tomo: msnc_tools.py annotate

author	rv43
date	Tue, 29 Mar 2022 16:10:16 +0000
parents
children	e4778148df6b

rev	line source
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1 #!/usr/bin/env python3
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	3 # -- coding: utf-8 --
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	4 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	5 Created on Mon Dec 6 15:36:22 2021
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	6
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	7 @author: rv43
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	8 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	9
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	10 import logging
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	11
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	12 import os
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	13 import sys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	14 import re
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	15 import yaml
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	16 import h5py
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	17 try:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	18 import pyinputplus as pyip
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	19 except:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	20 pass
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	21 import numpy as np
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	22 import imageio as img
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	23 import matplotlib.pyplot as plt
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	24 from time import time
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	25 from ast import literal_eval
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	26 try:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	27 from lmfit.models import StepModel, RectangleModel
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	28 except:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	29 pass
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	30
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	31 def depth_list(L): return isinstance(L, list) and max(map(depth_list, L))+1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	32 def depth_tuple(T): return isinstance(T, tuple) and max(map(depth_tuple, T))+1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	33
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	34 def is_int(v, v_min=None, v_max=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	35 """Value is an integer in range v_min <= v <= v_max.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	36 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	37 if not isinstance(v, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	38 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	39 if (v_min != None and v < v_min) or (v_max != None and v > v_max):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	40 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	41 return True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	42
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	43 def is_num(v, v_min=None, v_max=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	44 """Value is a number in range v_min <= v <= v_max.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	45 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	46 if not isinstance(v, (int,float)):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	47 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	48 if (v_min != None and v < v_min) or (v_max != None and v > v_max):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	49 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	50 return True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	51
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	52 def is_index(v, v_min=0, v_max=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	53 """Value is an array index in range v_min <= v < v_max.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	54 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	55 if not isinstance(v, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	56 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	57 if v < v_min or (v_max != None and v >= v_max):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	58 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	59 return True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	60
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	61 def is_index_range(v, v_min=0, v_max=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	62 """Value is an array index range in range v_min <= v[0] <= v[1] < v_max.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	63 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	64 if not (isinstance(v, list) and len(v) == 2 and isinstance(v[0], int) and
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	65 isinstance(v[1], int)):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	66 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	67 if not 0 <= v[0] < v[1] or (v_max != None and v[1] >= v_max):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	68 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	69 return True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	70
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	71 def illegal_value(name, value, location=None, exit_flag=False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	72 if not isinstance(location, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	73 location = ''
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	74 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	75 location = f'in {location} '
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	76 if isinstance(name, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	77 logging.error(f'Illegal value for {name} {location}({value}, {type(value)})')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	78 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	79 logging.error(f'Illegal value {location}({value}, {type(value)})')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	80 if exit_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	81 exit(1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	82
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	83 def get_trailing_int(string):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	84 indexRegex = re.compile(r'\d+$')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	85 mo = indexRegex.search(string)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	86 if mo == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	87 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	88 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	89 return int(mo.group())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	90
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	91 def findImageFiles(path, filetype, name=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	92 if isinstance(name, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	93 name = f' {name} '
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	94 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	95 name = ' '
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	96 # Find available index range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	97 if filetype == 'tif':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	98 if not isinstance(path, str) and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	99 illegal_value('path', path, 'findImageRange')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	100 return -1, 0, []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	101 indexRegex = re.compile(r'\d+')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	102 # At this point only tiffs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	103 files = sorted([f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f)) and
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	104 f.endswith('.tif') and indexRegex.search(f)])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	105 num_imgs = len(files)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	106 if num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	107 logging.warning('No available'+name+'files')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	108 return -1, 0, []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	109 first_index = indexRegex.search(files[0]).group()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	110 last_index = indexRegex.search(files[-1]).group()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	111 if first_index == None or last_index == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	112 logging.error('Unable to find correctly indexed'+name+'images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	113 return -1, 0, []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	114 first_index = int(first_index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	115 last_index = int(last_index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	116 if num_imgs != last_index-first_index+1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	117 logging.error('Non-consecutive set of indices for'+name+'images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	118 return -1, 0, []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	119 paths = [os.path.join(path, f) for f in files]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	120 elif filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	121 if not isinstance(path, str) or not os.path.isfile(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	122 illegal_value('path', path, 'findImageRange')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	123 return -1, 0, []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	124 # At this point only h5 in alamo2 detector style
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	125 first_index = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	126 with h5py.File(path, 'r') as f:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	127 num_imgs = f['entry/instrument/detector/data'].shape[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	128 last_index = num_imgs-1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	129 paths = [path]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	130 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	131 illegal_value('filetype', filetype, 'findImageRange')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	132 return -1, 0, []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	133 logging.debug('\nNumber of available'+name+f'images: {num_imgs}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	134 logging.debug('Index range of available'+name+f'images: [{first_index}, '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	135 f'{last_index}]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	136
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	137 return first_index, num_imgs, paths
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	138
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	139 def selectImageRange(first_index, offset, num_imgs, name=None, num_required=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	140 if isinstance(name, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	141 name = f' {name} '
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	142 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	143 name = ' '
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	144 # Check existing values
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	145 use_input = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	146 if (is_int(first_index, 0) and is_int(offset, 0) and is_int(num_imgs, 1)):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	147 if offset < 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	148 use_input = pyip.inputYesNo('\nCurrent'+name+f'first index = {first_index}, '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	149 'use this value ([y]/n)? ', blank=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	150 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	151 use_input = pyip.inputYesNo('\nCurrent'+name+'first index/offset = '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	152 f'{first_index}/{offset}, use these values ([y]/n)? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	153 blank=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	154 if use_input != 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	155 use_input = pyip.inputYesNo('Current number of'+name+'images = '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	156 f'{num_imgs}, use this value ([y]/n)? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	157 blank=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	158 if use_input == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	159 return first_index, offset, num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	160
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	161 # Check range against requirements
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	162 if num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	163 logging.warning('No available'+name+'images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	164 return -1, -1, 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	165 if num_required == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	166 if num_imgs == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	167 return first_index, 0, 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	168 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	169 if not is_int(num_required, 1):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	170 illegal_value('num_required', num_required, 'selectImageRange')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	171 return -1, -1, 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	172 if num_imgs < num_required:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	173 logging.error('Unable to find the required'+name+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	174 f'images ({num_imgs} out of {num_required})')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	175 return -1, -1, 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	176
