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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
author rv43
date Thu, 23 Mar 2023 13:39:14 +0000
parents fba792d5f83b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python3
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2
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3 #FIX write a function that returns a list of peak indices for a given plot
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4 #FIX use raise_error concept on more functions to optionally raise an error
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5
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6 # -*- coding: utf-8 -*-
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7 """
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8 Created on Mon Dec 6 15:36:22 2021
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10 @author: rv43
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11 """
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13 import logging
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14 logger=logging.getLogger(__name__)
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16 import os
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17 import sys
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18 import re
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19 try:
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20 from yaml import safe_load, safe_dump
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21 except:
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22 pass
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23 try:
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24 import h5py
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25 except:
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26 pass
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27 import numpy as np
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28 try:
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29 import matplotlib.pyplot as plt
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30 import matplotlib.lines as mlines
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31 from matplotlib import transforms
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32 from matplotlib.widgets import Button
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33 except:
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34 pass
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35
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36 from ast import literal_eval
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37 try:
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38 from asteval import Interpreter, get_ast_names
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39 except:
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40 pass
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41 from copy import deepcopy
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42 try:
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43 from sympy import diff, simplify
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44 except:
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45 pass
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46 from time import time
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49 def depth_list(L): return(isinstance(L, list) and max(map(depth_list, L))+1)
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50 def depth_tuple(T): return(isinstance(T, tuple) and max(map(depth_tuple, T))+1)
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51 def unwrap_tuple(T):
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52 if depth_tuple(T) > 1 and len(T) == 1:
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53 T = unwrap_tuple(*T)
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54 return(T)
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56 def illegal_value(value, name, location=None, raise_error=False, log=True):
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57 if not isinstance(location, str):
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58 location = ''
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59 else:
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60 location = f'in {location} '
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61 if isinstance(name, str):
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62 error_msg = f'Illegal value for {name} {location}({value}, {type(value)})'
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63 else:
69
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64 error_msg = f'Illegal value {location}({value}, {type(value)})'
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65 if log:
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66 logger.error(error_msg)
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67 if raise_error:
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68 raise ValueError(error_msg)
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69
69
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70 def illegal_combination(value1, name1, value2, name2, location=None, raise_error=False,
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71 log=True):
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72 if not isinstance(location, str):
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73 location = ''
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74 else:
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75 location = f'in {location} '
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76 if isinstance(name1, str):
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77 error_msg = f'Illegal combination for {name1} and {name2} {location}'+ \
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78 f'({value1}, {type(value1)} and {value2}, {type(value2)})'
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79 else:
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80 error_msg = f'Illegal combination {location}'+ \
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81 f'({value1}, {type(value1)} and {value2}, {type(value2)})'
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82 if log:
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83 logger.error(error_msg)
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84 if raise_error:
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85 raise ValueError(error_msg)
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86
69
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87 def test_ge_gt_le_lt(ge, gt, le, lt, func, location=None, raise_error=False, log=True):
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88 """Check individual and mutual validity of ge, gt, le, lt qualifiers
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89 func: is_int or is_num to test for int or numbers
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90 Return: True upon success or False when mutually exlusive
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91 """
69
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92 if ge is None and gt is None and le is None and lt is None:
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93 return(True)
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94 if ge is not None:
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95 if not func(ge):
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96 illegal_value(ge, 'ge', location, raise_error, log)
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97 return(False)
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98 if gt is not None:
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99 illegal_combination(ge, 'ge', gt, 'gt', location, raise_error, log)
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100 return(False)
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101 elif gt is not None and not func(gt):
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102 illegal_value(gt, 'gt', location, raise_error, log)
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103 return(False)
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104 if le is not None:
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105 if not func(le):
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106 illegal_value(le, 'le', location, raise_error, log)
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107 return(False)
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108 if lt is not None:
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109 illegal_combination(le, 'le', lt, 'lt', location, raise_error, log)
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110 return(False)
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111 elif lt is not None and not func(lt):
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112 illegal_value(lt, 'lt', location, raise_error, log)
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113 return(False)
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114 if ge is not None:
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115 if le is not None and ge > le:
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116 illegal_combination(ge, 'ge', le, 'le', location, raise_error, log)
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117 return(False)
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118 elif lt is not None and ge >= lt:
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119 illegal_combination(ge, 'ge', lt, 'lt', location, raise_error, log)
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120 return(False)
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121 elif gt is not None:
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122 if le is not None and gt >= le:
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123 illegal_combination(gt, 'gt', le, 'le', location, raise_error, log)
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124 return(False)
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125 elif lt is not None and gt >= lt:
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126 illegal_combination(gt, 'gt', lt, 'lt', location, raise_error, log)
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127 return(False)
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128 return(True)
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129
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130 def range_string_ge_gt_le_lt(ge=None, gt=None, le=None, lt=None):
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131 """Return a range string representation matching the ge, gt, le, lt qualifiers
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132 Does not validate the inputs, do that as needed before calling
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133 """
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134 range_string = ''
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135 if ge is not None:
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136 if le is None and lt is None:
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137 range_string += f'>= {ge}'
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138 else:
69
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139 range_string += f'[{ge}, '
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140 elif gt is not None:
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141 if le is None and lt is None:
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142 range_string += f'> {gt}'
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143 else:
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144 range_string += f'({gt}, '
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145 if le is not None:
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146 if ge is None and gt is None:
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147 range_string += f'<= {le}'
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148 else:
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149 range_string += f'{le}]'
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150 elif lt is not None:
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151 if ge is None and gt is None:
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152 range_string += f'< {lt}'
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153 else:
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154 range_string += f'{lt})'
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155 return(range_string)
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156
69
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157 def is_int(v, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
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158 """Value is an integer in range ge <= v <= le or gt < v < lt or some combination.
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159 Return: True if yes or False is no
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160 """
69
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161 return(_is_int_or_num(v, 'int', ge, gt, le, lt, raise_error, log))
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162
69
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163 def is_num(v, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
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164 """Value is a number in range ge <= v <= le or gt < v < lt or some combination.
