tomo: general.py annotate

annotate general.py @ 65:f31ef7bfb430 draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"

author	rv43
date	Thu, 18 Aug 2022 14:57:39 +0000
parents	98a83f03d91b
children	ba5866d0251d

rev	line source
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1 #!/usr/bin/env python3
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	2
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	3 # -- coding: utf-8 --
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	4 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	5 Created on Mon Dec 6 15:36:22 2021
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	6
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	7 @author: rv43
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	8 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	9
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	10 import logging
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	11
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	12 import os
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	13 import sys
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	14 import re
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	15 import yaml
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	16 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	17 import h5py
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	18 except:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	19 pass
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	20 import numpy as np
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	21 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	22 import matplotlib.pyplot as plt
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	23 from matplotlib.widgets import Button
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	24 except:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	25 pass
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	26
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	27 from ast import literal_eval
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	28 from copy import deepcopy
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	29 from time import time
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	30
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	31
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	32 def depth_list(L): return isinstance(L, list) and max(map(depth_list, L))+1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	33 def depth_tuple(T): return isinstance(T, tuple) and max(map(depth_tuple, T))+1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	34 def unwrap_tuple(T):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	35 if depth_tuple(T) > 1 and len(T) == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	36 T = unwrap_tuple(*T)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	37 return T
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	38
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	39 def illegal_value(value, name, location=None, exit_flag=False):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	40 if not isinstance(location, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	41 location = ''
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	42 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	43 location = f'in {location} '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	44 if isinstance(name, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	45 logging.error(f'Illegal value for {name} {location}({value}, {type(value)})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	46 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	47 logging.error(f'Illegal value {location}({value}, {type(value)})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	48 if exit_flag:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	49 raise ValueError
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	50
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	51 def is_int(v, v_min=None, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	52 """Value is an integer in range v_min <= v <= v_max.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	53 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	54 if not isinstance(v, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	55 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	56 if v_min is not None and not isinstance(v_min, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	57 illegal_value(v_min, 'v_min', 'is_int')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	58 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	59 if v_max is not None and not isinstance(v_max, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	60 illegal_value(v_max, 'v_max', 'is_int')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	61 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	62 if v_min is not None and v_max is not None and v_min > v_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	63 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	64 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	65 if (v_min is not None and v < v_min) or (v_max is not None and v > v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	66 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	67 return True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	68
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	69 def is_int_pair(v, v_min=None, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	70 """Value is an integer pair, each in range v_min <= v[i] <= v_max or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	71 v_min[i] <= v[i] <= v_max[i].
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	72 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	73 if not (isinstance(v, (tuple, list)) and len(v) == 2 and isinstance(v[0], int) and
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	74 isinstance(v[1], int)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	75 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	76 if v_min is not None or v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	77 if (v_min is None or isinstance(v_min, int)) and (v_max is None or isinstance(v_max, int)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	78 if True in [True if not is_int(vi, v_min=v_min, v_max=v_max) else False for vi in v]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	79 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	80 elif is_int_pair(v_min) and is_int_pair(v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	81 if True in [True if v_min[i] > v_max[i] else False for i in range(2)]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	82 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	83 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	84 if True in [True if not is_int(v[i], v_min[i], v_max[i]) else False for i in range(2)]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	85 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	86 elif is_int_pair(v_min) and (v_max is None or isinstance(v_max, int)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	87 if True in [True if not is_int(v[i], v_min=v_min[i], v_max=v_max) else False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	88 for i in range(2)]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	89 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	90 elif (v_min is None or isinstance(v_min, int)) and is_int_pair(v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	91 if True in [True if not is_int(v[i], v_min=v_min, v_max=v_max[i]) else False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	92 for i in range(2)]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	93 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	94 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	95 logging.error(f'Illegal v_min or v_max input ({v_min} {type(v_min)} and '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	96 f'{v_max} {type(v_max)})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	97 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	98 return True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	99
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	100 def is_int_series(l, v_min=None, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	101 """Value is a tuple or list of integers, each in range v_min <= l[i] <= v_max.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	102 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	103 if v_min is not None and not isinstance(v_min, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	104 illegal_value(v_min, 'v_min', 'is_int_series')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	105 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	106 if v_max is not None and not isinstance(v_max, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	107 illegal_value(v_max, 'v_max', 'is_int_series')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	108 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	109 if not isinstance(l, (tuple, list)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	110 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	111 if True in [True if not is_int(v, v_min=v_min, v_max=v_max) else False for v in l]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	112 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	113 return True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	114
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	115 def is_num(v, v_min=None, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	116 """Value is a number in range v_min <= v <= v_max.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	117 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	118 if not isinstance(v, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	119 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	120 if v_min is not None and not isinstance(v_min, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	121 illegal_value(v_min, 'v_min', 'is_num')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	122 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	123 if v_max is not None and not isinstance(v_max, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	124 illegal_value(v_max, 'v_max', 'is_num')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	125 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	126 if v_min is not None and v_max is not None and v_min > v_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	127 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	128 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	129 if (v_min is not None and v < v_min) or (v_max is not None and v > v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	130 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	131 return True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	132
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	133 def is_num_pair(v, v_min=None, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	134 """Value is a number pair, each in range v_min <= v[i] <= v_max or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	135 v_min[i] <= v[i] <= v_max[i].
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	136 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	137 if not (isinstance(v, (tuple, list)) and len(v) == 2 and isinstance(v[0], (int, float)) and
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	138 isinstance(v[1], (int, float))):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	139 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	140 if v_min is not None or v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	141 if ((v_min is None or isinstance(v_min, (int, float))) and
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	142 (v_max is None or isinstance(v_max, (int, float)))):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	143 if True in [True if not is_num(vi, v_min=v_min, v_max=v_max) else False for vi in v]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	144 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	145 elif is_num_pair(v_min) and is_num_pair(v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	146 if True in [True if v_min[i] > v_max[i] else False for i in range(2)]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	147 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	148 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	149 if True in [True if not is_num(v[i], v_min[i], v_max[i]) else False for i in range(2)]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	150 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	151 elif is_num_pair(v_min) and (v_max is None or isinstance(v_max, (int, float))):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	152 if True in [True if not is_num(v[i], v_min=v_min[i], v_max=v_max) else False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	153 for i in range(2)]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	154 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	155 elif (v_min is None or isinstance(v_min, (int, float))) and is_num_pair(v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	156 if True in [True if not is_num(v[i], v_min=v_min, v_max=v_max[i]) else False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	157 for i in range(2)]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	158 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	159 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	160 logging.error(f'Illegal v_min or v_max input ({v_min} {type(v_min)} and '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	161 f'{v_max} {type(v_max)})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	162 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	163 return True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	164
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	165 def is_num_series(l, v_min=None, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	166 """Value is a tuple or list of numbers, each in range v_min <= l[i] <= v_max.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	167 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	168 if v_min is not None and not isinstance(v_min, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	169 illegal_value(v_min, 'v_min', 'is_num_series')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	170 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	171 if v_max is not None and not isinstance(v_max, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	172 illegal_value(v_max, 'v_max', 'is_num_series')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	173 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	174 if not isinstance(l, (tuple, list)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	175 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	176 if True in [True if not is_num(v, v_min=v_min, v_max=v_max) else False for v in l]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	177 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	178 return True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	179
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	180 def is_index(v, v_min=0, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	181 """Value is an array index in range v_min <= v < v_max.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	182 NOTE v_max IS NOT included!