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	177 # Select index range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	178 if num_required == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	179 last_index = first_index+num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	180 use_all = f'Use all ([{first_index}, {last_index}])'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	181 pick_offset = 'Pick a first index offset and a number of images'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	182 pick_bounds = 'Pick the first and last index'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	183 menuchoice = pyip.inputMenu([use_all, pick_offset, pick_bounds], numbered=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	184 if menuchoice == use_all:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	185 offset = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	186 elif menuchoice == pick_offset:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	187 offset = pyip.inputInt('Enter the first index offset'+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	188 f' [0, {last_index-first_index}]: ', min=0, max=last_index-first_index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	189 first_index += offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	190 if first_index == last_index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	191 num_imgs = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	192 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	193 num_imgs = pyip.inputInt(f'Enter the number of images [1, {num_imgs-offset}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	194 min=1, max=num_imgs-offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	195 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	196 offset = pyip.inputInt(f'Enter the first index [{first_index}, {last_index}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	197 min=first_index, max=last_index)-first_index
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	198 first_index += offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	199 num_imgs = pyip.inputInt(f'Enter the last index [{first_index}, {last_index}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	200 min=first_index, max=last_index)-first_index+1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	201 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	202 use_all = f'Use ([{first_index}, {first_index+num_required-1}])'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	203 pick_offset = 'Pick the first index offset'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	204 menuchoice = pyip.inputMenu([use_all, pick_offset], numbered=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	205 offset = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	206 if menuchoice == pick_offset:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	207 offset = pyip.inputInt('Enter the first index offset'+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	208 f'[0, {num_imgs-num_required}]: ', min=0, max=num_imgs-num_required)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	209 first_index += offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	210 num_imgs = num_required
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	211
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	212 return first_index, offset, num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	213
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	214 def loadImage(f, img_x_bounds=None, img_y_bounds=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	215 """Load a single image from file.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	216 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	217 if not os.path.isfile(f):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	218 logging.error(f'Unable to load {f}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	219 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	220 img_read = img.imread(f)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	221 if not img_x_bounds:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	222 img_x_bounds = [0, img_read.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	223 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	224 if (not isinstance(img_x_bounds, list) or len(img_x_bounds) != 2 or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	225 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= img_read.shape[0])):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	226 logging.error(f'inconsistent row dimension in {f}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	227 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	228 if not img_y_bounds:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	229 img_y_bounds = [0, img_read.shape[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	230 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	231 if (not isinstance(img_y_bounds, list) or len(img_y_bounds) != 2 or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	232 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= img_read.shape[0])):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	233 logging.error(f'inconsistent column dimension in {f}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	234 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	235 return img_read[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	236
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	237 def loadImageStack(files, filetype, img_offset, num_imgs, num_img_skip=0,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	238 img_x_bounds=None, img_y_bounds=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	239 """Load a set of images and return them as a stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	240 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	241 logging.debug(f'img_offset = {img_offset}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	242 logging.debug(f'num_imgs = {num_imgs}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	243 logging.debug(f'num_img_skip = {num_img_skip}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	244 logging.debug(f'\nfiles:\n{files}\n')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	245 img_stack = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	246 if filetype == 'tif':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	247 img_read_stack = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	248 i = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	249 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	250 for f in files[img_offset:img_offset+num_imgs:num_img_skip+1]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	251 if not i%20:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	252 logging.info(f' loading {i}/{num_imgs}: {f}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	253 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	254 logging.debug(f' loading {i}/{num_imgs}: {f}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	255 img_read = loadImage(f, img_x_bounds, img_y_bounds)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	256 img_read_stack.append(img_read)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	257 i += num_img_skip+1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	258 img_stack = np.stack([img_read for img_read in img_read_stack])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	259 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	260 logging.debug(f'img_stack shape = {np.shape(img_stack)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	261 del img_read_stack, img_read
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	262 elif filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	263 if not isinstance(files[0], str) and not os.path.isfile(files[0]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	264 illegal_value('files[0]', files[0], 'loadImageStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	265 return img_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	266 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	267 with h5py.File(files[0], 'r') as f:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	268 shape = f['entry/instrument/detector/data'].shape
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	269 if len(shape) != 3:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	270 logging.error(f'inconsistent dimensions in {files[0]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	271 if not img_x_bounds:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	272 img_x_bounds = [0, shape[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	273 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	274 if (not isinstance(img_x_bounds, list) or len(img_x_bounds) != 2 or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	275 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= shape[1])):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	276 logging.error(f'inconsistent row dimension in {files[0]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	277 if not img_y_bounds:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	278 img_y_bounds = [0, shape[2]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	279 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	280 if (not isinstance(img_y_bounds, list) or len(img_y_bounds) != 2 or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	281 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= shape[2])):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	282 logging.error(f'inconsistent column dimension in {files[0]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	283 img_stack = f.get('entry/instrument/detector/data')[
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	284 img_offset:img_offset+num_imgs:num_img_skip+1,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	285 img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	286 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	287 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	288 illegal_value('filetype', filetype, 'findImageRange')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	289 return img_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	290
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	291 def clearFig(title):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	292 if not isinstance(title, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	293 illegal_value('title', title, 'clearFig')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	294 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	295 plt.close(fig=re.sub(r"\s+", '_', title))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	296
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	297 def quickImshow(a, title=None, path=None, name=None, save_fig=False, save_only=False,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	298 clear=True, **kwargs):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	299 if title != None and not isinstance(title, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	300 illegal_value('title', title, 'quickImshow')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	301 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	302 if path is not None and not isinstance(path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	303 illegal_value('path', path, 'quickImshow')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	304 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	305 if not isinstance(save_fig, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	306 illegal_value('save_fig', save_fig, 'quickImshow')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	307 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	308 if not isinstance(save_only, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	309 illegal_value('save_only', save_only, 'quickImshow')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	310 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	311 if not isinstance(clear, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	312 illegal_value('clear', clear, 'quickImshow')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	313 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	314 if not title:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	315 title='quick_imshow'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	316 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	317 title = re.sub(r"\s+", '_', title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	318 if name is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	319 if path is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	320 path = f'{title}.png'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	321 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	322 path = f'{path}/{title}.png'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	323 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	324 if path is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	325 path = name