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165 Return: True if yes or False is no
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166 """
69
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167 return(_is_int_or_num(v, 'num', ge, gt, le, lt, raise_error, log))
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168
69
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169 def _is_int_or_num(v, type_str, ge=None, gt=None, le=None, lt=None, raise_error=False,
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170 log=True):
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171 if type_str == 'int':
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172 if not isinstance(v, int):
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173 illegal_value(v, 'v', '_is_int_or_num', raise_error, log)
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174 return(False)
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175 if not test_ge_gt_le_lt(ge, gt, le, lt, is_int, '_is_int_or_num', raise_error, log):
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176 return(False)
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177 elif type_str == 'num':
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178 if not isinstance(v, (int, float)):
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179 illegal_value(v, 'v', '_is_int_or_num', raise_error, log)
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180 return(False)
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181 if not test_ge_gt_le_lt(ge, gt, le, lt, is_num, '_is_int_or_num', raise_error, log):
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182 return(False)
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183 else:
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184 illegal_value(type_str, 'type_str', '_is_int_or_num', raise_error, log)
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185 return(False)
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186 if ge is None and gt is None and le is None and lt is None:
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187 return(True)
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188 error = False
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189 if ge is not None and v < ge:
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190 error = True
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191 error_msg = f'Value {v} out of range: {v} !>= {ge}'
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192 if not error and gt is not None and v <= gt:
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193 error = True
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194 error_msg = f'Value {v} out of range: {v} !> {gt}'
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195 if not error and le is not None and v > le:
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196 error = True
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197 error_msg = f'Value {v} out of range: {v} !<= {le}'
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198 if not error and lt is not None and v >= lt:
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199 error = True
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200 error_msg = f'Value {v} out of range: {v} !< {lt}'
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201 if error:
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202 if log:
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203 logger.error(error_msg)
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204 if raise_error:
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205 raise ValueError(error_msg)
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206 return(False)
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207 return(True)
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208
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209 def is_int_pair(v, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
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210 """Value is an integer pair, each in range ge <= v[i] <= le or gt < v[i] < lt or
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211 ge[i] <= v[i] <= le[i] or gt[i] < v[i] < lt[i] or some combination.
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212 Return: True if yes or False is no
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213 """
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214 return(_is_int_or_num_pair(v, 'int', ge, gt, le, lt, raise_error, log))
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215
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216 def is_num_pair(v, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
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217 """Value is a number pair, each in range ge <= v[i] <= le or gt < v[i] < lt or
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218 ge[i] <= v[i] <= le[i] or gt[i] < v[i] < lt[i] or some combination.
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219 Return: True if yes or False is no
49
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220 """
69
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221 return(_is_int_or_num_pair(v, 'num', ge, gt, le, lt, raise_error, log))
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222
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223 def _is_int_or_num_pair(v, type_str, ge=None, gt=None, le=None, lt=None, raise_error=False,
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224 log=True):
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225 if type_str == 'int':
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226 if not (isinstance(v, (tuple, list)) and len(v) == 2 and isinstance(v[0], int) and
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227 isinstance(v[1], int)):
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228 illegal_value(v, 'v', '_is_int_or_num_pair', raise_error, log)
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229 return(False)
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230 func = is_int
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231 elif type_str == 'num':
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232 if not (isinstance(v, (tuple, list)) and len(v) == 2 and isinstance(v[0], (int, float)) and
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233 isinstance(v[1], (int, float))):
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234 illegal_value(v, 'v', '_is_int_or_num_pair', raise_error, log)
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235 return(False)
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236 func = is_num
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237 else:
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238 illegal_value(type_str, 'type_str', '_is_int_or_num_pair', raise_error, log)
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239 return(False)
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240 if ge is None and gt is None and le is None and lt is None:
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241 return(True)
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242 if ge is None or func(ge, log=True):
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243 ge = 2*[ge]
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244 elif not _is_int_or_num_pair(ge, type_str, raise_error=raise_error, log=log):
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245 return(False)
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246 if gt is None or func(gt, log=True):
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247 gt = 2*[gt]
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248 elif not _is_int_or_num_pair(gt, type_str, raise_error=raise_error, log=log):
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249 return(False)
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250 if le is None or func(le, log=True):
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251 le = 2*[le]
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252 elif not _is_int_or_num_pair(le, type_str, raise_error=raise_error, log=log):
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253 return(False)
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254 if lt is None or func(lt, log=True):
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255 lt = 2*[lt]
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256 elif not _is_int_or_num_pair(lt, type_str, raise_error=raise_error, log=log):
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257 return(False)
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258 if (not func(v[0], ge[0], gt[0], le[0], lt[0], raise_error, log) or
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259 not func(v[1], ge[1], gt[1], le[1], lt[1], raise_error, log)):
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260 return(False)
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261 return(True)
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262
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263 def is_int_series(l, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
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264 """Value is a tuple or list of integers, each in range ge <= l[i] <= le or
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265 gt < l[i] < lt or some combination.
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266 """
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267 if not test_ge_gt_le_lt(ge, gt, le, lt, is_int, 'is_int_series', raise_error, log):
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268 return(False)
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269 if not isinstance(l, (tuple, list)):
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270 illegal_value(l, 'l', 'is_int_series', raise_error, log)
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271 return(False)
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272 if any(True if not is_int(v, ge, gt, le, lt, raise_error, log) else False for v in l):
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273 return(False)
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274 return(True)
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275
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276 def is_num_series(l, ge=None, gt=None, le=None, lt=None, raise_error=False, log=True):
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277 """Value is a tuple or list of numbers, each in range ge <= l[i] <= le or
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278 gt < l[i] < lt or some combination.
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279 """
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280 if not test_ge_gt_le_lt(ge, gt, le, lt, is_int, 'is_int_series', raise_error, log):
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281 return(False)
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282 if not isinstance(l, (tuple, list)):
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283 illegal_value(l, 'l', 'is_num_series', raise_error, log)
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284 return(False)
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285 if any(True if not is_num(v, ge, gt, le, lt, raise_error, log) else False for v in l):
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286 return(False)
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287 return(True)
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288
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289 def is_str_series(l, raise_error=False, log=True):
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290 """Value is a tuple or list of strings.
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291 """
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292 if (not isinstance(l, (tuple, list)) or
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293 any(True if not isinstance(s, str) else False for s in l)):
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294 illegal_value(l, 'l', 'is_str_series', raise_error, log)
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295 return(False)
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296 return(True)
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297
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298 def is_dict_series(l, raise_error=False, log=True):
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299 """Value is a tuple or list of dictionaries.
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300 """
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301 if (not isinstance(l, (tuple, list)) or
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302 any(True if not isinstance(d, dict) else False for d in l)):
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303 illegal_value(l, 'l', 'is_dict_series', raise_error, log)
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304 return(False)
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305 return(True)
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306
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307 def is_dict_nums(l, raise_error=False, log=True):
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308 """Value is a dictionary with single number values
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309 """
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310 if (not isinstance(l, dict) or
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311 any(True if not is_num(v, log=False) else False for v in l.values())):
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312 illegal_value(l, 'l', 'is_dict_nums', raise_error, log)
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313 return(False)
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314 return(True)
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315
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316 def is_dict_strings(l, raise_error=False, log=True):
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317 """Value is a dictionary with single string values
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318 """
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319 if (not isinstance(l, dict) or
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320 any(True if not isinstance(v, str) else False for v in l.values())):
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321 illegal_value(l, 'l', 'is_dict_strings', raise_error, log)
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322 return(False)
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323 return(True)
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324
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325 def is_index(v, ge=0, lt=None, raise_error=False, log=True):
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326 """Value is an array index in range ge <= v < lt.
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327 NOTE lt IS NOT included!