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	183 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	184 if isinstance(v_max, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	185 if v_max <= v_min:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	186 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	187 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	188 v_max -= 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	189 return is_int(v, v_min, v_max)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	190
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	191 def is_index_range(v, v_min=0, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	192 """Value is an array index range in range v_min <= v[0] <= v[1] <= v_max.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	193 NOTE v_max IS included!
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	194 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	195 if not is_int_pair(v):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	196 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	197 if not isinstance(v_min, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	198 illegal_value(v_min, 'v_min', 'is_index_range')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	199 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	200 if v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	201 if not isinstance(v_max, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	202 illegal_value(v_max, 'v_max', 'is_index_range')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	203 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	204 if v_max < v_min:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	205 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	206 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	207 if not v_min <= v[0] <= v[1] or (v_max is not None and v[1] > v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	208 return False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	209 return True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	210
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	211 def index_nearest(a, value):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	212 a = np.asarray(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	213 if a.ndim > 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	214 logging.warning(f'Illegal input array ({a}, {type(a)})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	215 # Round up for .5
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	216 value *= 1.0+sys.float_info.epsilon
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	217 return (int)(np.argmin(np.abs(a-value)))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	218
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	219 def index_nearest_low(a, value):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	220 a = np.asarray(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	221 if a.ndim > 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	222 logging.warning(f'Illegal input array ({a}, {type(a)})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	223 index = int(np.argmin(np.abs(a-value)))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	224 if value < a[index] and index > 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	225 index -= 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	226 return index
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	227
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	228 def index_nearest_upp(a, value):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	229 a = np.asarray(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	230 if a.ndim > 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	231 logging.warning(f'Illegal input array ({a}, {type(a)})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	232 index = int(np.argmin(np.abs(a-value)))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	233 if value > a[index] and index < a.size-1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	234 index += 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	235 return index
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	236
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	237 def round_to_n(x, n=1):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	238 if x == 0.0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	239 return 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	240 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	241 return round(x, n-1-int(np.floor(np.log10(abs(x)))))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	242
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	243 def round_up_to_n(x, n=1):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	244 xr = round_to_n(x, n)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	245 if abs(x/xr) > 1.0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	246 xr += np.sign(x)10*(np.floor(np.log10(abs(x)))+1-n)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	247 return xr
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	248
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	249 def trunc_to_n(x, n=1):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	250 xr = round_to_n(x, n)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	251 if abs(xr/x) > 1.0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	252 xr -= np.sign(x)10*(np.floor(np.log10(abs(x)))+1-n)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	253 return xr
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	254
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	255 def string_to_list(s):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	256 """Return a list of numbers by splitting/expanding a string on any combination of
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	257 dashes, commas, and/or whitespaces
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	258 e.g: '1, 3, 5-8,12 ' -> [1, 3, 5, 6, 7, 8, 12]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	259 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	260 if not isinstance(s, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	261 illegal_value(s, location='string_to_list')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	262 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	263 if not len(s):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	264 return []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	265 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	266 list1 = [x for x in re.split('\s+,\s+\|\s+,\|,\s+\|\s+\|,', s.strip())]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	267 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	268 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	269 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	270 l = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	271 for l1 in list1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	272 l2 = [literal_eval(x) for x in re.split('\s+-\s+\|\s+-\|-\s+\|\s+\|-', l1)]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	273 if len(l2) == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	274 l += l2
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	275 elif len(l2) == 2 and l2[1] > l2[0]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	276 l += [i for i in range(l2[0], l2[1]+1)]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	277 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	278 raise ValueError
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	279 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	280 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	281 return sorted(set(l))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	282
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	283 def get_trailing_int(string):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	284 indexRegex = re.compile(r'\d+$')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	285 mo = indexRegex.search(string)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	286 if mo is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	287 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	288 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	289 return int(mo.group())
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	290
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	291 def input_int(s=None, v_min=None, v_max=None, default=None, inset=None):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	292 if default is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	293 if not isinstance(default, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	294 illegal_value(default, 'default', 'input_int')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	295 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	296 default_string = f' [{default}]'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	297 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	298 default_string = ''
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	299 if v_min is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	300 if not isinstance(v_min, int):
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	301 illegal_value(v_min, 'v_min', 'input_int')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	302 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	303 if default is not None and default < v_min:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	304 logging.error('Illegal v_min, default combination ({v_min}, {default})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	305 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	306 if v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	307 if not isinstance(v_max, int):
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	308 illegal_value(v_max, 'v_max', 'input_int')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	309 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	310 if v_min is not None and v_min > v_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	311 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	312 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	313 if default is not None and default > v_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	314 logging.error('Illegal default, v_max combination ({default}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	315 return None
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	316 if inset is not None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	317 if (not isinstance(inset, (tuple, list)) or False in [True if isinstance(i, int) else
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	318 False for i in inset]):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	319 illegal_value(inset, 'inset', 'input_int')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	320 return None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	321 if v_min is not None and v_max is not None:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	322 v_range = f' ({v_min}, {v_max})'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	323 elif v_min is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	324 v_range = f' (>= {v_min})'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	325 elif v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	326 v_range = f' (<= {v_max})'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	327 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	328 v_range = ''
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	329 if s is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	330 print(f'Enter an integer{v_range}{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	331 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	332 print(f'{s}{v_range}{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	333 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	334 i = input()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	335 if isinstance(i, str) and not len(i):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	336 v = default
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	337 print(f'{v}')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	338 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	339 v = literal_eval(i)
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	340 if inset and v not in inset:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	341 raise ValueError(f'{v} not part of the set {inset}')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	342 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	343 v = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	344 except:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	345 print('Unexpected error')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	346 raise
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	347 if not is_int(v, v_min, v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	348 print('Illegal input, enter a valid integer')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	349 v = input_int(s, v_min, v_max, default)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	350 return v
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	351
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	352 def input_num(s=None, v_min=None, v_max=None, default=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	353 if default is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	354 if not isinstance(default, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	355 illegal_value(default, 'default', 'input_num')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	356 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	357 default_string = f' [{default}]'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	358 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	359 default_string = ''