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	326 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	327 path = f'{path}/{name}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	328 if clear:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	329 plt.close(fig=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	330 if save_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	331 plt.figure(title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	332 plt.imshow(a, **kwargs)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	333 plt.savefig(path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	334 plt.close(fig=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	335 #plt.imsave(f'{title}.png', a, **kwargs)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	336 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	337 plt.ion()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	338 plt.figure(title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	339 plt.imshow(a, **kwargs)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	340 if save_fig:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	341 plt.savefig(path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	342 plt.pause(1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	343
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	344 def quickPlot(*args, title=None, path=None, name=None, save_fig=False, save_only=False,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	345 clear=True, **kwargs):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	346 if title != None and not isinstance(title, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	347 illegal_value('title', title, 'quickPlot')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	348 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	349 if path is not None and not isinstance(path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	350 illegal_value('path', path, 'quickPlot')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	351 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	352 if not isinstance(save_fig, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	353 illegal_value('save_fig', save_fig, 'quickPlot')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	354 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	355 if not isinstance(save_only, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	356 illegal_value('save_only', save_only, 'quickPlot')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	357 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	358 if not isinstance(clear, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	359 illegal_value('clear', clear, 'quickPlot')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	360 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	361 if not title:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	362 title = 'quick_plot'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	363 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	364 title = re.sub(r"\s+", '_', title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	365 if name is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	366 if path is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	367 path = f'{title}.png'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	368 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	369 path = f'{path}/{title}.png'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	370 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	371 if path is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	372 path = name
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	373 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	374 path = f'{path}/{name}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	375 if clear:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	376 plt.close(fig=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	377 if save_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	378 plt.figure(title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	379 if depth_tuple(args) > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	380 for y in args:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	381 plt.plot(y, *kwargs)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	382 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	383 plt.plot(args, *kwargs)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	384 plt.savefig(path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	385 plt.close(fig=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	386 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	387 plt.ion()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	388 plt.figure(title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	389 if depth_tuple(args) > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	390 for y in args:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	391 plt.plot(y, *kwargs)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	392 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	393 plt.plot(args, *kwargs)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	394 if save_fig:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	395 plt.savefig(path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	396 plt.pause(1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	397
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	398 def selectArrayBounds(a, x_low=None, x_upp=None, num_x_min=None,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	399 title='select array bounds'):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	400 """Interactively select the lower and upper data bounds for a numpy array.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	401 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	402 if not isinstance(a, np.ndarray) or a.ndim != 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	403 logging.error('Illegal array type or dimension in selectArrayBounds')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	404 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	405 if num_x_min == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	406 num_x_min = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	407 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	408 if num_x_min < 2 or num_x_min > a.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	409 logging.warning('Illegal input for num_x_min in selectArrayBounds, input ignored')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	410 num_x_min = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	411 if x_low == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	412 x_min = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	413 x_max = a.size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	414 x_low_max = a.size-num_x_min
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	415 while True:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	416 quickPlot(range(x_min, x_max), a[x_min:x_max], title=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	417 zoom_flag = pyip.inputInt('Set lower data bound (0) or zoom in (1)?: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	418 min=0, max=1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	419 if zoom_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	420 x_min = pyip.inputInt(f' Set lower zoom index [0, {x_low_max}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	421 min=0, max=x_low_max)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	422 x_max = pyip.inputInt(f' Set upper zoom index [{x_min+1}, {x_low_max+1}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	423 min=x_min+1, max=x_low_max+1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	424 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	425 x_low = pyip.inputInt(f' Set lower data bound [0, {x_low_max}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	426 min=0, max=x_low_max)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	427 break
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	428 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	429 if not is_int(x_low, 0, a.size-num_x_min):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	430 illegal_value('x_low', x_low, 'selectArrayBounds')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	431 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	432 if x_upp == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	433 x_min = x_low+num_x_min
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	434 x_max = a.size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	435 x_upp_min = x_min
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	436 while True:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	437 quickPlot(range(x_min, x_max), a[x_min:x_max], title=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	438 zoom_flag = pyip.inputInt('Set upper data bound (0) or zoom in (1)?: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	439 min=0, max=1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	440 if zoom_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	441 x_min = pyip.inputInt(f' Set upper zoom index [{x_upp_min}, {a.size-1}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	442 min=x_upp_min, max=a.size-1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	443 x_max = pyip.inputInt(f' Set upper zoom index [{x_min+1}, {a.size}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	444 min=x_min+1, max=a.size)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	445 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	446 x_upp = pyip.inputInt(f' Set upper data bound [{x_upp_min}, {a.size}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	447 min=x_upp_min, max=a.size)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	448 break
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	449 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	450 if not is_int(x_upp, x_low+num_x_min, a.size):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	451 illegal_value('x_upp', x_upp, 'selectArrayBounds')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	452 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	453 bounds = [x_low, x_upp]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	454 print(f'lower bound = {x_low} (inclusive)\nupper bound = {x_upp} (exclusive)]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	455 #quickPlot(range(bounds[0], bounds[1]), a[bounds[0]:bounds[1]], title=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	456 quickPlot((range(a.size), a), ([bounds[0], bounds[0]], [a.min(), a.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	457 ([bounds[1], bounds[1]], [a.min(), a.max()], 'r-'), title=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	458 if pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	459 bounds = selectArrayBounds(a, title=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	460 return bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	461
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	462 def selectImageBounds(a, axis, low=None, upp=None, num_min=None,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	463 title='select array bounds'):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	464 """Interactively select the lower and upper data bounds for a 2D numpy array.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	465 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	466 if not isinstance(a, np.ndarray) or a.ndim != 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	467 logging.error('Illegal array type or dimension in selectImageBounds')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	468 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	469 if axis < 0 or axis >= a.ndim:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	470 illegal_value('axis', axis, 'selectImageBounds')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	471 return None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	472 if num_min == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	473 num_min = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	474 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	475 if num_min < 2 or num_min > a.shape[axis]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	476 logging.warning('Illegal input for num_min in selectImageBounds, input ignored')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	477 num_min = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	478 if low == None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	479 min_ = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	480 max_ = a.shape[axis]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	481 low_max = a.shape[axis]-num_min
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	482 while True:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	483 if axis:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	484 quickImshow(a[:,min_:max_], title=title, aspect='auto',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	485 extent=[min_,max_,a.shape[0],0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	486 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	487 quickImshow(a[min_:max_,:], title=title, aspect='auto',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	488 extent=[0,a.shape[1], max_,min_])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	489 zoom_flag = pyip.inputInt('Set lower data bound (0) or zoom in (1)?: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	490 min=0, max=1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	491 if zoom_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	492 min_ = pyip.inputInt(f' Set lower zoom index [0, {low_max}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	493 min=0, max=low_max)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	494 max_ = pyip.inputInt(f' Set upper zoom index [{min_+1}, {low_max+1}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	495 min=min_+1, max=low_max+1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	496 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	497 low = pyip.inputInt(f' Set lower data bound [0, {low_max}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	498 min=0, max=low_max)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	499 break
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	500 else:

