path = name
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1497 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1498 path = f'{path}/{name}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1499 if 'cmap' in kwargs and a.ndim == 3 and (a.shape[2] == 3 or a.shape[2] == 4):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1500 use_cmap = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1501 if a.shape[2] == 4 and a[:,:,-1].min() != a[:,:,-1].max():
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1502 use_cmap = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1503 if any(True if a[i,j,0] != a[i,j,1] and a[i,j,0] != a[i,j,2] else False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1504 for i in range(a.shape[0]) for j in range(a.shape[1])):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1505 use_cmap = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1506 if use_cmap:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1507 a = a[:,:,0]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1508 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1509 logger.warning('Image incompatible with cmap option, ignore cmap')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1510 kwargs.pop('cmap')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1511 if extent is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1512 extent = (0, a.shape[1], a.shape[0], 0)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1513 if clear:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1514 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1515 plt.close(fig=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1516 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1517 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1518 if not save_only:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1519 if block:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1520 plt.ioff()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1521 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1522 plt.ion()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1523 plt.figure(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1524 plt.imshow(a, extent=extent, **kwargs)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1525 if show_grid:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1526 ax = plt.gca()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1527 ax.grid(color=grid_color, linewidth=grid_linewidth)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1528 # if title != 'quick imshow':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1529 # plt.title = title
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1530 if save_only:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1531 plt.savefig(path)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1532 plt.close(fig=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1533 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1534 if save_fig:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1535 plt.savefig(path)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1536 if block:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1537 plt.show(block=block)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1538
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1539 def quick_plot(*args, xerr=None, yerr=None, vlines=None, title=None, xlim=None, ylim=None,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1540 xlabel=None, ylabel=None, legend=None, path=None, name=None, show_grid=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1541 save_fig=False, save_only=False, clear=True, block=False, **kwargs):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1542 if title is not None and not isinstance(title, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1543 illegal_value(title, 'title', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1544 title = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1545 if xlim is not None and not isinstance(xlim, (tuple, list)) and len(xlim) != 2:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1546 illegal_value(xlim, 'xlim', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1547 xlim = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1548 if ylim is not None and not isinstance(ylim, (tuple, list)) and len(ylim) != 2:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1549 illegal_value(ylim, 'ylim', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1550 ylim = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1551 if xlabel is not None and not isinstance(xlabel, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1552 illegal_value(xlabel, 'xlabel', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1553 xlabel = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1554 if ylabel is not None and not isinstance(ylabel, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1555 illegal_value(ylabel, 'ylabel', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1556 ylabel = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1557 if legend is not None and not isinstance(legend, (tuple, list)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1558 illegal_value(legend, 'legend', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1559 legend = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1560 if path is not None and not isinstance(path, str):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1561 illegal_value(path, 'path', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1562 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1563 if not isinstance(show_grid, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1564 illegal_value(show_grid, 'show_grid', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1565 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1566 if not isinstance(save_fig, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1567 illegal_value(save_fig, 'save_fig', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1568 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1569 if not isinstance(save_only, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1570 illegal_value(save_only, 'save_only', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1571 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1572 if not isinstance(clear, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1573 illegal_value(clear, 'clear', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1574 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1575 if not isinstance(block, bool):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1576 illegal_value(block, 'block', 'quick_plot')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1577 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1578 if title is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1579 title = 'quick plot'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1580 # else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1581 # title = re.sub(r"\s+", '_', title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1582 if name is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1583 ttitle = re.sub(r"\s+", '_', title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1584 if path is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1585 path = f'{ttitle}.png'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1586 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1587 path = f'{path}/{ttitle}.png'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1588 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1589 if path is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1590 path = name