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	360 if v_min is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	361 if not isinstance(v_min, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	362 illegal_value(vmin, 'vmin', 'input_num')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	363 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	364 if default is not None and default < v_min:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	365 logging.error('Illegal v_min, default combination ({v_min}, {default})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	366 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	367 if v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	368 if not isinstance(v_max, (int, float)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	369 illegal_value(vmax, 'vmax', 'input_num')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	370 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	371 if v_min is not None and v_max < v_min:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	372 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	373 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	374 if default is not None and default > v_max:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	375 logging.error('Illegal default, v_max combination ({default}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	376 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	377 if v_min is not None and v_max is not None:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	378 v_range = f' ({v_min}, {v_max})'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	379 elif v_min is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	380 v_range = f' (>= {v_min})'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	381 elif v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	382 v_range = f' (<= {v_max})'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	383 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	384 v_range = ''
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	385 if s is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	386 print(f'Enter a number{v_range}{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	387 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	388 print(f'{s}{v_range}{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	389 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	390 i = input()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	391 if isinstance(i, str) and not len(i):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	392 v = default
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	393 print(f'{v}')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	394 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	395 v = literal_eval(i)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	396 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	397 v = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	398 except:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	399 print('Unexpected error')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	400 raise
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	401 if not is_num(v, v_min, v_max):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	402 print('Illegal input, enter a valid number')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	403 v = input_num(s, v_min, v_max, default)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	404 return v
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	405
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	406 def input_int_list(s=None, v_min=None, v_max=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	407 if v_min is not None and not isinstance(v_min, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	408 illegal_value(vmin, 'vmin', 'input_int_list')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	409 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	410 if v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	411 if not isinstance(v_max, int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	412 illegal_value(vmax, 'vmax', 'input_int_list')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	413 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	414 if v_max < v_min:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	415 logging.error(f'Illegal v_min, v_max combination ({v_min}, {v_max})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	416 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	417 if v_min is not None and v_max is not None:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	418 v_range = f' (each value in ({v_min}, {v_max}))'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	419 elif v_min is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	420 v_range = f' (each value >= {v_min})'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	421 elif v_max is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	422 v_range = f' (each value <= {v_max})'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	423 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	424 v_range = ''
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	425 if s is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	426 print(f'Enter a series of integers{v_range}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	427 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	428 print(f'{s}{v_range}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	429 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	430 l = string_to_list(input())
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	431 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	432 l = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	433 except:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	434 print('Unexpected error')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	435 raise
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	436 if (not isinstance(l, list) or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	437 True in [True if not is_int(v, v_min, v_max) else False for v in l]):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	438 print('Illegal input: enter a valid set of dash/comma/whitespace separated integers '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	439 'e.g. 2,3,5-8,10')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	440 l = input_int_list(s, v_min, v_max)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	441 return l
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	442
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	443 def input_yesno(s=None, default=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	444 if default is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	445 if not isinstance(default, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	446 illegal_value(default, 'default', 'input_yesno')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	447 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	448 if default.lower() in 'yes':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	449 default = 'y'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	450 elif default.lower() in 'no':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	451 default = 'n'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	452 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	453 illegal_value(default, 'default', 'input_yesno')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	454 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	455 default_string = f' [{default}]'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	456 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	457 default_string = ''
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	458 if s is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	459 print(f'Enter yes or no{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	460 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	461 print(f'{s}{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	462 i = input()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	463 if isinstance(i, str) and not len(i):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	464 i = default
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	465 print(f'{i}')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	466 if i is not None and i.lower() in 'yes':
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	467 v = True
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	468 elif i is not None and i.lower() in 'no':
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	469 v = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	470 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	471 print('Illegal input, enter yes or no')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	472 v = input_yesno(s, default)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	473 return v
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	474
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	475 def input_menu(items, default=None, header=None):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	476 if not isinstance(items, (tuple, list)) or False in [True if isinstance(i, str) else False
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	477 for i in items]:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	478 illegal_value(items, 'items', 'input_menu')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	479 return None
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	480 if default is not None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	481 if not (isinstance(default, str) and default in items):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	482 logging.error(f'Illegal value for default ({default}), must be in {items}')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	483 return None
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	484 default_string = f' [{items.index(default)+1}]'
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	485 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	486 default_string = ''
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	487 if header is None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	488 print(f'Choose one of the following items (1, {len(items)}){default_string}:')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	489 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	490 print(f'{header} (1, {len(items)}){default_string}:')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	491 for i, choice in enumerate(items):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	492 print(f' {i+1}: {choice}')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	493 try:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	494 choice = input()
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	495 if isinstance(choice, str) and not len(choice):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	496 choice = items.index(default)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	497 print(f'{choice+1}')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	498 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	499 choice = literal_eval(choice)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	500 if isinstance(choice, int) and 1 <= choice <= len(items):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	501 choice -= 1
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	502 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	503 raise ValueError
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	504 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	505 choice = None
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	506 except:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	507 print('Unexpected error')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	508 raise
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	509 if choice is None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	510 print(f'Illegal choice, enter a number between 1 and {len(items)}')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	511 choice = input_menu(items, default)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	512 return choice
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	513
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	514 def create_mask(x, bounds=None, reverse_mask=False, current_mask=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	515 # bounds is a pair of number in the same units a x
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	516 if not isinstance(x, (tuple, list, np.ndarray)) or not len(x):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	517 logging.warning(f'Illegal input array ({x}, {type(x)})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	518 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	519 if bounds is not None and not is_num_pair(bounds):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	520 logging.warning(f'Illegal bounds parameter ({bounds} {type(bounds)}, input ignored')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	521 bounds = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	522 if bounds is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	523 if not reverse_mask:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	524 mask = np.logical_and(x > min(bounds), x < max(bounds))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	525 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	526 mask = np.logical_or(x < min(bounds), x > max(bounds))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	527 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	528 mask = np.ones(len(x), dtype=bool)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	529 if current_mask is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	530 if not isinstance(current_mask, (tuple, list, np.ndarray)) or len(current_mask) != len(x):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	531 logging.warning(f'Illegal current_mask ({current_mask}, {type(current_mask)}), '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	532 'input ignored')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	533 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	534 mask = np.logical_and(mask, current_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	535 if not True in mask:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	536 logging.warning('Entire data array is masked')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	537 return mask
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	538
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	539 def draw_mask_1d(ydata, xdata=None, current_index_ranges=None, current_mask=None,
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	540 select_mask=True, num_index_ranges_max=None, title=None, legend=None, test_mode=False):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	541 def draw_selections(ax):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	542 ax.clear()
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	543 ax.set_title(title)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	544 ax.legend([legend])