0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1 #!/usr/bin/env python3

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2

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3 # -*- coding: utf-8 -*-

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4 """

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5 Created on Mon Dec 6 15:36:22 2021

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6

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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7 @author: rv43

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8 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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9

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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10 import logging

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11

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12 import os

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13 import sys

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14 import re

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15 import yaml

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16 import h5py

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17 try:

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18 import pyinputplus as pyip

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19 except:

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20 pass

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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21 import numpy as np

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22 import imageio as img

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23 import matplotlib.pyplot as plt

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24 from time import time

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25 from ast import literal_eval

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26 try:

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27 from lmfit.models import StepModel, RectangleModel

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28 except:

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29 pass

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30

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31 def depth_list(L): return isinstance(L, list) and max(map(depth_list, L))+1

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32 def depth_tuple(T): return isinstance(T, tuple) and max(map(depth_tuple, T))+1

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33

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34 def is_int(v, v_min=None, v_max=None):

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35 """Value is an integer in range v_min <= v <= v_max.

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36 """

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37 if not isinstance(v, int):

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38 return False

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39 if (v_min != None and v < v_min) or (v_max != None and v > v_max):

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40 return False

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41 return True

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42

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43 def is_num(v, v_min=None, v_max=None):

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44 """Value is a number in range v_min <= v <= v_max.

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45 """

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46 if not isinstance(v, (int,float)):

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47 return False

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48 if (v_min != None and v < v_min) or (v_max != None and v > v_max):

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49 return False

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50 return True

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51

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52 def is_index(v, v_min=0, v_max=None):

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53 """Value is an array index in range v_min <= v < v_max.

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54 """

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55 if not isinstance(v, int):

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56 return False

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57 if v < v_min or (v_max != None and v >= v_max):

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58 return False

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59 return True

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60

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61 def is_index_range(v, v_min=0, v_max=None):

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62 """Value is an array index range in range v_min <= v[0] <= v[1] < v_max.

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63 """

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64 if not (isinstance(v, list) and len(v) == 2 and isinstance(v[0], int) and

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65 isinstance(v[1], int)):

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66 return False

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67 if not 0 <= v[0] < v[1] or (v_max != None and v[1] >= v_max):

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68 return False

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69 return True

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70

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71 def illegal_value(name, value, location=None, exit_flag=False):

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72 if not isinstance(location, str):

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73 location = ''

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74 else:

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75 location = f'in {location} '

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76 if isinstance(name, str):

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77 logging.error(f'Illegal value for {name} {location}({value}, {type(value)})')

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78 else:

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79 logging.error(f'Illegal value {location}({value}, {type(value)})')

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80 if exit_flag:

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81 exit(1)

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82

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83 def get_trailing_int(string):

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84 indexRegex = re.compile(r'\d+$')

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85 mo = indexRegex.search(string)

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86 if mo == None:

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87 return None

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88 else:

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89 return int(mo.group())

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90

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91 def findImageFiles(path, filetype, name=None):

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92 if isinstance(name, str):

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93 name = f' {name} '

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94 else:

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95 name = ' '

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96 # Find available index range

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97 if filetype == 'tif':

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98 if not isinstance(path, str) and not os.path.isdir(path):

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99 illegal_value('path', path, 'findImageRange')

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100 return -1, 0, []

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101 indexRegex = re.compile(r'\d+')

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102 # At this point only tiffs

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103 files = sorted([f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f)) and

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104 f.endswith('.tif') and indexRegex.search(f)])

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105 num_imgs = len(files)

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106 if num_imgs < 1:

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107 logging.warning('No available'+name+'files')

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108 return -1, 0, []

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109 first_index = indexRegex.search(files[0]).group()

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110 last_index = indexRegex.search(files[-1]).group()

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111 if first_index == None or last_index == None:

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112 logging.error('Unable to find correctly indexed'+name+'images')

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113 return -1, 0, []

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114 first_index = int(first_index)

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115 last_index = int(last_index)

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116 if num_imgs != last_index-first_index+1:

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117 logging.error('Non-consecutive set of indices for'+name+'images')

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118 return -1, 0, []

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119 paths = [os.path.join(path, f) for f in files]

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120 elif filetype == 'h5':

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121 if not isinstance(path, str) or not os.path.isfile(path):

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122 illegal_value('path', path, 'findImageRange')

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123 return -1, 0, []

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124 # At this point only h5 in alamo2 detector style

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125 first_index = 0

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126 with h5py.File(path, 'r') as f:

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127 num_imgs = f['entry/instrument/detector/data'].shape[0]

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128 last_index = num_imgs-1

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129 paths = [path]

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130 else:

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131 illegal_value('filetype', filetype, 'findImageRange')

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132 return -1, 0, []

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133 logging.debug('\nNumber of available'+name+f'images: {num_imgs}')

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134 logging.debug('Index range of available'+name+f'images: [{first_index}, '+

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135 f'{last_index}]')

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136

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137 return first_index, num_imgs, paths

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138

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139 def selectImageRange(first_index, offset, num_imgs, name=None, num_required=None):

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140 if isinstance(name, str):

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141 name = f' {name} '

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142 else:

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143 name = ' '

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144 # Check existing values

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145 use_input = 'no'

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146 if (is_int(first_index, 0) and is_int(offset, 0) and is_int(num_imgs, 1)):

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147 if offset < 0:

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148 use_input = pyip.inputYesNo('\nCurrent'+name+f'first index = {first_index}, '+

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149 'use this value ([y]/n)? ', blank=True)

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150 else:

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151 use_input = pyip.inputYesNo('\nCurrent'+name+'first index/offset = '+

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152 f'{first_index}/{offset}, use these values ([y]/n)? ',

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153 blank=True)

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154 if use_input != 'no':

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155 use_input = pyip.inputYesNo('Current number of'+name+'images = '+

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156 f'{num_imgs}, use this value ([y]/n)? ',

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157 blank=True)

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158 if use_input == 'yes':

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159 return first_index, offset, num_imgs

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160

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161 # Check range against requirements

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162 if num_imgs < 1:

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163 logging.warning('No available'+name+'images')

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164 return -1, -1, 0

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165 if num_required == None:

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166 if num_imgs == 1:

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167 return first_index, 0, 1

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168 else:

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169 if not is_int(num_required, 1):

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170 illegal_value('num_required', num_required, 'selectImageRange')

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171 return -1, -1, 0

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172 if num_imgs < num_required:

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173 logging.error('Unable to find the required'+name+

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174 f'images ({num_imgs} out of {num_required})')

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175 return -1, -1, 0

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176

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177 # Select index range

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178 if num_required == None:

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179 last_index = first_index+num_imgs

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180 use_all = f'Use all ([{first_index}, {last_index}])'

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181 pick_offset = 'Pick a first index offset and a number of images'

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182 pick_bounds = 'Pick the first and last index'

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183 menuchoice = pyip.inputMenu([use_all, pick_offset, pick_bounds], numbered=True)

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184 if menuchoice == use_all:

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185 offset = 0

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186 elif menuchoice == pick_offset:

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187 offset = pyip.inputInt('Enter the first index offset'+

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188 f' [0, {last_index-first_index}]: ', min=0, max=last_index-first_index)

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189 first_index += offset

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190 if first_index == last_index:

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191 num_imgs = 1

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192 else:

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193 num_imgs = pyip.inputInt(f'Enter the number of images [1, {num_imgs-offset}]: ',

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194 min=1, max=num_imgs-offset)

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195 else:

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196 offset = pyip.inputInt(f'Enter the first index [{first_index}, {last_index}]: ',

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197 min=first_index, max=last_index)-first_index

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198 first_index += offset

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199 num_imgs = pyip.inputInt(f'Enter the last index [{first_index}, {last_index}]: ',

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200 min=first_index, max=last_index)-first_index+1

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201 else:

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202 use_all = f'Use ([{first_index}, {first_index+num_required-1}])'

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203 pick_offset = 'Pick the first index offset'

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204 menuchoice = pyip.inputMenu([use_all, pick_offset], numbered=True)

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205 offset = 0

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206 if menuchoice == pick_offset:

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207 offset = pyip.inputInt('Enter the first index offset'+

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208 f'[0, {num_imgs-num_required}]: ', min=0, max=num_imgs-num_required)

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209 first_index += offset

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210 num_imgs = num_required

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211

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212 return first_index, offset, num_imgs

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213

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214 def loadImage(f, img_x_bounds=None, img_y_bounds=None):

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215 """Load a single image from file.