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328 """
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329 if isinstance(lt, int):
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330 if lt <= ge:
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331 illegal_combination(ge, 'ge', lt, 'lt', 'is_index', raise_error, log)
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332 return(False)
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333 return(is_int(v, ge=ge, lt=lt, raise_error=raise_error, log=log))
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334
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335 def is_index_range(v, ge=0, le=None, lt=None, raise_error=False, log=True):
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336 """Value is an array index range in range ge <= v[0] <= v[1] <= le or ge <= v[0] <= v[1] < lt.
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337 NOTE le IS included!
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338 """
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339 if not is_int_pair(v, raise_error=raise_error, log=log):
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340 return(False)
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341 if not test_ge_gt_le_lt(ge, None, le, lt, is_int, 'is_index_range', raise_error, log):
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342 return(False)
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343 if not ge <= v[0] <= v[1] or (le is not None and v[1] > le) or (lt is not None and v[1] >= lt):
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344 if le is not None:
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345 error_msg = f'Value {v} out of range: !({ge} <= {v[0]} <= {v[1]} <= {le})'
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346 else:
69
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347 error_msg = f'Value {v} out of range: !({ge} <= {v[0]} <= {v[1]} < {lt})'
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348 if log:
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349 logger.error(error_msg)
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350 if raise_error:
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351 raise ValueError(error_msg)
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352 return(False)
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353 return(True)
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354
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355 def index_nearest(a, value):
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356 a = np.asarray(a)
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357 if a.ndim > 1:
69
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358 raise ValueError(f'Invalid array dimension for parameter a ({a.ndim}, {a})')
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359 # Round up for .5
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360 value *= 1.0+sys.float_info.epsilon
69
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361 return((int)(np.argmin(np.abs(a-value))))
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362
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363 def index_nearest_low(a, value):
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364 a = np.asarray(a)
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365 if a.ndim > 1:
69
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366 raise ValueError(f'Invalid array dimension for parameter a ({a.ndim}, {a})')
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367 index = int(np.argmin(np.abs(a-value)))
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368 if value < a[index] and index > 0:
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369 index -= 1
69
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370 return(index)
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371
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372 def index_nearest_upp(a, value):
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373 a = np.asarray(a)
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374 if a.ndim > 1:
69
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375 raise ValueError(f'Invalid array dimension for parameter a ({a.ndim}, {a})')
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376 index = int(np.argmin(np.abs(a-value)))
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377 if value > a[index] and index < a.size-1:
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378 index += 1
69
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379 return(index)
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380
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381 def round_to_n(x, n=1):
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382 if x == 0.0:
69
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diff changeset
383 return(0)
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384 else:
69
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385 return(type(x)(round(x, n-1-int(np.floor(np.log10(abs(x)))))))
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386
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diff changeset
387 def round_up_to_n(x, n=1):
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388 xr = round_to_n(x, n)
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389 if abs(x/xr) > 1.0:
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390 xr += np.sign(x)*10**(np.floor(np.log10(abs(x)))+1-n)
69
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391 return(type(x)(xr))
49
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392
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393 def trunc_to_n(x, n=1):
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394 xr = round_to_n(x, n)
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395 if abs(xr/x) > 1.0:
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396 xr -= np.sign(x)*10**(np.floor(np.log10(abs(x)))+1-n)
69
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397 return(type(x)(xr))
49
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diff changeset
398
69
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399 def almost_equal(a, b, sig_figs):
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diff changeset
400 if is_num(a) and is_num(b):
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diff changeset
401 return(abs(round_to_n(a-b, sig_figs)) < pow(10, -sig_figs+1))
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diff changeset
402 else:
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403 raise ValueError(f'Invalid value for a or b in almost_equal (a: {a}, {type(a)}, '+
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diff changeset
404 f'b: {b}, {type(b)})')
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diff changeset
405 return(False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
406
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diff changeset
407 def string_to_list(s, split_on_dash=True, remove_duplicates=True, sort=True):
49
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408 """Return a list of numbers by splitting/expanding a string on any combination of
69
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409 commas, whitespaces, or dashes (when split_on_dash=True)
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410 e.g: '1, 3, 5-8, 12 ' -> [1, 3, 5, 6, 7, 8, 12]
49
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411 """
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412 if not isinstance(s, str):
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413 illegal_value(s, location='string_to_list')
69
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diff changeset
414 return(None)
49
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415 if not len(s):
69
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diff changeset
416 return([])
49
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417 try:
69
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418 ll = [x for x in re.split('\s+,\s+|\s+,|,\s+|\s+|,', s.strip())]
49
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419 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
69
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diff changeset
420 return(None)
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diff changeset
421 if split_on_dash:
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diff changeset
422 try:
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diff changeset
423 l = []
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diff changeset
424 for l1 in ll:
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diff changeset
425 l2 = [literal_eval(x) for x in re.split('\s+-\s+|\s+-|-\s+|\s+|-', l1)]
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diff changeset
426 if len(l2) == 1:
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diff changeset
427 l += l2
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diff changeset
428 elif len(l2) == 2 and l2[1] > l2[0]:
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429 l += [i for i in range(l2[0], l2[1]+1)]
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diff changeset
430 else:
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diff changeset
431 raise ValueError
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diff changeset
432 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
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diff changeset
433 return(None)
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diff changeset
434 else:
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diff changeset
435 l = [literal_eval(x) for x in ll]
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diff changeset
436 if remove_duplicates:
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diff changeset
437 l = list(dict.fromkeys(l))
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diff changeset
438 if sort:
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diff changeset
439 l = sorted(l)
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diff changeset
440 return(l)
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diff changeset
441
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diff changeset
442 def get_trailing_int(string):
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diff changeset
443 indexRegex = re.compile(r'\d+$')
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diff changeset
444 mo = indexRegex.search(string)
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diff changeset
445 if mo is None:
69
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diff changeset
446 return(None)
49
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diff changeset
447 else:
69
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diff changeset
448 return(int(mo.group()))
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diff changeset
449
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diff changeset
450 def input_int(s=None, ge=None, gt=None, le=None, lt=None, default=None, inset=None,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
451 raise_error=False, log=True):
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diff changeset
452 return(_input_int_or_num('int', s, ge, gt, le, lt, default, inset, raise_error, log))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
453
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
454 def input_num(s=None, ge=None, gt=None, le=None, lt=None, default=None, raise_error=False,
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diff changeset
455 log=True):
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diff changeset
456 return(_input_int_or_num('num', s, ge, gt, le, lt, default, None, raise_error,log))
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diff changeset
457
69
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diff changeset
458 def _input_int_or_num(type_str, s=None, ge=None, gt=None, le=None, lt=None, default=None,
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diff changeset
459 inset=None, raise_error=False, log=True):
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diff changeset
460 if type_str == 'int':
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diff changeset
461 if not test_ge_gt_le_lt(ge, gt, le, lt, is_int, '_input_int_or_num', raise_error, log):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
462 return(None)
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diff changeset
463 elif type_str == 'num':
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diff changeset
464 if not test_ge_gt_le_lt(ge, gt, le, lt, is_num, '_input_int_or_num', raise_error, log):
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diff changeset
465 return(None)
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diff changeset
466 else:
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diff changeset
467 illegal_value(type_str, 'type_str', '_input_int_or_num', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
468 return(None)
49
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diff changeset
469 if default is not None:
69
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diff changeset
470 if not _is_int_or_num(default, type_str, raise_error=raise_error, log=log):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
471 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
472 if ge is not None and default < ge:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