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	545 ax.plot(xdata, ydata, 'k')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	546 for (low, upp) in current_include:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	547 xlow = 0.5*(xdata[max(0, low-1)]+xdata[low])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	548 xupp = 0.5*(xdata[upp]+xdata[min(num_data-1, upp+1)])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	549 ax.axvspan(xlow, xupp, facecolor='green', alpha=0.5)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	550 for (low, upp) in current_exclude:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	551 xlow = 0.5*(xdata[max(0, low-1)]+xdata[low])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	552 xupp = 0.5*(xdata[upp]+xdata[min(num_data-1, upp+1)])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	553 ax.axvspan(xlow, xupp, facecolor='red', alpha=0.5)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	554 for (low, upp) in selected_index_ranges:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	555 xlow = 0.5*(xdata[max(0, low-1)]+xdata[low])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	556 xupp = 0.5*(xdata[upp]+xdata[min(num_data-1, upp+1)])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	557 ax.axvspan(xlow, xupp, facecolor=selection_color, alpha=0.5)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	558 ax.get_figure().canvas.draw()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	559
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	560 def onclick(event):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	561 if event.inaxes in [fig.axes[0]]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	562 selected_index_ranges.append(index_nearest_upp(xdata, event.xdata))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	563
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	564 def onrelease(event):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	565 if len(selected_index_ranges) > 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	566 if isinstance(selected_index_ranges[-1], int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	567 if event.inaxes in [fig.axes[0]]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	568 event.xdata = index_nearest_low(xdata, event.xdata)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	569 if selected_index_ranges[-1] <= event.xdata:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	570 selected_index_ranges[-1] = (selected_index_ranges[-1], event.xdata)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	571 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	572 selected_index_ranges[-1] = (event.xdata, selected_index_ranges[-1])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	573 draw_selections(event.inaxes)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	574 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	575 selected_index_ranges.pop(-1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	576
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	577 def confirm_selection(event):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	578 plt.close()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	579
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	580 def clear_last_selection(event):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	581 if len(selected_index_ranges):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	582 selected_index_ranges.pop(-1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	583 draw_selections(ax)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	584
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	585 def update_mask(mask):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	586 for (low, upp) in selected_index_ranges:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	587 selected_mask = np.logical_and(xdata >= xdata[low], xdata <= xdata[upp])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	588 mask = np.logical_or(mask, selected_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	589 for (low, upp) in unselected_index_ranges:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	590 unselected_mask = np.logical_and(xdata >= xdata[low], xdata <= xdata[upp])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	591 mask[unselected_mask] = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	592 return mask
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	593
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	594 def update_index_ranges(mask):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	595 # Update the currently included index ranges (where mask is True)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	596 current_include = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	597 for i, m in enumerate(mask):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	598 if m == True:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	599 if len(current_include) == 0 or type(current_include[-1]) == tuple:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	600 current_include.append(i)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	601 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	602 if len(current_include) > 0 and isinstance(current_include[-1], int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	603 current_include[-1] = (current_include[-1], i-1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	604 if len(current_include) > 0 and isinstance(current_include[-1], int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	605 current_include[-1] = (current_include[-1], num_data-1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	606 return current_include
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	607
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	608 # Check for valid inputs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	609 ydata = np.asarray(ydata)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	610 if ydata.ndim > 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	611 logging.warning(f'Illegal ydata dimension ({ydata.ndim})')
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	612 return None, None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	613 num_data = ydata.size
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	614 if xdata is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	615 xdata = np.arange(num_data)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	616 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	617 xdata = np.asarray(xdata, dtype=np.float64)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	618 if xdata.ndim > 1 or xdata.size != num_data:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	619 logging.warning(f'Illegal xdata shape ({xdata.shape})')
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	620 return None, None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	621 if not np.all(xdata[:-1] < xdata[1:]):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	622 logging.warning('Illegal xdata: must be monotonically increasing')
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	623 return None, None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	624 if current_index_ranges is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	625 if not isinstance(current_index_ranges, (tuple, list)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	626 logging.warning('Illegal current_index_ranges parameter ({current_index_ranges}, '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	627 f'{type(current_index_ranges)})')
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	628 return None, None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	629 if not isinstance(select_mask, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	630 logging.warning('Illegal select_mask parameter ({select_mask}, {type(select_mask)})')
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	631 return None, None
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	632 if num_index_ranges_max is not None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	633 logging.warning('num_index_ranges_max input not yet implemented in draw_mask_1d')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	634 if title is None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	635 title = 'select ranges of data'
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	636 elif not isinstance(title, str):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	637 illegal(title, 'title')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	638 title = ''
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	639 if legend is None and not isinstance(title, str):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	640 illegal(legend, 'legend')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	641 legend = None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	642
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	643 if select_mask:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	644 title = f'Click and drag to {title} you wish to include'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	645 selection_color = 'green'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	646 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	647 title = f'Click and drag to {title} you wish to exclude'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	648 selection_color = 'red'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	649
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	650 # Set initial selected mask and the selected/unselected index ranges as needed
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	651 selected_index_ranges = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	652 unselected_index_ranges = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	653 selected_mask = np.full(xdata.shape, False, dtype=bool)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	654 if current_index_ranges is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	655 if current_mask is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	656 if not select_mask:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	657 selected_index_ranges = [(0, num_data-1)]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	658 selected_mask = np.full(xdata.shape, True, dtype=bool)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	659 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	660 selected_mask = np.copy(np.asarray(current_mask, dtype=bool))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	661 if current_index_ranges is not None and len(current_index_ranges):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	662 current_index_ranges = sorted([(low, upp) for (low, upp) in current_index_ranges])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	663 for (low, upp) in current_index_ranges:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	664 if low > upp or low >= num_data or upp < 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	665 continue
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	666 if low < 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	667 low = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	668 if upp >= num_data:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	669 upp = num_data-1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	670 selected_index_ranges.append((low, upp))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	671 selected_mask = update_mask(selected_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	672 if current_index_ranges is not None and current_mask is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	673 selected_mask = np.logical_and(current_mask, selected_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	674 if current_mask is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	675 selected_index_ranges = update_index_ranges(selected_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	676
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	677 # Set up range selections for display
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	678 current_include = selected_index_ranges
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	679 current_exclude = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	680 selected_index_ranges = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	681 if not len(current_include):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	682 if select_mask:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	683 current_exclude = [(0, num_data-1)]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	684 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	685 current_include = [(0, num_data-1)]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	686 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	687 if current_include[0][0] > 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	688 current_exclude.append((0, current_include[0][0]-1))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	689 for i in range(1, len(current_include)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	690 current_exclude.append((current_include[i-1][1]+1, current_include[i][0]-1))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	691 if current_include[-1][1] < num_data-1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	692 current_exclude.append((current_include[-1][1]+1, num_data-1))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	693
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	694 if not test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	695
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	696 # Set up matplotlib figure
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	697 plt.close('all')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	698 fig, ax = plt.subplots()
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	699 plt.subplots_adjust(bottom=0.2)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	700 draw_selections(ax)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	701
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	702 # Set up event handling for click-and-drag range selection
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	703 cid_click = fig.canvas.mpl_connect('button_press_event', onclick)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	704 cid_release = fig.canvas.mpl_connect('button_release_event', onrelease)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	705
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	706 # Set up confirm / clear range selection buttons