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216 """

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217 if not os.path.isfile(f):

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218 logging.error(f'Unable to load {f}')

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219 return None

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220 img_read = img.imread(f)

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221 if not img_x_bounds:

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222 img_x_bounds = [0, img_read.shape[0]]

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223 else:

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224 if (not isinstance(img_x_bounds, list) or len(img_x_bounds) != 2 or

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225 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= img_read.shape[0])):

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226 logging.error(f'inconsistent row dimension in {f}')

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227 return None

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228 if not img_y_bounds:

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229 img_y_bounds = [0, img_read.shape[1]]

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230 else:

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231 if (not isinstance(img_y_bounds, list) or len(img_y_bounds) != 2 or

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232 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= img_read.shape[0])):

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233 logging.error(f'inconsistent column dimension in {f}')

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234 return None

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235 return img_read[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]

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236

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237 def loadImageStack(files, filetype, img_offset, num_imgs, num_img_skip=0,

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238 img_x_bounds=None, img_y_bounds=None):

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239 """Load a set of images and return them as a stack.

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240 """

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241 logging.debug(f'img_offset = {img_offset}')

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242 logging.debug(f'num_imgs = {num_imgs}')

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243 logging.debug(f'num_img_skip = {num_img_skip}')

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244 logging.debug(f'\nfiles:\n{files}\n')

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245 img_stack = np.array([])

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246 if filetype == 'tif':

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247 img_read_stack = []

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248 i = 1

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249 t0 = time()

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250 for f in files[img_offset:img_offset+num_imgs:num_img_skip+1]:

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251 if not i%20:

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252 logging.info(f' loading {i}/{num_imgs}: {f}')

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253 else:

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254 logging.debug(f' loading {i}/{num_imgs}: {f}')

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255 img_read = loadImage(f, img_x_bounds, img_y_bounds)

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256 img_read_stack.append(img_read)

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257 i += num_img_skip+1

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258 img_stack = np.stack([img_read for img_read in img_read_stack])

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259 logging.info(f'... done in {time()-t0:.2f} seconds!')

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260 logging.debug(f'img_stack shape = {np.shape(img_stack)}')

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261 del img_read_stack, img_read

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262 elif filetype == 'h5':

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263 if not isinstance(files[0], str) and not os.path.isfile(files[0]):

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264 illegal_value('files[0]', files[0], 'loadImageStack')

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265 return img_stack

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266 t0 = time()

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267 with h5py.File(files[0], 'r') as f:

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268 shape = f['entry/instrument/detector/data'].shape

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269 if len(shape) != 3:

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270 logging.error(f'inconsistent dimensions in {files[0]}')

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271 if not img_x_bounds:

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272 img_x_bounds = [0, shape[1]]

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273 else:

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274 if (not isinstance(img_x_bounds, list) or len(img_x_bounds) != 2 or

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275 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= shape[1])):

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276 logging.error(f'inconsistent row dimension in {files[0]}')

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277 if not img_y_bounds:

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278 img_y_bounds = [0, shape[2]]

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279 else:

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280 if (not isinstance(img_y_bounds, list) or len(img_y_bounds) != 2 or

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281 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= shape[2])):

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282 logging.error(f'inconsistent column dimension in {files[0]}')

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283 img_stack = f.get('entry/instrument/detector/data')[

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284 img_offset:img_offset+num_imgs:num_img_skip+1,

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285 img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]

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286 logging.info(f'... done in {time()-t0:.2f} seconds!')

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287 else:

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288 illegal_value('filetype', filetype, 'findImageRange')

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289 return img_stack

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290

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291 def clearFig(title):

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292 if not isinstance(title, str):

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293 illegal_value('title', title, 'clearFig')

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294 return

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295 plt.close(fig=re.sub(r"\s+", '_', title))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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296

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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297 def quickImshow(a, title=None, path=None, name=None, save_fig=False, save_only=False,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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298 clear=True, **kwargs):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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299 if title != None and not isinstance(title, str):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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300 illegal_value('title', title, 'quickImshow')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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301 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

302 if path is not None and not isinstance(path, str):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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303 illegal_value('path', path, 'quickImshow')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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304 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

305 if not isinstance(save_fig, bool):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

306 illegal_value('save_fig', save_fig, 'quickImshow')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

307 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

308 if not isinstance(save_only, bool):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

309 illegal_value('save_only', save_only, 'quickImshow')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

310 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

311 if not isinstance(clear, bool):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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312 illegal_value('clear', clear, 'quickImshow')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

313 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

314 if not title:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

315 title='quick_imshow'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

316 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

317 title = re.sub(r"\s+", '_', title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

318 if name is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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319 if path is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

320 path = f'{title}.png'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

321 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

322 path = f'{path}/{title}.png'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

323 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

324 if path is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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325 path = name

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

326 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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327 path = f'{path}/{name}'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

328 if clear:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

329 plt.close(fig=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

330 if save_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

331 plt.figure(title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

332 plt.imshow(a, **kwargs)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

333 plt.savefig(path)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

334 plt.close(fig=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

335 #plt.imsave(f'{title}.png', a, **kwargs)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

336 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

337 plt.ion()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

338 plt.figure(title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

339 plt.imshow(a, **kwargs)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

340 if save_fig:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

341 plt.savefig(path)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

342 plt.pause(1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

343

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

344 def quickPlot(*args, title=None, path=None, name=None, save_fig=False, save_only=False,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

345 clear=True, **kwargs):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

346 if title != None and not isinstance(title, str):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

347 illegal_value('title', title, 'quickPlot')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

348 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

349 if path is not None and not isinstance(path, str):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

350 illegal_value('path', path, 'quickPlot')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

351 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

352 if not isinstance(save_fig, bool):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

353 illegal_value('save_fig', save_fig, 'quickPlot')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

354 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

355 if not isinstance(save_only, bool):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

356 illegal_value('save_only', save_only, 'quickPlot')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