473 illegal_combination(ge, 'ge', default, 'default', '_input_int_or_num', raise_error,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
474 log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
475 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
476 if gt is not None and default <= gt:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
477 illegal_combination(gt, 'gt', default, 'default', '_input_int_or_num', raise_error,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
478 log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
479 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
480 if le is not None and default > le:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
481 illegal_combination(le, 'le', default, 'default', '_input_int_or_num', raise_error,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
482 log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
483 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
484 if lt is not None and default >= lt:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
485 illegal_combination(lt, 'lt', default, 'default', '_input_int_or_num', raise_error,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
486 log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
487 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
488 default_string = f' [{default}]'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
489 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
490 default_string = ''
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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diff changeset
491 if inset is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
492 if (not isinstance(inset, (tuple, list)) or any(True if not isinstance(i, int) else
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
493 False for i in inset)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
494 illegal_value(inset, 'inset', '_input_int_or_num', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
495 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
496 v_range = f'{range_string_ge_gt_le_lt(ge, gt, le, lt)}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
497 if len(v_range):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
498 v_range = f' {v_range}'
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
499 if s is None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
500 if type_str == 'int':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
501 print(f'Enter an integer{v_range}{default_string}: ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
502 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
503 print(f'Enter a number{v_range}{default_string}: ')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
504 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
505 print(f'{s}{v_range}{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
506 try:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
507 i = input()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
508 if isinstance(i, str) and not len(i):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
509 v = default
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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diff changeset
510 print(f'{v}')
49
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parents:
diff changeset
511 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
512 v = literal_eval(i)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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diff changeset
513 if inset and v not in inset:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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parents: 63
diff changeset
514 raise ValueError(f'{v} not part of the set {inset}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
515 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
516 v = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
517 except:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
518 if log:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
519 logger.error('Unexpected error')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
520 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
521 raise ValueError('Unexpected error')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
522 if not _is_int_or_num(v, type_str, ge, gt, le, lt):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
523 v = _input_int_or_num(type_str, s, ge, gt, le, lt, default, inset, raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
524 return(v)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
525
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
526 def input_int_list(s=None, ge=None, le=None, split_on_dash=True, remove_duplicates=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
527 sort=True, raise_error=False, log=True):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
528 """Prompt the user to input a list of interger and split the entered string on any combination
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
529 of commas, whitespaces, or dashes (when split_on_dash is True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
530 e.g: '1 3,5-8 , 12 ' -> [1, 3, 5, 6, 7, 8, 12]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
531 remove_duplicates: removes duplicates if True (may also change the order)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
532 sort: sort in ascending order if True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
533 return None upon an illegal input
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
534 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
535 return(_input_int_or_num_list('int', s, ge, le, split_on_dash, remove_duplicates, sort,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
536 raise_error, log))
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
537
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
538 def input_num_list(s=None, ge=None, le=None, remove_duplicates=True, sort=True, raise_error=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
539 log=True):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
540 """Prompt the user to input a list of numbers and split the entered string on any combination
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
541 of commas or whitespaces
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
542 e.g: '1.0, 3, 5.8, 12 ' -> [1.0, 3.0, 5.8, 12.0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
543 remove_duplicates: removes duplicates if True (may also change the order)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
544 sort: sort in ascending order if True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
545 return None upon an illegal input
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
546 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
547 return(_input_int_or_num_list('num', s, ge, le, False, remove_duplicates, sort, raise_error,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
548 log))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
549
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
550 def _input_int_or_num_list(type_str, s=None, ge=None, le=None, split_on_dash=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
551 remove_duplicates=True, sort=True, raise_error=False, log=True):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
552 #FIX do we want a limit on max dimension?
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
553 if type_str == 'int':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
554 if not test_ge_gt_le_lt(ge, None, le, None, is_int, 'input_int_or_num_list', raise_error,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
555 log):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
556 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
557 elif type_str == 'num':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
558 if not test_ge_gt_le_lt(ge, None, le, None, is_num, 'input_int_or_num_list', raise_error,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
559 log):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
560 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
561 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
562 illegal_value(type_str, 'type_str', '_input_int_or_num_list')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
563 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
564 v_range = f'{range_string_ge_gt_le_lt(ge=ge, le=le)}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
565 if len(v_range):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
566 v_range = f' (each value in {v_range})'
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
567 if s is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
568 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
569 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
570 print(f'{s}{v_range}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
571 try:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
572 l = string_to_list(input(), split_on_dash, remove_duplicates, sort)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
573 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
574 l = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
575 except:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
576 print('Unexpected error')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
577 raise
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
578 if (not isinstance(l, list) or
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
579 any(True if not _is_int_or_num(v, type_str, ge=ge, le=le) else False for v in l)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
580 if split_on_dash:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
581 print('Invalid input: enter a valid set of dash/comma/whitespace separated integers '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
582 'e.g. 1 3,5-8 , 12')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
583 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
584 print('Invalid input: enter a valid set of comma/whitespace separated integers '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
585 'e.g. 1 3,5 8 , 12')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
586 l = _input_int_or_num_list(type_str, s, ge, le, split_on_dash, remove_duplicates, sort,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
587 raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
588 return(l)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
589
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
590 def input_yesno(s=None, default=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
591 if default is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
592 if not isinstance(default, str):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
593 illegal_value(default, 'default', 'input_yesno')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
594 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
595 if default.lower() in 'yes':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
596 default = 'y'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
597 elif default.lower() in 'no':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
598 default = 'n'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
599 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
600 illegal_value(default, 'default', 'input_yesno')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
601 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
602 default_string = f' [{default}]'
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 default_string = ''
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
605 if s is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
606 print(f'Enter yes or no{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
607 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
608 print(f'{s}{default_string}: ')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
609 i = input()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
610 if isinstance(i, str) and not len(i):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
611 i = default
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
612 print(f'{i}')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
613 if i is not None and i.lower() in 'yes':
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
614 v = True
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
615 elif i is not None and i.lower() in 'no':
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
616 v = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
617 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
618 print('Invalid input, enter yes or no')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
619 v = input_yesno(s, default)
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
620 return(v)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
621
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
622 def input_menu(items, default=None, header=None):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
623 if not isinstance(items, (tuple, list)) or any(True if not isinstance(i, str) else False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
624 for i in items):
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
625 illegal_value(items, 'items', 'input_menu')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
626 return(None)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
627 if default is not None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