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	707 confirm_b = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	708 clear_b = Button(plt.axes([0.59, 0.05, 0.15, 0.075]), 'Clear')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	709 cid_confirm = confirm_b.on_clicked(confirm_selection)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	710 cid_clear = clear_b.on_clicked(clear_last_selection)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	711
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	712 # Show figure
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	713 plt.show(block=True)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	714
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	715 # Disconnect callbacks when figure is closed
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	716 fig.canvas.mpl_disconnect(cid_click)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	717 fig.canvas.mpl_disconnect(cid_release)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	718 confirm_b.disconnect(cid_confirm)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	719 clear_b.disconnect(cid_clear)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	720
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	721 # Swap selection depending on select_mask
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	722 if not select_mask:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	723 selected_index_ranges, unselected_index_ranges = unselected_index_ranges, \
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	724 selected_index_ranges
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	725
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	726 # Update the mask with the currently selected/unselected x-ranges
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	727 selected_mask = update_mask(selected_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	728
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	729 # Update the currently included index ranges (where mask is True)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	730 current_include = update_index_ranges(selected_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	731
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	732 return selected_mask, current_include
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	733
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	734 def findImageFiles(path, filetype, name=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	735 if isinstance(name, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	736 name = f' {name} '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	737 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	738 name = ' '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	739 # Find available index range
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	740 if filetype == 'tif':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	741 if not isinstance(path, str) or not os.path.isdir(path):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	742 illegal_value(path, 'path', 'findImageRange')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	743 return -1, 0, []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	744 indexRegex = re.compile(r'\d+')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	745 # At this point only tiffs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	746 files = sorted([f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f)) and
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	747 f.endswith('.tif') and indexRegex.search(f)])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	748 num_imgs = len(files)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	749 if num_imgs < 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	750 logging.warning('No available'+name+'files')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	751 return -1, 0, []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	752 first_index = indexRegex.search(files[0]).group()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	753 last_index = indexRegex.search(files[-1]).group()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	754 if first_index is None or last_index is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	755 logging.error('Unable to find correctly indexed'+name+'images')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	756 return -1, 0, []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	757 first_index = int(first_index)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	758 last_index = int(last_index)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	759 if num_imgs != last_index-first_index+1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	760 logging.error('Non-consecutive set of indices for'+name+'images')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	761 return -1, 0, []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	762 paths = [os.path.join(path, f) for f in files]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	763 elif filetype == 'h5':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	764 if not isinstance(path, str) or not os.path.isfile(path):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	765 illegal_value(path, 'path', 'findImageRange')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	766 return -1, 0, []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	767 # At this point only h5 in alamo2 detector style
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	768 first_index = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	769 with h5py.File(path, 'r') as f:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	770 num_imgs = f['entry/instrument/detector/data'].shape[0]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	771 last_index = num_imgs-1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	772 paths = [path]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	773 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	774 illegal_value(filetype, 'filetype', 'findImageRange')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	775 return -1, 0, []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	776 logging.debug('\nNumber of available'+name+f'images: {num_imgs}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	777 logging.debug('Index range of available'+name+f'images: [{first_index}, '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	778 f'{last_index}]')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	779
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	780 return first_index, num_imgs, paths
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	781
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	782 def selectImageRange(first_index, offset, num_imgs, name=None, num_required=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	783 if isinstance(name, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	784 name = f' {name} '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	785 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	786 name = ' '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	787 # Check existing values
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	788 use_input = False
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	789 if (is_int(first_index, 0) and is_int(offset, 0) and is_int(num_imgs, 1)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	790 if offset < 0:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	791 use_input = input_yesno(f'\nCurrent{name}first index = {first_index}, '+
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	792 'use this value (y/n)?', 'y')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	793 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	794 use_input = input_yesno(f'\nCurrent{name}first index/offset = '+
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	795 f'{first_index}/{offset}, use these values (y/n)?', 'y')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	796 if num_required is None:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	797 if use_input:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	798 use_input = input_yesno(f'Current number of{name}images = '+
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	799 f'{num_imgs}, use this value (y/n)? ', 'y')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	800 if use_input:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	801 return first_index, offset, num_imgs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	802
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	803 # Check range against requirements
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	804 if num_imgs < 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	805 logging.warning('No available'+name+'images')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	806 return -1, -1, 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	807 if num_required is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	808 if num_imgs == 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	809 return first_index, 0, 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	810 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	811 if not is_int(num_required, 1):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	812 illegal_value(num_required, 'num_required', 'selectImageRange')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	813 return -1, -1, 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	814 if num_imgs < num_required:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	815 logging.error('Unable to find the required'+name+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	816 f'images ({num_imgs} out of {num_required})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	817 return -1, -1, 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	818
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	819 # Select index range
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	820 print('\nThe number of available'+name+f'images is {num_imgs}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	821 if num_required is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	822 last_index = first_index+num_imgs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	823 use_all = f'Use all ([{first_index}, {last_index}])'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	824 pick_offset = 'Pick a first index offset and a number of images'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	825 pick_bounds = 'Pick the first and last index'
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	826 choice = input_menu([use_all, pick_offset, pick_bounds], default=pick_offset)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	827 if not choice:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	828 offset = 0
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	829 elif choice == 1:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	830 offset = input_int('Enter the first index offset', 0, last_index-first_index)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	831 first_index += offset
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	832 if first_index == last_index:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	833 num_imgs = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	834 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	835 num_imgs = input_int('Enter the number of images', 1, num_imgs-offset)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	836 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	837 offset = input_int('Enter the first index', first_index, last_index)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	838 first_index += offset
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	839 num_imgs = input_int('Enter the last index', first_index, last_index)-first_index+1
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	840 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	841 use_all = f'Use ([{first_index}, {first_index+num_required-1}])'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	842 pick_offset = 'Pick the first index offset'
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	843 choice = input_menu([use_all, pick_offset], pick_offset)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	844 offset = 0
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	845 if choice == 1:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	846 offset = input_int('Enter the first index offset', 0, num_imgs-num_required)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	847 first_index += offset
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	848 num_imgs = num_required
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	849
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	850 return first_index, offset, num_imgs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	851
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	852 def loadImage(f, img_x_bounds=None, img_y_bounds=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	853 """Load a single image from file.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	854 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	855 if not os.path.isfile(f):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	856 logging.error(f'Unable to load {f}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	857 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	858 img_read = plt.imread(f)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	859 if not img_x_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	860 img_x_bounds = (0, img_read.shape[0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	861 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	862 if (not isinstance(img_x_bounds, (tuple, list)) or len(img_x_bounds) != 2 or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	863 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= img_read.shape[0])):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	864 logging.error(f'inconsistent row dimension in {f}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	865 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	866 if not img_y_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	867 img_y_bounds = (0, img_read.shape[1])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	868 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	869 if (not isinstance(img_y_bounds, list) or len(img_y_bounds) != 2 or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	870 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= img_read.shape[1])):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	871 logging.error(f'inconsistent column dimension in {f}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	872 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	873 return img_read[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	874