357 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

358 if not isinstance(clear, bool):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

359 illegal_value('clear', clear, 'quickPlot')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

360 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

361 if not title:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

362 title = 'quick_plot'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

363 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

364 title = re.sub(r"\s+", '_', title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

365 if name is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

366 if path is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

367 path = f'{title}.png'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

368 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

369 path = f'{path}/{title}.png'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

370 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

371 if path is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

372 path = name

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

373 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

374 path = f'{path}/{name}'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

375 if clear:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

376 plt.close(fig=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

377 if save_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

378 plt.figure(title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

379 if depth_tuple(args) > 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

380 for y in args:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

381 plt.plot(*y, **kwargs)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

382 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

383 plt.plot(*args, **kwargs)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

384 plt.savefig(path)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

385 plt.close(fig=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

386 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

387 plt.ion()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

388 plt.figure(title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

389 if depth_tuple(args) > 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

390 for y in args:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

391 plt.plot(*y, **kwargs)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

392 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

393 plt.plot(*args, **kwargs)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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394 if save_fig:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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395 plt.savefig(path)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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396 plt.pause(1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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397

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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398 def selectArrayBounds(a, x_low=None, x_upp=None, num_x_min=None,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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399 title='select array bounds'):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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400 """Interactively select the lower and upper data bounds for a numpy array.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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401 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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402 if not isinstance(a, np.ndarray) or a.ndim != 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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403 logging.error('Illegal array type or dimension in selectArrayBounds')

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404 return None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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405 if num_x_min == None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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406 num_x_min = 1

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407 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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408 if num_x_min < 2 or num_x_min > a.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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409 logging.warning('Illegal input for num_x_min in selectArrayBounds, input ignored')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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410 num_x_min = 1

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411 if x_low == None:

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412 x_min = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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413 x_max = a.size

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414 x_low_max = a.size-num_x_min

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415 while True:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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416 quickPlot(range(x_min, x_max), a[x_min:x_max], title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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417 zoom_flag = pyip.inputInt('Set lower data bound (0) or zoom in (1)?: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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418 min=0, max=1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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419 if zoom_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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420 x_min = pyip.inputInt(f' Set lower zoom index [0, {x_low_max}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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421 min=0, max=x_low_max)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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422 x_max = pyip.inputInt(f' Set upper zoom index [{x_min+1}, {x_low_max+1}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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423 min=x_min+1, max=x_low_max+1)

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424 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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425 x_low = pyip.inputInt(f' Set lower data bound [0, {x_low_max}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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426 min=0, max=x_low_max)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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427 break

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428 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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429 if not is_int(x_low, 0, a.size-num_x_min):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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430 illegal_value('x_low', x_low, 'selectArrayBounds')

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431 return None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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432 if x_upp == None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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433 x_min = x_low+num_x_min

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434 x_max = a.size

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435 x_upp_min = x_min

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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436 while True:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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437 quickPlot(range(x_min, x_max), a[x_min:x_max], title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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438 zoom_flag = pyip.inputInt('Set upper data bound (0) or zoom in (1)?: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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439 min=0, max=1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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440 if zoom_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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441 x_min = pyip.inputInt(f' Set upper zoom index [{x_upp_min}, {a.size-1}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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442 min=x_upp_min, max=a.size-1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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443 x_max = pyip.inputInt(f' Set upper zoom index [{x_min+1}, {a.size}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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444 min=x_min+1, max=a.size)

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445 else:

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446 x_upp = pyip.inputInt(f' Set upper data bound [{x_upp_min}, {a.size}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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447 min=x_upp_min, max=a.size)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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448 break

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449 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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450 if not is_int(x_upp, x_low+num_x_min, a.size):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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451 illegal_value('x_upp', x_upp, 'selectArrayBounds')

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452 return None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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453 bounds = [x_low, x_upp]

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454 print(f'lower bound = {x_low} (inclusive)\nupper bound = {x_upp} (exclusive)]')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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455 #quickPlot(range(bounds[0], bounds[1]), a[bounds[0]:bounds[1]], title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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456 quickPlot((range(a.size), a), ([bounds[0], bounds[0]], [a.min(), a.max()], 'r-'),

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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457 ([bounds[1], bounds[1]], [a.min(), a.max()], 'r-'), title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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458 if pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True) == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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459 bounds = selectArrayBounds(a, title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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460 return bounds

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461

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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462 def selectImageBounds(a, axis, low=None, upp=None, num_min=None,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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463 title='select array bounds'):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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464 """Interactively select the lower and upper data bounds for a 2D numpy array.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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465 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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466 if not isinstance(a, np.ndarray) or a.ndim != 2:

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467 logging.error('Illegal array type or dimension in selectImageBounds')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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468 return None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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469 if axis < 0 or axis >= a.ndim:

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470 illegal_value('axis', axis, 'selectImageBounds')

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471 return None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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472 if num_min == None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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473 num_min = 1

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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474 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

475 if num_min < 2 or num_min > a.shape[axis]:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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476 logging.warning('Illegal input for num_min in selectImageBounds, input ignored')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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477 num_min = 1

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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478 if low == None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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479 min_ = 0

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480 max_ = a.shape[axis]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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481 low_max = a.shape[axis]-num_min

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482 while True:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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483 if axis:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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484 quickImshow(a[:,min_:max_], title=title, aspect='auto',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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485 extent=[min_,max_,a.shape[0],0])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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486 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

487 quickImshow(a[min_:max_,:], title=title, aspect='auto',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

488 extent=[0,a.shape[1], max_,min_])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

489 zoom_flag = pyip.inputInt('Set lower data bound (0) or zoom in (1)?: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

490 min=0, max=1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

491 if zoom_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

492 min_ = pyip.inputInt(f' Set lower zoom index [0, {low_max}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

493 min=0, max=low_max)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

494 max_ = pyip.inputInt(f' Set upper zoom index [{min_+1}, {low_max+1}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

495 min=min_+1, max=low_max+1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

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diff changeset

496 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

497 low = pyip.inputInt(f' Set lower data bound [0, {low_max}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

498 min=0, max=low_max)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

499 break

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

500 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

501 if not is_int(low, 0, a.shape[axis]-num_min):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

502 illegal_value('low', low, 'selectImageBounds')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

503 return None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

504 if upp == None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

505 min_ = low+num_min

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

506 max_ = a.shape[axis]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

507 upp_min = min_

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

508 while True:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

509 if axis:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

510 quickImshow(a[:,min_:max_], title=title, aspect='auto',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

511 extent=[min_,max_,a.shape[0],0])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

512 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

513 quickImshow(a[min_:max_,:], title=title, aspect='auto',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

514 extent=[0,a.shape[1], max_,min_])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

515 zoom_flag = pyip.inputInt('Set upper data bound (0) or zoom in (1)?: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