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1591 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1592 path = f'{path}/{name}'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1593 if clear:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1594 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1595 plt.close(fig=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1596 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1597 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1598 args = unwrap_tuple(args)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1599 if depth_tuple(args) > 1 and (xerr is not None or yerr is not None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1600 logger.warning('Error bars ignored form multiple curves')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1601 if not save_only:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1602 if block:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1603 plt.ioff()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1604 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1605 plt.ion()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1606 plt.figure(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1607 if depth_tuple(args) > 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1608 for y in args:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1609 plt.plot(y, *kwargs)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1610 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1611 if xerr is None and yerr is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1612 plt.plot(args, *kwargs)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1613 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1614 plt.errorbar(args, xerr=xerr, yerr=yerr, *kwargs)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1615 if vlines is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1616 if isinstance(vlines, (int, float)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1617 vlines = [vlines]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1618 for v in vlines:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1619 plt.axvline(v, color='r', linestyle='--', **kwargs)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1620 # if vlines is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1621 # for s in tuple(([x, x], list(plt.gca().get_ylim())) for x in vlines):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1622 # plt.plot(s, color='red', *kwargs)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1623 if xlim is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1624 plt.xlim(xlim)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1625 if ylim is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1626 plt.ylim(ylim)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1627 if xlabel is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1628 plt.xlabel(xlabel)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1629 if ylabel is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1630 plt.ylabel(ylabel)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1631 if show_grid:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1632 ax = plt.gca()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1633 ax.grid(color='k')#, linewidth=1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1634 if legend is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1635 plt.legend(legend)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1636 if save_only:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1637 plt.savefig(path)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1638 plt.close(fig=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1639 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1640 if save_fig:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1641 plt.savefig(path)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1642 if block:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1643 plt.show(block=block)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1644
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1645 def select_array_bounds(a, x_low=None, x_upp=None, num_x_min=None, ask_bounds=False,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1646 title='select array bounds'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1647 """Interactively select the lower and upper data bounds for a numpy array.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1648 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1649 if isinstance(a, (tuple, list)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1650 a = np.array(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1651 if not isinstance(a, np.ndarray) or a.ndim != 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1652 illegal_value(a.ndim, 'array type or dimension', 'select_array_bounds')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1653 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1654 len_a = len(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1655 if num_x_min is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1656 num_x_min = 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1657 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1658 if num_x_min < 2 or num_x_min > len_a:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1659 logger.warning('Invalid value for num_x_min in select_array_bounds, input ignored')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1660 num_x_min = 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1661
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1662 # Ask to use current bounds
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1663 if ask_bounds and (x_low is not None or x_upp is not None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1664 if x_low is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1665 x_low = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1666 if not is_int(x_low, ge=0, le=len_a-num_x_min):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1667 illegal_value(x_low, 'x_low', 'select_array_bounds')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1668 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1669 if x_upp is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1670 x_upp = len_a
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1671 if not is_int(x_upp, ge=x_low+num_x_min, le=len_a):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1672 illegal_value(x_upp, 'x_upp', 'select_array_bounds')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1673 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1674 quick_plot((range(len_a), a), vlines=(x_low,x_upp), title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1675 if not input_yesno(f'\nCurrent array bounds: [{x_low}, {x_upp}] '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1676 'use these values (y/n)?', 'y'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1677 x_low = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1678 x_upp = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1679 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1680 clear_plot(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1681 return(x_low, x_upp)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1682
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1683 if x_low is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1684 x_min = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1685 x_max = len_a
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1686 x_low_max = len_a-num_x_min
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1687 while True:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1688 quick_plot(range(x_min, x_max), a[x_min:x_max], title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1689 zoom_flag = input_yesno('Set lower data bound (y) or zoom in (n)?', 'y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1690 if zoom_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1691 x_low = input_int(' Set lower data bound', ge=0, le=x_low_max)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1692 break