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	875 def loadImageStack(files, filetype, img_offset, num_imgs, num_img_skip=0,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	876 img_x_bounds=None, img_y_bounds=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	877 """Load a set of images and return them as a stack.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	878 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	879 logging.debug(f'img_offset = {img_offset}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	880 logging.debug(f'num_imgs = {num_imgs}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	881 logging.debug(f'num_img_skip = {num_img_skip}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	882 logging.debug(f'\nfiles:\n{files}\n')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	883 img_stack = np.array([])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	884 if filetype == 'tif':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	885 img_read_stack = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	886 i = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	887 t0 = time()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	888 for f in files[img_offset:img_offset+num_imgs:num_img_skip+1]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	889 if not i%20:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	890 logging.info(f' loading {i}/{num_imgs}: {f}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	891 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	892 logging.debug(f' loading {i}/{num_imgs}: {f}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	893 img_read = loadImage(f, img_x_bounds, img_y_bounds)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	894 img_read_stack.append(img_read)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	895 i += num_img_skip+1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	896 img_stack = np.stack([img_read for img_read in img_read_stack])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	897 logging.info(f'... done in {time()-t0:.2f} seconds!')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	898 logging.debug(f'img_stack shape = {np.shape(img_stack)}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	899 del img_read_stack, img_read
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	900 elif filetype == 'h5':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	901 if not isinstance(files[0], str) and not os.path.isfile(files[0]):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	902 illegal_value(files[0], 'files[0]', 'loadImageStack')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	903 return img_stack
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	904 t0 = time()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	905 logging.info(f'Loading {files[0]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	906 with h5py.File(files[0], 'r') as f:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	907 shape = f['entry/instrument/detector/data'].shape
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	908 if len(shape) != 3:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	909 logging.error(f'inconsistent dimensions in {files[0]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	910 if not img_x_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	911 img_x_bounds = (0, shape[1])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	912 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	913 if (not isinstance(img_x_bounds, (tuple, list)) or len(img_x_bounds) != 2 or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	914 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= shape[1])):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	915 logging.error(f'inconsistent row dimension in {files[0]} {img_x_bounds} '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	916 f'{shape[1]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	917 if not img_y_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	918 img_y_bounds = (0, shape[2])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	919 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	920 if (not isinstance(img_y_bounds, list) or len(img_y_bounds) != 2 or
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	921 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= shape[2])):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	922 logging.error(f'inconsistent column dimension in {files[0]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	923 img_stack = f.get('entry/instrument/detector/data')[
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	924 img_offset:img_offset+num_imgs:num_img_skip+1,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	925 img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	926 logging.info(f'... done in {time()-t0:.2f} seconds!')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	927 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	928 illegal_value(filetype, 'filetype', 'loadImageStack')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	929 return img_stack
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	930
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	931 def combine_tiffs_in_h5(files, num_imgs, h5_filename):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	932 img_stack = loadImageStack(files, 'tif', 0, num_imgs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	933 with h5py.File(h5_filename, 'w') as f:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	934 f.create_dataset('entry/instrument/detector/data', data=img_stack)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	935 del img_stack
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	936 return [h5_filename]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	937
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	938 def clearImshow(title=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	939 plt.ioff()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	940 if title is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	941 title = 'quick imshow'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	942 elif not isinstance(title, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	943 illegal_value(title, 'title', 'clearImshow')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	944 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	945 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	946
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	947 def clearPlot(title=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	948 plt.ioff()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	949 if title is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	950 title = 'quick plot'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	951 elif not isinstance(title, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	952 illegal_value(title, 'title', 'clearPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	953 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	954 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	955
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	956 def quickImshow(a, title=None, path=None, name=None, save_fig=False, save_only=False,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	957 clear=True, extent=None, show_grid=False, grid_color='w', grid_linewidth=1, **kwargs):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	958 if title is not None and not isinstance(title, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	959 illegal_value(title, 'title', 'quickImshow')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	960 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	961 if path is not None and not isinstance(path, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	962 illegal_value(path, 'path', 'quickImshow')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	963 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	964 if not isinstance(save_fig, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	965 illegal_value(save_fig, 'save_fig', 'quickImshow')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	966 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	967 if not isinstance(save_only, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	968 illegal_value(save_only, 'save_only', 'quickImshow')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	969 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	970 if not isinstance(clear, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	971 illegal_value(clear, 'clear', 'quickImshow')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	972 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	973 if not title:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	974 title='quick imshow'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	975 # else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	976 # title = re.sub(r"\s+", '_', title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	977 if name is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	978 ttitle = re.sub(r"\s+", '_', title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	979 if path is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	980 path = f'{ttitle}.png'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	981 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	982 path = f'{path}/{ttitle}.png'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	983 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	984 if path is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	985 path = name
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	986 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	987 path = f'{path}/{name}'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	988 if extent is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	989 extent = (0, a.shape[1], a.shape[0], 0)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	990 if clear:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	991 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	992 if not save_only:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	993 plt.ion()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	994 plt.figure(title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	995 plt.imshow(a, extent=extent, **kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	996 if show_grid:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	997 ax = plt.gca()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	998 ax.grid(color=grid_color, linewidth=grid_linewidth)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	999 # if title != 'quick imshow':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1000 # plt.title = title
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1001 if save_only:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1002 plt.savefig(path)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1003 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1004 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1005 if save_fig:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1006 plt.savefig(path)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1007
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1008 def quickPlot(*args, xerr=None, yerr=None, vlines=None, title=None, xlim=None, ylim=None,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1009 xlabel=None, ylabel=None, legend=None, path=None, name=None, show_grid=False,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1010 save_fig=False, save_only=False, clear=True, block=False, **kwargs):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1011 if title is not None and not isinstance(title, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1012 illegal_value(title, 'title', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1013 title = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1014 if xlim is not None and not isinstance(xlim, (tuple, list)) and len(xlim) != 2:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1015 illegal_value(xlim, 'xlim', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1016 xlim = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1017 if ylim is not None and not isinstance(ylim, (tuple, list)) and len(ylim) != 2:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1018 illegal_value(ylim, 'ylim', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1019 ylim = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1020 if xlabel is not None and not isinstance(xlabel, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1021 illegal_value(xlabel, 'xlabel', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1022 xlabel = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1023 if ylabel is not None and not isinstance(ylabel, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1024 illegal_value(ylabel, 'ylabel', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1025 ylabel = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1026 if legend is not None and not isinstance(legend, (tuple, list)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1027 illegal_value(legend, 'legend', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1028 legend = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1029 if path is not None and not isinstance(path, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1030 illegal_value(path, 'path', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1031 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1032 if not isinstance(show_grid, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1033 illegal_value(show_grid, 'show_grid', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1034 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1035 if not isinstance(save_fig, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1036 illegal_value(save_fig, 'save_fig', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1037 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1038 if not isinstance(save_only, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1039 illegal_value(save_only, 'save_only', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1040 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1041 if not isinstance(clear, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1042 illegal_value(clear, 'clear', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1043 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1044 if not isinstance(block, bool):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1045 illegal_value(block, 'block', 'quickPlot')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1046 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1047 if title is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1048 title = 'quick plot'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1049 # else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1050 # title = re.sub(r"\s+", '_', title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1051 if name is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1052 ttitle = re.sub(r"\s+", '_', title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1053 if path is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1054 path = f'{ttitle}.png'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1055 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1056 path = f'{path}/{ttitle}.png'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1057 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1058 if path is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1059 path = name