516 min=0, max=1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

517 if zoom_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

518 min_ = pyip.inputInt(f' Set upper zoom index [{upp_min}, {a.shape[axis]-1}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

519 min=upp_min, max=a.shape[axis]-1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

520 max_ = pyip.inputInt(f' Set upper zoom index [{min_+1}, {a.shape[axis]}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

521 min=min_+1, max=a.shape[axis])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

522 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

523 upp = pyip.inputInt(f' Set upper data bound [{upp_min}, {a.shape[axis]}]: ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

524 min=upp_min, max=a.shape[axis])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

525 break

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

526 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

527 if not is_int(upp, low+num_min, a.shape[axis]):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

528 illegal_value('upp', upp, 'selectImageBounds')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

529 return None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

530 bounds = [low, upp]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

531 a_tmp = a

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

532 if axis:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

533 a_tmp[:,bounds[0]] = a.max()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

534 a_tmp[:,bounds[1]] = a.max()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

535 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

536 a_tmp[bounds[0],:] = a.max()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

537 a_tmp[bounds[1],:] = a.max()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

538 print(f'lower bound = {low} (inclusive)\nupper bound = {upp} (exclusive)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

539 quickImshow(a_tmp, title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

540 if pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True) == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

541 bounds = selectImageBounds(a, title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

542 return bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

543

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

544 def fitStep(x=None, y=None, model='step', form='arctan'):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

545 if not isinstance(y, np.ndarray) or y.ndim != 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

546 logging.error('Illegal array type or dimension for y in fitStep')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

547 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

548 if isinstance(x, type(None)):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

549 x = np.array(range(y.size))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

550 elif not isinstance(x, np.ndarray) or x.ndim != 1 or x.size != y.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

551 logging.error('Illegal array type or dimension for x in fitStep')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

552 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

553 if not isinstance(model, str) or not model in ('step', 'rectangle'):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

554 illegal_value('model', model, 'fitStepModel')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

555 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

556 if not isinstance(form, str) or not form in ('linear', 'atan', 'arctan', 'erf', 'logistic'):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

557 illegal_value('form', form, 'fitStepModel')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

558 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

559

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

560 if model == 'step':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

561 mod = StepModel(form=form)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

562 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

563 mod = RectangleModel(form=form)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

564 pars = mod.guess(y, x=x)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

565 out = mod.fit(y, pars, x=x)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

566 #print(out.fit_report())

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

567 #quickPlot((x,y),(x,out.best_fit))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

568 return out.best_values

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

569

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

570 class Config:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

571 """Base class for processing a config file or dictionary.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

572 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

573 def __init__(self, config_file=None, config_dict=None):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

574 self.config = {}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

575 self.load_flag = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

576 self.suffix = None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

577

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

578 # Load config file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

579 if config_file is not None and config_dict is not None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

580 logging.warning('Ignoring config_dict (both config_file and config_dict are specified)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

581 if config_file is not None:

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582 self.loadFile(config_file)

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583 elif config_dict is not None:

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584 self.loadDict(config_dict)

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585

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586 def loadFile(self, config_file):

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587 """Load a config file.

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588 """

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589 if self.load_flag:

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590 logging.warning('Overwriting any previously loaded config file')

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591 self.config = {}

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592

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593 # Ensure config file exists

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594 if not os.path.isfile(config_file):

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595 logging.error(f'Unable to load {config_file}')

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596 return

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597

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598 # Load config file

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599 self.suffix = os.path.splitext(config_file)[1]

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600 if self.suffix == '.yml' or self.suffix == '.yaml':

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601 with open(config_file, 'r') as f:

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602 self.config = yaml.safe_load(f)

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603 elif self.suffix == '.txt':

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604 with open(config_file, 'r') as f:

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605 lines = f.read().splitlines()

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606 self.config = {item[0].strip():literal_eval(item[1].strip()) for item in

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607 [line.split('#')[0].split('=') for line in lines if '=' in line.split('#')[0]]}

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608 else:

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609 logging.error(f'Illegal config file extension: {self.suffix}')

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610

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611 # Make sure config file was correctly loaded

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612 if isinstance(self.config, dict):

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613 self.load_flag = True

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614 else:

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615 logging.error(f'Unable to load dictionary from config file: {config_file}')

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616 self.config = {}

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617

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618 def loadDict(self, config_dict):

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619 """Takes a dictionary and places it into self.config.

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620 """

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621 exit('loadDict not tested yet, what format do we follow: txt or yaml?')

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622 if self.load_flag:

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623 logging.warning('Overwriting the previously loaded config file')

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624

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625 if isinstance(config_dict, dict):

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626 self.config = config_dict

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627 self.load_flag = True

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628 else:

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629 logging.error(f'Illegal dictionary config object: {config_dict}')

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630 self.config = {}

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631

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632 def saveFile(self, config_file):

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633 """Save the config file (as a yaml file only right now).

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634 """

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635 suffix = os.path.splitext(config_file)[1]

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636 if suffix != '.yml' and suffix != '.yaml':

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637 logging.error(f'Illegal config file extension: {suffix}')

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638

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639 # Check if config file exists

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640 if os.path.isfile(config_file):

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641 logging.info(f'Updating {config_file}')

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642 else:

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643 logging.info(f'Saving {config_file}')

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644

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645 # Save config file

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646 with open(config_file, 'w') as f:

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647 yaml.dump(self.config, f)

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648

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649 def validate(self, pars_required, pars_missing=None):

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650 """Returns False if any required first level keys are missing.

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651 """

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652 if not self.load_flag:

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653 logging.error('Load a config file prior to calling Config.validate')

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654 pars = [p for p in pars_required if p not in self.config]

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655 if isinstance(pars_missing, list):

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656 pars_missing.extend(pars)

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657 elif pars_missing is not None:

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658 illegal_value('pars_missing', pars_missing, 'Config.validate')

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659 if len(pars) > 0:

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660 return False

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661 return True

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662

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663 #RV FIX this is for a txt file, obsolete?

