tomo: general.py annotate

annotate general.py @ 63:98a83f03d91b draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877"

author	rv43
date	Thu, 18 Aug 2022 14:36:46 +0000
parents	ca61007a60fa
children	f31ef7bfb430

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

Mercurial > repos > rv43 > tomo

annotate general.py @ 63:98a83f03d91b draft