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1060 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1061 path = f'{path}/{name}'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1062 if clear:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1063 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1064 args = unwrap_tuple(args)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1065 if depth_tuple(args) > 1 and (xerr is not None or yerr is not None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1066 logging.warning('Error bars ignored form multiple curves')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1067 if not save_only:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1068 if block:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1069 plt.ioff()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1070 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1071 plt.ion()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1072 plt.figure(title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1073 if depth_tuple(args) > 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1074 for y in args:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1075 plt.plot(y, *kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1076 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1077 if xerr is None and yerr is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1078 plt.plot(args, *kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1079 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1080 plt.errorbar(args, xerr=xerr, yerr=yerr, *kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1081 if vlines is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1082 for v in vlines:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1083 plt.axvline(v, color='r', linestyle='--', **kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1084 # if vlines is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1085 # for s in tuple(([x, x], list(plt.gca().get_ylim())) for x in vlines):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1086 # plt.plot(s, color='red', *kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1087 if xlim is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1088 plt.xlim(xlim)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1089 if ylim is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1090 plt.ylim(ylim)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1091 if xlabel is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1092 plt.xlabel(xlabel)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1093 if ylabel is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1094 plt.ylabel(ylabel)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1095 if show_grid:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1096 ax = plt.gca()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1097 ax.grid(color='k')#, linewidth=1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1098 if legend is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1099 plt.legend(legend)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1100 if save_only:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1101 plt.savefig(path)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1102 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1103 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1104 if save_fig:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1105 plt.savefig(path)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1106 if block:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1107 plt.show(block=block)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1108
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1109 def selectArrayBounds(a, x_low=None, x_upp=None, num_x_min=None, ask_bounds=False,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1110 title='select array bounds'):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1111 """Interactively select the lower and upper data bounds for a numpy array.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1112 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1113 if isinstance(a, (tuple, list)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1114 a = np.array(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1115 if not isinstance(a, np.ndarray) or a.ndim != 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1116 illegal_value(a.ndim, 'array type or dimension', 'selectArrayBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1117 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1118 len_a = len(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1119 if num_x_min is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1120 num_x_min = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1121 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1122 if num_x_min < 2 or num_x_min > len_a:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1123 logging.warning('Illegal value for num_x_min in selectArrayBounds, input ignored')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1124 num_x_min = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1125
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1126 # Ask to use current bounds
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1127 if ask_bounds and (x_low is not None or x_upp is not None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1128 if x_low is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1129 x_low = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1130 if not is_int(x_low, 0, len_a-num_x_min):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1131 illegal_value(x_low, 'x_low', 'selectArrayBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1132 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1133 if x_upp is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1134 x_upp = len_a
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1135 if not is_int(x_upp, x_low+num_x_min, len_a):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1136 illegal_value(x_upp, 'x_upp', 'selectArrayBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1137 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1138 quickPlot((range(len_a), a), vlines=(x_low,x_upp), title=title)
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1139 if not input_yesno(f'\nCurrent array bounds: [{x_low}, {x_upp}] '+
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1140 'use these values (y/n)?', 'y'):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1141 x_low = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1142 x_upp = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1143 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1144 clearPlot(title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1145 return x_low, x_upp
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1146
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1147 if x_low is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1148 x_min = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1149 x_max = len_a
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1150 x_low_max = len_a-num_x_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1151 while True:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1152 quickPlot(range(x_min, x_max), a[x_min:x_max], title=title)
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1153 zoom_flag = input_yesno('Set lower data bound (y) or zoom in (n)?', 'y')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1154 if zoom_flag:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1155 x_low = input_int(' Set lower data bound', 0, x_low_max)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1156 break
63 98a83f03d91b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877" rv43 parents: 56 diff changeset	1157 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1158 x_min = input_int(' Set lower zoom index', 0, x_low_max)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1159 x_max = input_int(' Set upper zoom index', x_min+1, x_low_max+1)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1160 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1161 if not is_int(x_low, 0, len_a-num_x_min):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1162 illegal_value(x_low, 'x_low', 'selectArrayBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1163 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1164 if x_upp is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1165 x_min = x_low+num_x_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1166 x_max = len_a
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1167 x_upp_min = x_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1168 while True:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1169 quickPlot(range(x_min, x_max), a[x_min:x_max], title=title)
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1170 zoom_flag = input_yesno('Set upper data bound (y) or zoom in (n)?', 'y')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1171 if zoom_flag:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1172 x_upp = input_int(' Set upper data bound', x_upp_min, len_a)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1173 break
63 98a83f03d91b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877" rv43 parents: 56 diff changeset	1174 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1175 x_min = input_int(' Set upper zoom index', x_upp_min, len_a-1)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1176 x_max = input_int(' Set upper zoom index', x_min+1, len_a)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1177 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1178 if not is_int(x_upp, x_low+num_x_min, len_a):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1179 illegal_value(x_upp, 'x_upp', 'selectArrayBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1180 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1181 print(f'lower bound = {x_low} (inclusive)\nupper bound = {x_upp} (exclusive)]')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1182 quickPlot((range(len_a), a), vlines=(x_low,x_upp), title=title)
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1183 if not input_yesno('Accept these bounds (y/n)?', 'y'):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1184 x_low, x_upp = selectArrayBounds(a, None, None, num_x_min, title=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1185 clearPlot(title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1186 return x_low, x_upp
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1187
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1188 def selectImageBounds(a, axis, low=None, upp=None, num_min=None,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1189 title='select array bounds'):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1190 """Interactively select the lower and upper data bounds for a 2D numpy array.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1191 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1192 if isinstance(a, np.ndarray):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1193 if a.ndim != 2:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1194 illegal_value(a.ndim, 'array dimension', 'selectImageBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1195 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1196 elif isinstance(a, (tuple, list)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1197 if len(a) != 2:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1198 illegal_value(len(a), 'array dimension', 'selectImageBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1199 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1200 if len(a[0]) != len(a[1]) or not (isinstance(a[0], (tuple, list, np.ndarray)) and
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1201 isinstance(a[1], (tuple, list, np.ndarray))):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1202 logging.error(f'Illegal array type in selectImageBounds ({type(a[0])} {type(a[1])})')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1203 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1204 a = np.array(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1205 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1206 illegal_value(a, 'array type', 'selectImageBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1207 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1208 if axis < 0 or axis >= a.ndim:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1209 illegal_value(axis, 'axis', 'selectImageBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1210 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1211 low_save = low
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1212 upp_save = upp