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664 # def update_txt(self, config_file, key, value, search_string=None, header=None):

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665 # if not self.load_flag:

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666 # logging.error('Load a config file prior to calling Config.update')

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667 #

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668 # if not os.path.isfile(config_file):

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669 # logging.error(f'Unable to load {config_file}')

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670 # lines = []

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671 # else:

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672 # with open(config_file, 'r') as f:

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673 # lines = f.read().splitlines()

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674 # config = {item[0].strip():literal_eval(item[1].strip()) for item in

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675 # [line.split('#')[0].split('=') for line in lines if '=' in line.split('#')[0]]}

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676 # if not isinstance(key, str):

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677 # illegal_value('key', key, 'Config.update')

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678 # return config

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679 # if isinstance(value, str):

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680 # newline = f"{key} = '{value}'"

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681 # else:

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682 # newline = f'{key} = {value}'

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683 # if key in config.keys():

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684 # # Update key with value

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685 # for index,line in enumerate(lines):

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686 # if '=' in line:

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687 # item = line.split('#')[0].split('=')

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688 # if item[0].strip() == key:

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689 # lines[index] = newline

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690 # break

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691 # else:

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692 # # Insert new key/value pair

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693 # if search_string != None:

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694 # if isinstance(search_string, str):

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695 # search_string = [search_string]

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696 # elif not isinstance(search_string, (tuple, list)):

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diff changeset

697 # illegal_value('search_string', search_string, 'Config.update')

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698 # search_string = None

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diff changeset

699 # update_flag = False

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700 # if search_string != None:

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diff changeset

701 # indices = [[index for index,line in enumerate(lines) if item in line]

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702 # for item in search_string]

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703 # for i,index in enumerate(indices):

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704 # if index:

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705 # if len(search_string) > 1 and key < search_string[i]:

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diff changeset

706 # lines.insert(index[0], newline)

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diff changeset

707 # else:

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diff changeset

708 # lines.insert(index[0]+1, newline)

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709 # update_flag = True

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710 # break

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711 # if not update_flag:

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712 # if isinstance(header, str):

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diff changeset

713 # lines += ['', header, newline]

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714 # else:

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715 # lines += ['', newline]

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diff changeset

716 # # Write updated config file

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717 # with open(config_file, 'w') as f:

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diff changeset

718 # for line in lines:

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diff changeset

719 # f.write(f'{line}\n')

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diff changeset

720 # # Update loaded config

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diff changeset

721 # config['key'] = value

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722 #

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

723 #RV update and bring into Config if needed again

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diff changeset

724 #def search(config_file, search_string):

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725 # if not os.path.isfile(config_file):

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726 # logging.error(f'Unable to load {config_file}')

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727 # return False

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728 # with open(config_file, 'r') as f:

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729 # lines = f.read()

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730 # if search_string in lines:

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731 # return True

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732 # return False

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733

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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734 class Detector:

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735 """Class for processing a detector info file or dictionary.

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736 """

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737 def __init__(self, detector_id):

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738 self.detector = {}

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diff changeset

739 self.load_flag = False

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740 self.validate_flag = False

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741

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

742 # Load detector file

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diff changeset

743 self.loadFile(detector_id)

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diff changeset

744

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

745 def loadFile(self, detector_id):

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diff changeset

746 """Load a detector file.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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747 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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748 if self.load_flag:

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diff changeset

749 logging.warning('Overwriting the previously loaded detector file')

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diff changeset

750 self.detector = {}

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751

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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752 # Ensure detector file exists

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753 if not isinstance(detector_id, str):

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754 illegal_value('detector_id', detector_id, 'Detector.loadFile')

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755 return

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756 detector_file = f'{detector_id}.yaml'

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757 if not os.path.isfile(detector_file):

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758 detector_file = self.config['detector_id']+'.yaml'

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759 if not os.path.isfile(detector_file):

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760 logging.error(f'Unable to load detector info file for {detector_id}')

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diff changeset

761 return

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762

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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763 # Load detector file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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764 with open(detector_file, 'r') as f:

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765 self.detector = yaml.safe_load(f)

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766

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767 # Make sure detector file was correctly loaded

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768 if isinstance(self.detector, dict):

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769 self.load_flag = True

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770 else:

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771 logging.error(f'Unable to load dictionary from detector file: {detector_file}')

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772 self.detector = {}

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773

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diff changeset

774 def validate(self):

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diff changeset

775 """Returns False if any config parameters is illegal or missing.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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776 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

777 if not self.load_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

778 logging.error('Load a detector file prior to calling Detector.validate')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

779

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

780 # Check for required first-level keys

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

781 pars_required = ['detector', 'lens_magnification']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

782 pars_missing = [p for p in pars_required if p not in self.detector]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

783 if len(pars_missing) > 0:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

784 logging.error(f'Missing item(s) in detector file: {", ".join(pars_missing)}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

785 return False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

786

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

787 is_valid = True

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

788

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

789 # Check detector pixel config keys

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

790 pixels = self.detector['detector'].get('pixels')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

791 if not pixels:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

792 pars_missing.append('detector:pixels')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

793 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

794 rows = pixels.get('rows')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

795 if not rows:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

796 pars_missing.append('detector:pixels:rows')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

797 columns = pixels.get('columns')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

798 if not columns:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

799 pars_missing.append('detector:pixels:columns')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

800 size = pixels.get('size')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

801 if not size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

802 pars_missing.append('detector:pixels:size')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

803

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

804 if not len(pars_missing):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

805 self.validate_flag = True

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

806 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

807 is_valid = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

808

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

809 return is_valid

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

810

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

811 def getPixelSize(self):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

812 """Returns the detector pixel size.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

813 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

814 if not self.validate_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

815 logging.error('Validate detector file info prior to calling Detector.getPixelSize')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

816

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

817 lens_magnification = self.detector.get('lens_magnification')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

818 if not isinstance(lens_magnification, (int,float)) or lens_magnification <= 0.:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

819 illegal_value('lens_magnification', lens_magnification, 'detector file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

820 return 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

821 pixel_size = self.detector['detector'].get('pixels').get('size')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

822 if isinstance(pixel_size, (int,float)):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

823 if pixel_size <= 0.:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

824 illegal_value('pixel_size', pixel_size, 'detector file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

825 return 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

826 pixel_size /= lens_magnification

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

827 elif isinstance(pixel_size, list):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

828 if ((len(pixel_size) > 2) or

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

829 (len(pixel_size) == 2 and pixel_size[0] != pixel_size[1])):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

830 illegal_value('pixel size', pixel_size, 'detector file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

831 return 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

832 elif not is_num(pixel_size[0], 0.):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

833 illegal_value('pixel size', pixel_size, 'detector file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

834 return 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

835 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

836 pixel_size = pixel_size[0]/lens_magnification

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

837 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

838 illegal_value('pixel size', pixel_size, 'detector file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

839 return 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

840

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

841 return pixel_size

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

842

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

843 def getDimensions(self):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

844 """Returns the detector pixel dimensions.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

845 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

846 if not self.validate_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

847 logging.error('Validate detector file info prior to calling Detector.getDimensions')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

848

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

849 pixels = self.detector['detector'].get('pixels')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

850 num_rows = pixels.get('rows')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

851 if not is_int(num_rows, 1):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

852 illegal_value('rows', num_rows, 'detector file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

853 return (0, 0)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

854 num_columns = pixels.get('columns')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

855 if not is_int(num_columns, 1):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

856 illegal_value('columns', num_columns, 'detector file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

857 return (0, 0)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

858

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

859 return num_rows, num_columns

Mercurial > repos > rv43 > tomo

annotate msnc_tools.py @ 0:cb1b0d757704 draft