628 if not (isinstance(default, str) and default in items):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
629 logger.error(f'Invalid value for default ({default}), must be in {items}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
630 return(None)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
631 default_string = f' [{items.index(default)+1}]'
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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parents: 63
diff changeset
632 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
633 default_string = ''
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
634 if header is None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
635 print(f'Choose one of the following items (1, {len(items)}){default_string}:')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
636 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
637 print(f'{header} (1, {len(items)}){default_string}:')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
638 for i, choice in enumerate(items):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
639 print(f' {i+1}: {choice}')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
640 try:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
641 choice = input()
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
642 if isinstance(choice, str) and not len(choice):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
643 choice = items.index(default)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
644 print(f'{choice+1}')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
645 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
646 choice = literal_eval(choice)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
647 if isinstance(choice, int) and 1 <= choice <= len(items):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
648 choice -= 1
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
649 else:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
650 raise ValueError
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
651 except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
652 choice = None
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
653 except:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
654 print('Unexpected error')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
655 raise
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
656 if choice is None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
657 print(f'Invalid choice, enter a number between 1 and {len(items)}')
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
658 choice = input_menu(items, default)
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
659 return(choice)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
660
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
661 def assert_no_duplicates_in_list_of_dicts(l: list, raise_error=False) -> list:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
662 if not isinstance(l, list):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
663 illegal_value(l, 'l', 'assert_no_duplicates_in_list_of_dicts', raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
664 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
665 if any(True if not isinstance(d, dict) else False for d in l):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
666 illegal_value(l, 'l', 'assert_no_duplicates_in_list_of_dicts', raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
667 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
668 if len(l) != len([dict(t) for t in {tuple(sorted(d.items())) for d in l}]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
669 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
670 raise ValueError(f'Duplicate items found in {l}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
671 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
672 logger.error(f'Duplicate items found in {l}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
673 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
674 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
675 return(l)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
676
69
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diff changeset
677 def assert_no_duplicate_key_in_list_of_dicts(l: list, key: str, raise_error=False) -> list:
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diff changeset
678 if not isinstance(key, str):
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diff changeset
679 illegal_value(key, 'key', 'assert_no_duplicate_key_in_list_of_dicts', raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
680 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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681 if not isinstance(l, list):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
682 illegal_value(l, 'l', 'assert_no_duplicate_key_in_list_of_dicts', raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
683 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
684 if any(True if not isinstance(d, dict) else False for d in l):
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diff changeset
685 illegal_value(l, 'l', 'assert_no_duplicates_in_list_of_dicts', raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
686 return(None)
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diff changeset
687 keys = [d.get(key, None) for d in l]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
688 if None in keys or len(set(keys)) != len(l):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
689 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
690 raise ValueError(f'Duplicate or missing key ({key}) found in {l}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
691 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
692 logger.error(f'Duplicate or missing key ({key}) found in {l}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
693 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
694 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
695 return(l)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
696
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
697 def assert_no_duplicate_attr_in_list_of_objs(l: list, attr: str, raise_error=False) -> list:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
698 if not isinstance(attr, str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
699 illegal_value(attr, 'attr', 'assert_no_duplicate_attr_in_list_of_objs', raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
700 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
701 if not isinstance(l, list):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
702 illegal_value(l, 'l', 'assert_no_duplicate_key_in_list_of_objs', raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
703 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
704 attrs = [getattr(obj, attr, None) for obj in l]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
705 if None in attrs or len(set(attrs)) != len(l):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
706 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
707 raise ValueError(f'Duplicate or missing attr ({attr}) found in {l}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
708 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
709 logger.error(f'Duplicate or missing attr ({attr}) found in {l}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
710 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
711 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
712 return(l)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
713
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
714 def file_exists_and_readable(path):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
715 if not os.path.isfile(path):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
716 raise ValueError(f'{path} is not a valid file')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
717 elif not os.access(path, os.R_OK):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
718 raise ValueError(f'{path} is not accessible for reading')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
719 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
720 return(path)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
721
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
722 def create_mask(x, bounds=None, exclude_bounds=False, current_mask=None):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
723 # bounds is a pair of number in the same units a x
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
724 if not isinstance(x, (tuple, list, np.ndarray)) or not len(x):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
725 logger.warning(f'Invalid input array ({x}, {type(x)})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
726 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
727 if bounds is not None and not is_num_pair(bounds):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
728 logger.warning(f'Invalid bounds parameter ({bounds} {type(bounds)}, input ignored')
49
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rv43
parents:
diff changeset
729 bounds = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
730 if bounds is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
731 if exclude_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
732 mask = np.logical_or(x < min(bounds), x > max(bounds))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
733 else:
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
734 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
735 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
736 mask = np.ones(len(x), dtype=bool)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
737 if current_mask is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
738 if not isinstance(current_mask, (tuple, list, np.ndarray)) or len(current_mask) != len(x):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
739 logger.warning(f'Invalid current_mask ({current_mask}, {type(current_mask)}), '+
49
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rv43
parents:
diff changeset
740 'input ignored')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
741 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
742 mask = np.logical_or(mask, current_mask)
49
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parents:
diff changeset
743 if not True in mask:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
744 logger.warning('Entire data array is masked')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
745 return(mask)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
746
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
747 def eval_expr(name, expr, expr_variables, user_variables=None, max_depth=10, raise_error=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
748 log=True, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
749 """Evaluate an expression of expressions
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
750 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
751 if not isinstance(name, str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
752 illegal_value(name, 'name', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
753 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
754 if not isinstance(expr, str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
755 illegal_value(expr, 'expr', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
756 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
757 if not is_dict_strings(expr_variables, log=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
758 illegal_value(expr_variables, 'expr_variables', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
759 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
760 if user_variables is not None and not is_dict_nums(user_variables, log=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
761 illegal_value(user_variables, 'user_variables', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
762 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
763 if not is_int(max_depth, gt=1, log=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
764 illegal_value(max_depth, 'max_depth', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
765 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
766 if not isinstance(raise_error, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
767 illegal_value(raise_error, 'raise_error', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
768 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
769 if not isinstance(log, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
770 illegal_value(log, 'log', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
771 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
772 # print(f'\nEvaluate the full expression for {expr}')
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773 if 'chain' in kwargs:
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774 chain = kwargs.pop('chain')
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diff changeset
775 if not is_str_series(chain):
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diff changeset
776 illegal_value(chain, 'chain', 'eval_expr', raise_error, log)
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diff changeset
777 return(None)
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diff changeset
778 else:
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diff changeset
779 chain = []
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780 if len(chain) > max_depth:
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diff changeset
781 error_msg = 'Exceeded maximum depth ({max_depth}) in eval_expr'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
782 if log:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
783 logger.error(error_msg)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
784 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
785 raise ValueError(error_msg)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
786 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
787 if name not in chain:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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788 chain.append(name)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
789 # print(f'start: chain = {chain}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
790 if 'ast' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
791 ast = kwargs.pop('ast')
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792 else:
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793 ast = Interpreter()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
794 if user_variables is not None:
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795 ast.symtable.update(user_variables)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
796 chain_vars = [var for var in get_ast_names(ast.parse(expr))
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797 if var in expr_variables and var not in ast.symtable]
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798 # print(f'chain_vars: {chain_vars}')
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diff changeset
799 save_chain = chain.copy()
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diff changeset
800 for var in chain_vars:
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801 # print(f'\n\tname = {name}, var = {var}:\n\t\t{expr_variables[var]}')
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802 # print(f'\tchain = {chain}')
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diff changeset
803 if var in chain:
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diff changeset
804 error_msg = f'Circular variable {var} in eval_expr'
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diff changeset
805 if log:
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diff changeset
806 logger.error(error_msg)
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diff changeset
807 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
808 raise ValueError(error_msg)
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diff changeset
809 return(None)
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diff changeset
810 # print(f'\tknown symbols:\n\t\t{ast.user_defined_symbols()}\n')
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diff changeset
811 if var in ast.user_defined_symbols():
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diff changeset
812 val = ast.symtable[var]
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diff changeset
813 else:
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diff changeset
814 #val = eval_expr(var, expr_variables[var], expr_variables, user_variables=user_variables,
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diff changeset
815 val = eval_expr(var, expr_variables[var], expr_variables, max_depth=max_depth,
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diff changeset
816 raise_error=raise_error, log=log, chain=chain, ast=ast)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
817 if val is None:
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diff changeset
818 return(None)
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diff changeset
819 ast.symtable[var] = val
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diff changeset
820 # print(f'\tval = {val}')
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diff changeset
821 # print(f'\t{var} = {ast.symtable[var]}')
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diff changeset
822 chain = save_chain.copy()
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diff changeset
823 # print(f'\treset loop for {var}: chain = {chain}')
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diff changeset
824 val = ast.eval(expr)
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diff changeset
825 # print(f'return val for {expr} = {val}\n')
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diff changeset
826 return(val)
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diff changeset
827
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diff changeset
828 def full_gradient(expr, x, expr_name=None, expr_variables=None, valid_variables=None, max_depth=10,
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diff changeset
829 raise_error=False, log=True, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
830 """Compute the full gradient dexpr/dx
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831 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
832 if not isinstance(x, str):
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diff changeset
833 illegal_value(x, 'x', 'full_gradient', raise_error, log)
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diff changeset
834 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
835 if expr_name is not None and not isinstance(expr_name, str):
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diff changeset
836 illegal_value(expr_name, 'expr_name', 'eval_expr', raise_error, log)
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diff changeset
837 return(None)
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diff changeset
838 if expr_variables is not None and not is_dict_strings(expr_variables, log=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
839 illegal_value(expr_variables, 'expr_variables', 'full_gradient', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
840 return(None)
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diff changeset
841 if valid_variables is not None and not is_str_series(valid_variables, log=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
842 illegal_value(valid_variables, 'valid_variables', 'full_gradient', raise_error, log)
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diff changeset
843 if not is_int(max_depth, gt=1, log=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
844 illegal_value(max_depth, 'max_depth', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
845 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
846 if not isinstance(raise_error, bool):
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diff changeset
847 illegal_value(raise_error, 'raise_error', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
848 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
849 if not isinstance(log, bool):
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diff changeset
850 illegal_value(log, 'log', 'eval_expr', raise_error, log)
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diff changeset
851 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
852 # print(f'\nGet full gradient of {expr_name} = {expr} with respect to {x}')
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diff changeset
853 if expr_name is not None and expr_name == x:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
854 return(1.0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
855 if 'chain' in kwargs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
856 chain = kwargs.pop('chain')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
857 if not is_str_series(chain):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
858 illegal_value(chain, 'chain', 'eval_expr', raise_error, log)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
859 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
860 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
861 chain = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
862 if len(chain) > max_depth:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
863 error_msg = 'Exceeded maximum depth ({max_depth}) in eval_expr'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
864 if log:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
865 logger.error(error_msg)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
866 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
867 raise ValueError(error_msg)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
868 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
869 if expr_name is not None and expr_name not in chain:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
870 chain.append(expr_name)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
871 # print(f'start ({x}): chain = {chain}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
872 ast = Interpreter()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
873 if expr_variables is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
874 chain_vars = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
875 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
876 chain_vars = [var for var in get_ast_names(ast.parse(f'{expr}'))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
877 if var in expr_variables and var != x and var not in ast.symtable]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
878 # print(f'chain_vars: {chain_vars}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
879 if valid_variables is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
880 unknown_vars = [var for var in chain_vars if var not in valid_variables]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
881 if len(unknown_vars):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
882 error_msg = f'Unknown variable {unknown_vars} in {expr}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
883 if log:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
884 logger.error(error_msg)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
885 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
886 raise ValueError(error_msg)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
887 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
888 dexpr_dx = diff(expr, x)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
889 # print(f'direct gradient: d({expr})/d({x}) = {dexpr_dx} ({type(dexpr_dx)})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
890 save_chain = chain.copy()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
891 for var in chain_vars:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
892 # print(f'\n\texpr_name = {expr_name}, var = {var}:\n\t\t{expr}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
893 # print(f'\tchain = {chain}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
894 if var in chain:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
895 error_msg = f'Circular variable {var} in full_gradient'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
896 if log:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
897 logger.error(error_msg)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
898 if raise_error:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
899 raise ValueError(error_msg)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
900 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
901 dexpr_dvar = diff(expr, var)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
902 # print(f'\td({expr})/d({var}) = {dexpr_dvar}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
903 if dexpr_dvar:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
904 dvar_dx = full_gradient(expr_variables[var], x, expr_name=var,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
905 expr_variables=expr_variables, valid_variables=valid_variables,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
906 max_depth=max_depth, raise_error=raise_error, log=log, chain=chain)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
907 # print(f'\t\td({var})/d({x}) = {dvar_dx}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
908 if dvar_dx:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
909 dexpr_dx = f'{dexpr_dx}+({dexpr_dvar})*({dvar_dx})'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
910 # print(f'\t\t2: chain = {chain}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
911 chain = save_chain.copy()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
912 # print(f'\treset loop for {var}: chain = {chain}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
913 # print(f'full gradient: d({expr})/d({x}) = {dexpr_dx} ({type(dexpr_dx)})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
914 # print(f'reset end: chain = {chain}\n\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
915 return(simplify(dexpr_dx))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
916
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
917 def bounds_from_mask(mask, return_include_bounds:bool=True):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
918 bounds = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
919 for i, m in enumerate(mask):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
920 if m == return_include_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
921 if len(bounds) == 0 or type(bounds[-1]) == tuple:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
922 bounds.append(i)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
923 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
924 if len(bounds) > 0 and isinstance(bounds[-1], int):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
925 bounds[-1] = (bounds[-1], i-1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