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1693 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1694 x_min = input_int(' Set lower zoom index', ge=0, le=x_low_max)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1695 x_max = input_int(' Set upper zoom index', ge=x_min+1, le=x_low_max+1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1696 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1697 if not is_int(x_low, ge=0, le=len_a-num_x_min):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1698 illegal_value(x_low, 'x_low', 'select_array_bounds')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1699 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1700 if x_upp is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1701 x_min = x_low+num_x_min
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1702 x_max = len_a
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1703 x_upp_min = x_min
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1704 while True:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1705 quick_plot(range(x_min, x_max), a[x_min:x_max], title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1706 zoom_flag = input_yesno('Set upper data bound (y) or zoom in (n)?', 'y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1707 if zoom_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1708 x_upp = input_int(' Set upper data bound', ge=x_upp_min, le=len_a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1709 break
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1710 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1711 x_min = input_int(' Set upper zoom index', ge=x_upp_min, le=len_a-1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1712 x_max = input_int(' Set upper zoom index', ge=x_min+1, le=len_a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1713 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1714 if not is_int(x_upp, ge=x_low+num_x_min, le=len_a):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1715 illegal_value(x_upp, 'x_upp', 'select_array_bounds')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1716 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1717 print(f'lower bound = {x_low} (inclusive)\nupper bound = {x_upp} (exclusive)]')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1718 quick_plot((range(len_a), a), vlines=(x_low,x_upp), title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1719 if not input_yesno('Accept these bounds (y/n)?', 'y'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1720 x_low, x_upp = select_array_bounds(a, None, None, num_x_min, title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1721 clear_plot(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1722 return(x_low, x_upp)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1723
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1724 def select_image_bounds(a, axis, low=None, upp=None, num_min=None, title='select array bounds',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1725 raise_error=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1726 """Interactively select the lower and upper data bounds for a 2D numpy array.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1727 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1728 a = np.asarray(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1729 if a.ndim != 2:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1730 illegal_value(a.ndim, 'array dimension', location='select_image_bounds',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1731 raise_error=raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1732 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1733 if axis < 0 or axis >= a.ndim:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1734 illegal_value(axis, 'axis', location='select_image_bounds', raise_error=raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1735 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1736 low_save = low
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1737 upp_save = upp
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1738 num_min_save = num_min
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1739 if num_min is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1740 num_min = 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1741 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1742 if num_min < 2 or num_min > a.shape[axis]:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1743 logger.warning('Invalid input for num_min in select_image_bounds, input ignored')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1744 num_min = 1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1745 if low is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1746 min_ = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1747 max_ = a.shape[axis]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1748 low_max = a.shape[axis]-num_min
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1749 while True:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1750 if axis:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1751 quick_imshow(a[:,min_:max_], title=title, aspect='auto',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1752 extent=[min_,max_,a.shape[0],0])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1753 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1754 quick_imshow(a[min_:max_,:], title=title, aspect='auto',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1755 extent=[0,a.shape[1], max_,min_])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1756 zoom_flag = input_yesno('Set lower data bound (y) or zoom in (n)?', 'y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1757 if zoom_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1758 low = input_int(' Set lower data bound', ge=0, le=low_max)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1759 break
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1760 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1761 min_ = input_int(' Set lower zoom index', ge=0, le=low_max)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1762 max_ = input_int(' Set upper zoom index', ge=min_+1, le=low_max+1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1763 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1764 if not is_int(low, ge=0, le=a.shape[axis]-num_min):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1765 illegal_value(low, 'low', location='select_image_bounds', raise_error=raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1766 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1767 if upp is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1768 min_ = low+num_min
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1769 max_ = a.shape[axis]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1770 upp_min = min_
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1771 while True:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1772 if axis:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1773 quick_imshow(a[:,min_:max_], title=title, aspect='auto',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1774 extent=[min_,max_,a.shape[0],0])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1775 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1776 quick_imshow(a[min_:max_,:], title=title, aspect='auto',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1777 extent=[0,a.shape[1], max_,min_])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1778 zoom_flag = input_yesno('Set upper data bound (y) or zoom in (n)?', 'y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1779 if zoom_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1780 upp = input_int(' Set upper data bound', ge=upp_min, le=a.shape[axis])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1781 break