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1213 num_min_save = num_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1214 if num_min is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1215 num_min = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1216 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1217 if num_min < 2 or num_min > a.shape[axis]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1218 logging.warning('Illegal input for num_min in selectImageBounds, input ignored')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1219 num_min = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1220 if low is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1221 min_ = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1222 max_ = a.shape[axis]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1223 low_max = a.shape[axis]-num_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1224 while True:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1225 if axis:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1226 quickImshow(a[:,min_:max_], title=title, aspect='auto',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1227 extent=[min_,max_,a.shape[0],0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1228 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1229 quickImshow(a[min_:max_,:], title=title, aspect='auto',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1230 extent=[0,a.shape[1], max_,min_])
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1231 zoom_flag = input_yesno('Set lower data bound (y) or zoom in (n)?', 'y')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1232 if zoom_flag:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1233 low = input_int(' Set lower data bound', 0, low_max)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1234 break
63 98a83f03d91b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877" rv43 parents: 56 diff changeset	1235 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1236 min_ = input_int(' Set lower zoom index', 0, low_max)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1237 max_ = input_int(' Set upper zoom index', min_+1, low_max+1)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1238 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1239 if not is_int(low, 0, a.shape[axis]-num_min):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1240 illegal_value(low, 'low', 'selectImageBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1241 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1242 if upp is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1243 min_ = low+num_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1244 max_ = a.shape[axis]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1245 upp_min = min_
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1246 while True:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1247 if axis:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1248 quickImshow(a[:,min_:max_], title=title, aspect='auto',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1249 extent=[min_,max_,a.shape[0],0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1250 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1251 quickImshow(a[min_:max_,:], title=title, aspect='auto',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1252 extent=[0,a.shape[1], max_,min_])
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1253 zoom_flag = input_yesno('Set upper data bound (y) or zoom in (n)?', 'y')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1254 if zoom_flag:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1255 upp = input_int(' Set upper data bound', upp_min, a.shape[axis])
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1256 break
63 98a83f03d91b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877" rv43 parents: 56 diff changeset	1257 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1258 min_ = input_int(' Set upper zoom index', upp_min, a.shape[axis]-1)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1259 max_ = input_int(' Set upper zoom index', min_+1, a.shape[axis])
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1260 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1261 if not is_int(upp, low+num_min, a.shape[axis]):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1262 illegal_value(upp, 'upp', 'selectImageBounds')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1263 return None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1264 bounds = (low, upp)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1265 a_tmp = np.copy(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1266 a_tmp_max = a.max()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1267 if axis:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1268 a_tmp[:,bounds[0]] = a_tmp_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1269 a_tmp[:,bounds[1]-1] = a_tmp_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1270 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1271 a_tmp[bounds[0],:] = a_tmp_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1272 a_tmp[bounds[1]-1,:] = a_tmp_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1273 print(f'lower bound = {low} (inclusive)\nupper bound = {upp} (exclusive)')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1274 quickImshow(a_tmp, title=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1275 del a_tmp
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1276 if not input_yesno('Accept these bounds (y/n)?', 'y'):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1277 bounds = selectImageBounds(a, axis, low=low_save, upp=upp_save, num_min=num_min_save,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1278 title=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1279 return bounds
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1280
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1281
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1282 class Config:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1283 """Base class for processing a config file or dictionary.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1284 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1285 def __init__(self, config_file=None, config_dict=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1286 self.config = {}
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1287 self.load_flag = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1288 self.suffix = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1289
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1290 # Load config file
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1291 if config_file is not None and config_dict is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1292 logging.warning('Ignoring config_dict (both config_file and config_dict are specified)')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1293 if config_file is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1294 self.loadFile(config_file)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1295 elif config_dict is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1296 self.loadDict(config_dict)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1297
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1298 def loadFile(self, config_file):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1299 """Load a config file.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1300 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1301 if self.load_flag:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1302 logging.warning('Overwriting any previously loaded config file')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1303 self.config = {}
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1304
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1305 # Ensure config file exists
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1306 if not os.path.isfile(config_file):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1307 logging.error(f'Unable to load {config_file}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1308 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1309
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1310 # Load config file (for now for Galaxy, allow .dat extension)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1311 self.suffix = os.path.splitext(config_file)[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1312 if self.suffix == '.yml' or self.suffix == '.yaml' or self.suffix == '.dat':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1313 with open(config_file, 'r') as f:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1314 self.config = yaml.safe_load(f)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1315 elif self.suffix == '.txt':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1316 with open(config_file, 'r') as f:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1317 lines = f.read().splitlines()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1318 self.config = {item[0].strip():literal_eval(item[1].strip()) for item in
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1319 [line.split('#')[0].split('=') for line in lines if '=' in line.split('#')[0]]}
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1320 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1321 illegal_value(self.suffix, 'config file extension', 'Config.loadFile')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1322
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1323 # Make sure config file was correctly loaded
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1324 if isinstance(self.config, dict):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1325 self.load_flag = True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1326 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1327 logging.error(f'Unable to load dictionary from config file: {config_file}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1328 self.config = {}
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1329
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1330 def loadDict(self, config_dict):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1331 """Takes a dictionary and places it into self.config.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1332 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1333 if self.load_flag:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1334 logging.warning('Overwriting the previously loaded config file')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1335
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1336 if isinstance(config_dict, dict):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1337 self.config = config_dict
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1338 self.load_flag = True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1339 else:
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1340 illegal_value(config_dict, 'dictionary config object', 'Config.loadDict')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1341 self.config = {}
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1342
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1343 def saveFile(self, config_file):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1344 """Save the config file (as a yaml file only right now).
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1345 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1346 suffix = os.path.splitext(config_file)[1]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1347 if suffix != '.yml' and suffix != '.yaml':
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1348 illegal_value(suffix, 'config file extension', 'Config.saveFile')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1349
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1350 # Check if config file exists
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1351 if os.path.isfile(config_file):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1352 logging.info(f'Updating {config_file}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1353 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1354 logging.info(f'Saving {config_file}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1355
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1356 # Save config file
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1357 with open(config_file, 'w') as f:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1358 yaml.safe_dump(self.config, f)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1359
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1360 def validate(self, pars_required, pars_missing=None):
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1361 """Returns False if any required keys are missing.
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1362 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1363 if not self.load_flag:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1364 logging.error('Load a config file prior to calling Config.validate')
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1365
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1366 def validate_nested_pars(config, par):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1367 par_levels = par.split(':')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1368 first_level_par = par_levels[0]
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1369 try:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1370 first_level_par = int(first_level_par)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1371 except:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1372 pass
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1373 try:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1374 next_level_config = config[first_level_par]
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1375 if len(par_levels) > 1:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1376 next_level_par = ':'.join(par_levels[1:])
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1377 return validate_nested_pars(next_level_config, next_level_par)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1378 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1379 return True
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1380 except:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1381 return False
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1382
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1383 pars_missing = [p for p in pars_required if not validate_nested_pars(self.config, p)]
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1384 if len(pars_missing) > 0:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1385 logging.error(f'Missing item(s) in configuration: {", ".join(pars_missing)}')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: diff changeset	1386 return False
65 f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1387 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7" rv43 parents: 63 diff changeset	1388 return True

Mercurial > repos > rv43 > tomo

annotate general.py @ 65:f31ef7bfb430 draft