926 if len(bounds) > 0 and isinstance(bounds[-1], int):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
927 bounds[-1] = (bounds[-1], mask.size-1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
928 return(bounds)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
929
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
930 def draw_mask_1d(ydata, xdata=None, current_index_ranges=None, current_mask=None,
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
931 select_mask=True, num_index_ranges_max=None, title=None, legend=None, test_mode=False):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
932 #FIX make color blind friendly
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
933 def draw_selections(ax, current_include, current_exclude, selected_index_ranges):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
934 ax.clear()
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
935 ax.set_title(title)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
936 ax.legend([legend])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
937 ax.plot(xdata, ydata, 'k')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
938 for (low, upp) in current_include:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
939 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
940 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
941 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
942 for (low, upp) in current_exclude:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
943 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
944 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
945 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
946 for (low, upp) in selected_index_ranges:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
947 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
948 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
949 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
950 ax.get_figure().canvas.draw()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
951
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
952 def onclick(event):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
953 if event.inaxes in [fig.axes[0]]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
954 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
955
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
956 def onrelease(event):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
957 if len(selected_index_ranges) > 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
958 if isinstance(selected_index_ranges[-1], int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
959 if event.inaxes in [fig.axes[0]]:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
960 event.xdata = index_nearest_low(xdata, event.xdata)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
961 if selected_index_ranges[-1] <= event.xdata:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
962 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
963 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
964 selected_index_ranges[-1] = (event.xdata, selected_index_ranges[-1])
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
965 draw_selections(event.inaxes, current_include, current_exclude, selected_index_ranges)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
966 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
967 selected_index_ranges.pop(-1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
968
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
969 def confirm_selection(event):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
970 plt.close()
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
971
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
972 def clear_last_selection(event):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
973 if len(selected_index_ranges):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
974 selected_index_ranges.pop(-1)
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
975 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
976 while len(current_include):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
977 current_include.pop()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
978 while len(current_exclude):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
979 current_exclude.pop()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
980 selected_mask.fill(False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
981 draw_selections(ax, current_include, current_exclude, selected_index_ranges)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
982
69
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diff changeset
983 def update_mask(mask, selected_index_ranges, unselected_index_ranges):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
984 for (low, upp) in selected_index_ranges:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
985 selected_mask = np.logical_and(xdata >= xdata[low], xdata <= xdata[upp])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
986 mask = np.logical_or(mask, selected_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
987 for (low, upp) in unselected_index_ranges:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
988 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
989 mask[unselected_mask] = False
69
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diff changeset
990 return(mask)
49
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rv43
parents:
diff changeset
991
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
992 def update_index_ranges(mask):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
993 # 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
994 current_include = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
995 for i, m in enumerate(mask):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
996 if m == True:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
997 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
998 current_include.append(i)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
999 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1000 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
1001 current_include[-1] = (current_include[-1], i-1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1002 if len(current_include) > 0 and isinstance(current_include[-1], int):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1003 current_include[-1] = (current_include[-1], num_data-1)
69
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parents: 68
diff changeset
1004 return(current_include)
49
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rv43
parents:
diff changeset
1005
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1006 # Check inputs
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1007 ydata = np.asarray(ydata)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1008 if ydata.ndim > 1:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1009 logger.warning(f'Invalid ydata dimension ({ydata.ndim})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1010 return(None, None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1011 num_data = ydata.size
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1012 if xdata is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1013 xdata = np.arange(num_data)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1014 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1015 xdata = np.asarray(xdata, dtype=np.float64)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1016 if xdata.ndim > 1 or xdata.size != num_data:
69
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diff changeset
1017 logger.warning(f'Invalid xdata shape ({xdata.shape})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1018 return(None, None)
49
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rv43
parents:
diff changeset
1019 if not np.all(xdata[:-1] < xdata[1:]):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1020 logger.warning('Invalid xdata: must be monotonically increasing')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1021 return(None, None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1022 if current_index_ranges is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1023 if not isinstance(current_index_ranges, (tuple, list)):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1024 logger.warning('Invalid current_index_ranges parameter ({current_index_ranges}, '+
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1025 f'{type(current_index_ranges)})')
69
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rv43
parents: 68
diff changeset
1026 return(None, None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1027 if not isinstance(select_mask, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1028 logger.warning('Invalid select_mask parameter ({select_mask}, {type(select_mask)})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1029 return(None, None)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1030 if num_index_ranges_max is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1031 logger.warning('num_index_ranges_max input not yet implemented in draw_mask_1d')
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1032 if title is None:
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1033 title = 'select ranges of data'
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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parents: 63
diff changeset
1034 elif not isinstance(title, str):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1035 illegal(title, 'title')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1036 title = ''
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1037 if legend is None and not isinstance(title, str):
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1038 illegal(legend, 'legend')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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parents: 63
diff changeset
1039 legend = None
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1040
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1041 if select_mask:
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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parents: 63
diff changeset
1042 title = f'Click and drag to {title} you wish to include'
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1043 selection_color = 'green'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1044 else:
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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parents: 63
diff changeset
1045 title = f'Click and drag to {title} you wish to exclude'
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1046 selection_color = 'red'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1047
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1048 # Set initial selected mask and the selected/unselected index ranges as needed
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1049 selected_index_ranges = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1050 unselected_index_ranges = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1051 selected_mask = np.full(xdata.shape, False, dtype=bool)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1052 if current_index_ranges is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1053 if current_mask is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1054 if not select_mask:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1055 selected_index_ranges = [(0, num_data-1)]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1056 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
1057 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1058 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
1059 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
1060 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
1061 for (low, upp) in current_index_ranges:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1062 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
1063 continue
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1064 if low < 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1065 low = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1066 if upp >= num_data:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1067 upp = num_data-1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1068 selected_index_ranges.append((low, upp))
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1069 selected_mask = update_mask(selected_mask, selected_index_ranges, unselected_index_ranges)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1070 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
1071 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
1072 if current_mask is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1073 selected_index_ranges = update_index_ranges(selected_mask)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1074
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1075 # Set up range selections for display
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1076 current_include = selected_index_ranges