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1782 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1783 min_ = input_int(' Set upper zoom index', ge=upp_min, le=a.shape[axis]-1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1784 max_ = input_int(' Set upper zoom index', ge=min_+1, le=a.shape[axis])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1785 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1786 if not is_int(upp, ge=low+num_min, le=a.shape[axis]):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1787 illegal_value(upp, 'upp', location='select_image_bounds', raise_error=raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1788 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1789 bounds = (low, upp)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1790 a_tmp = np.copy(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1791 a_tmp_max = a.max()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1792 if axis:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1793 a_tmp[:,bounds[0]] = a_tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1794 a_tmp[:,bounds[1]-1] = a_tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1795 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1796 a_tmp[bounds[0],:] = a_tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1797 a_tmp[bounds[1]-1,:] = a_tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1798 print(f'lower bound = {low} (inclusive)\nupper bound = {upp} (exclusive)')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1799 quick_imshow(a_tmp, title=title, aspect='auto')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1800 del a_tmp
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1801 if not input_yesno('Accept these bounds (y/n)?', 'y'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1802 bounds = select_image_bounds(a, axis, low=low_save, upp=upp_save, num_min=num_min_save,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1803 title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1804 return(bounds)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1805
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1806 def select_one_image_bound(a, axis, bound=None, bound_name=None, title='select array bounds',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1807 default='y', raise_error=False):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1808 """Interactively select a data boundary for a 2D numpy array.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1809 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1810 a = np.asarray(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1811 if a.ndim != 2:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1812 illegal_value(a.ndim, 'array dimension', location='select_one_image_bound',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1813 raise_error=raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1814 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1815 if axis < 0 or axis >= a.ndim:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1816 illegal_value(axis, 'axis', location='select_one_image_bound', raise_error=raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1817 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1818 if bound_name is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1819 bound_name = 'data bound'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1820 if bound is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1821 min_ = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1822 max_ = a.shape[axis]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1823 bound_max = a.shape[axis]-1
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1824 while True:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1825 if axis:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1826 quick_imshow(a[:,min_:max_], title=title, aspect='auto',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1827 extent=[min_,max_,a.shape[0],0])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1828 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1829 quick_imshow(a[min_:max_,:], title=title, aspect='auto',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1830 extent=[0,a.shape[1], max_,min_])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1831 zoom_flag = input_yesno(f'Set {bound_name} (y) or zoom in (n)?', 'y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1832 if zoom_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1833 bound = input_int(f' Set {bound_name}', ge=0, le=bound_max)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1834 clear_imshow(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1835 break
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1836 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1837 min_ = input_int(' Set lower zoom index', ge=0, le=bound_max)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1838 max_ = input_int(' Set upper zoom index', ge=min_+1, le=bound_max+1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1839
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1840 elif not is_int(bound, ge=0, le=a.shape[axis]-1):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1841 illegal_value(bound, 'bound', location='select_one_image_bound', raise_error=raise_error)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1842 return(None)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1843 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1844 print(f'Current {bound_name} = {bound}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1845 a_tmp = np.copy(a)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1846 a_tmp_max = a.max()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1847 if axis:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1848 a_tmp[:,bound] = a_tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1849 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1850 a_tmp[bound,:] = a_tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1851 quick_imshow(a_tmp, title=title, aspect='auto')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1852 del a_tmp
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1853 if not input_yesno(f'Accept this {bound_name} (y/n)?', default):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1854 bound = select_one_image_bound(a, axis, bound_name=bound_name, title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1855 clear_imshow(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1856 return(bound)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1857
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1858
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1859 class Config:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1860 """Base class for processing a config file or dictionary.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1861 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1862 def __init__(self, config_file=None, config_dict=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1863 self.config = {}
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1864 self.load_flag = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1865 self.suffix = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1866
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1867 # Load config file
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1868 if config_file is not None and config_dict is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1869 logger.warning('Ignoring config_dict (both config_file and config_dict are specified)')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1870 if config_file is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1871 self.load_file(config_file)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1872 elif config_dict is not None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1873 self.load_dict(config_dict)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1874
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1875 def load_file(self, config_file):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1876 """Load a config file.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1877 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1878 if self.load_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1879 logger.warning('Overwriting any previously loaded config file')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1880 self.config = {}
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1881
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1882 # Ensure config file exists
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1883 if not os.path.isfile(config_file):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1884 logger.error(f'Unable to load {config_file}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1885 return
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1886
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1887 # Load config file (for now for Galaxy, allow .dat extension)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1888 self.suffix = os.path.splitext(config_file)[1]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1889 if self.suffix == '.yml' or self.suffix == '.yaml' or self.suffix == '.dat':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1890 with open(config_file, 'r') as f:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1891 self.config = safe_load(f)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1892 elif self.suffix == '.txt':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1893 with open(config_file, 'r') as f:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1894 lines = f.read().splitlines()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1895 self.config = {item[0].strip():literal_eval(item[1].strip()) for item in
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1896 [line.split('#')[0].split('=') for line in lines if '=' in line.split('#')[0]]}
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1897 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1898 illegal_value(self.suffix, 'config file extension', 'Config.load_file')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1899
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1900 # Make sure config file was correctly loaded
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1901 if isinstance(self.config, dict):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1902 self.load_flag = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1903 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1904 logger.error(f'Unable to load dictionary from config file: {config_file}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1905 self.config = {}
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1906
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1907 def load_dict(self, config_dict):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1908 """Takes a dictionary and places it into self.config.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1909 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1910 if self.load_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1911 logger.warning('Overwriting the previously loaded config file')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1912
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1913 if isinstance(config_dict, dict):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1914 self.config = config_dict
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1915 self.load_flag = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1916 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1917 illegal_value(config_dict, 'dictionary config object', 'Config.load_dict')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1918 self.config = {}
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1919
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1920 def save_file(self, config_file):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1921 """Save the config file (as a yaml file only right now).
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1922 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1923 suffix = os.path.splitext(config_file)[1]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1924 if suffix != '.yml' and suffix != '.yaml':
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1925 illegal_value(suffix, 'config file extension', 'Config.save_file')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1926
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1927 # Check if config file exists
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1928 if os.path.isfile(config_file):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1929 logger.info(f'Updating {config_file}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1930 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1931 logger.info(f'Saving {config_file}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1932
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1933 # Save config file
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1934 with open(config_file, 'w') as f:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1935 safe_dump(self.config, f)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1936
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1937 def validate(self, pars_required, pars_missing=None):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1938 """Returns False if any required keys are missing.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1939 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1940 if not self.load_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1941 logger.error('Load a config file prior to calling Config.validate')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1942
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1943 def validate_nested_pars(config, par):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1944 par_levels = par.split(':')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1945 first_level_par = par_levels[0]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1946 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1947 first_level_par = int(first_level_par)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1948 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1949 pass
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1950 try:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1951 next_level_config = config[first_level_par]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1952 if len(par_levels) > 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1953 next_level_par = ':'.join(par_levels[1:])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1954 return(validate_nested_pars(next_level_config, next_level_par))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1955 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1956 return(True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1957 except:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1958 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1959
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1960 pars_missing = [p for p in pars_required if not validate_nested_pars(self.config, p)]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1961 if len(pars_missing) > 0:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1962 logger.error(f'Missing item(s) in configuration: {", ".join(pars_missing)}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1963 return(False)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1964 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty rv43 parents: diff changeset	1965 return(True)

Mercurial > repos > rv43 > test_tomo_reconstruct

annotate general.py @ 0:98e23dff1de2 draft default tip