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1077 current_exclude = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1078 selected_index_ranges = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1079 if not len(current_include):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1080 if select_mask:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1081 current_exclude = [(0, num_data-1)]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1082 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1083 current_include = [(0, num_data-1)]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1084 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1085 if current_include[0][0] > 0:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1086 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
1087 for i in range(1, len(current_include)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1088 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
1089 if current_include[-1][1] < num_data-1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1090 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
1091
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1092 if not test_mode:
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1093
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1094 # Set up matplotlib figure
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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parents: 63
diff changeset
1095 plt.close('all')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1096 fig, ax = plt.subplots()
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1097 plt.subplots_adjust(bottom=0.2)
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1098 draw_selections(ax, current_include, current_exclude, selected_index_ranges)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1099
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1100 # Set up event handling for click-and-drag range selection
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1101 cid_click = fig.canvas.mpl_connect('button_press_event', onclick)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1102 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
1103
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1104 # Set up confirm / clear range selection buttons
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1105 confirm_b = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1106 clear_b = Button(plt.axes([0.59, 0.05, 0.15, 0.075]), 'Clear')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1107 cid_confirm = confirm_b.on_clicked(confirm_selection)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1108 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
1109
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1110 # Show figure
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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parents: 63
diff changeset
1111 plt.show(block=True)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1112
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1113 # Disconnect callbacks when figure is closed
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1114 fig.canvas.mpl_disconnect(cid_click)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1115 fig.canvas.mpl_disconnect(cid_release)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1116 confirm_b.disconnect(cid_confirm)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1117 clear_b.disconnect(cid_clear)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1118
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1119 # Swap selection depending on select_mask
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1120 if not select_mask:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1121 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
1122 selected_index_ranges
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1123
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1124 # Update the mask with the currently selected/unselected x-ranges
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1125 selected_mask = update_mask(selected_mask, selected_index_ranges, unselected_index_ranges)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1126
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1127 # 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
1128 current_include = update_index_ranges(selected_mask)
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1129
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1130 return(selected_mask, current_include)
49
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rv43
parents:
diff changeset
1131
69
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parents: 68
diff changeset
1132 def select_peaks(ydata:np.ndarray, x_values:np.ndarray=None, x_mask:np.ndarray=None,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1133 peak_x_values:np.ndarray=np.array([]), peak_x_indices:np.ndarray=np.array([]),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1134 return_peak_x_values:bool=False, return_peak_x_indices:bool=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1135 return_peak_input_indices:bool=False, return_sorted:bool=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1136 title:str=None, xlabel:str=None, ylabel:str=None) -> list :
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1137
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1138 # Check arguments
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1139 if (len(peak_x_values) > 0 or return_peak_x_values) and not len(x_values) > 0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1140 raise RuntimeError('Cannot use peak_x_values or return_peak_x_values without x_values')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1141 if not ((len(peak_x_values) > 0) ^ (len(peak_x_indices) > 0)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1142 raise RuntimeError('Use exactly one of peak_x_values or peak_x_indices')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1143 return_format_iter = iter((return_peak_x_values, return_peak_x_indices, return_peak_input_indices))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1144 if not (any(return_format_iter) and not any(return_format_iter)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1145 raise RuntimeError('Exactly one of return_peak_x_values, return_peak_x_indices, or '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1146 'return_peak_input_indices must be True')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1147
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1148 EXCLUDE_PEAK_PROPERTIES = {'color': 'black', 'linestyle': '--','linewidth': 1,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1149 'marker': 10, 'markersize': 5, 'fillstyle': 'none'}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1150 INCLUDE_PEAK_PROPERTIES = {'color': 'green', 'linestyle': '-', 'linewidth': 2,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1151 'marker': 10, 'markersize': 10, 'fillstyle': 'full'}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1152 MASKED_PEAK_PROPERTIES = {'color': 'gray', 'linestyle': ':', 'linewidth': 1}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1153
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1154 # Setup reference data & plot
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1155 x_indices = np.arange(len(ydata))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1156 if x_values is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1157 x_values = x_indices
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1158 if x_mask is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1159 x_mask = np.full(x_values.shape, True, dtype=bool)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1160 fig, ax = plt.subplots()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1161 handles = ax.plot(x_values, ydata, label='Reference data')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1162 handles.append(mlines.Line2D([], [], label='Excluded / unselected HKL', **EXCLUDE_PEAK_PROPERTIES))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1163 handles.append(mlines.Line2D([], [], label='Included / selected HKL', **INCLUDE_PEAK_PROPERTIES))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1164 handles.append(mlines.Line2D([], [], label='HKL in masked region (unselectable)', **MASKED_PEAK_PROPERTIES))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1165 ax.legend(handles=handles, loc='upper right')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1166 ax.set(title=title, xlabel=xlabel, ylabel=ylabel)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1167
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1168
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1169 # Plot vertical line at each peak
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1170 value_to_index = lambda x_value: int(np.argmin(abs(x_values - x_value)))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1171 if len(peak_x_indices) > 0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1172 peak_x_values = x_values[peak_x_indices]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1173 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1174 peak_x_indices = np.array(list(map(value_to_index, peak_x_values)))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1175 peak_vlines = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1176 for loc in peak_x_values:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1177 nearest_index = value_to_index(loc)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1178 if nearest_index in x_indices[x_mask]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1179 peak_vline = ax.axvline(loc, **EXCLUDE_PEAK_PROPERTIES)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1180 peak_vline.set_picker(5)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1181 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1182 peak_vline = ax.axvline(loc, **MASKED_PEAK_PROPERTIES)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1183 peak_vlines.append(peak_vline)
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diff changeset
1184
69
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diff changeset
1185 # Indicate masked regions by gray-ing out the axes facecolor
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diff changeset
1186 mask_exclude_bounds = bounds_from_mask(x_mask, return_include_bounds=False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1187 for (low, upp) in mask_exclude_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1188 xlow = x_values[low]
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diff changeset
1189 xupp = x_values[upp]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1190 ax.axvspan(xlow, xupp, facecolor='gray', alpha=0.5)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1191
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1192 # Setup peak picking
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1193 selected_peak_input_indices = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1194 def onpick(event):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1195 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1196 peak_index = peak_vlines.index(event.artist)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1197 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1198 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1199 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1200 peak_vline = event.artist
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1201 if peak_index in selected_peak_input_indices:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1202 peak_vline.set(**EXCLUDE_PEAK_PROPERTIES)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1203 selected_peak_input_indices.remove(peak_index)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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diff changeset
1204 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1205 peak_vline.set(**INCLUDE_PEAK_PROPERTIES)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1206 selected_peak_input_indices.append(peak_index)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1207 plt.draw()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1208 cid_pick_peak = fig.canvas.mpl_connect('pick_event', onpick)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1209
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1210 # Setup "Confirm" button
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1211 def confirm_selection(event):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1212 plt.close()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1213 plt.subplots_adjust(bottom=0.2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1214 confirm_b = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1215 cid_confirm = confirm_b.on_clicked(confirm_selection)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1216
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1217 # Show figure for user interaction
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diff changeset
1218 plt.show()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1219
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1220 # Disconnect callbacks when figure is closed
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1221 fig.canvas.mpl_disconnect(cid_pick_peak)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1222 confirm_b.disconnect(cid_confirm)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1223
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1224 if return_peak_input_indices:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1225 selected_peaks = np.array(selected_peak_input_indices)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1226 if return_peak_x_values:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1227 selected_peaks = peak_x_values[selected_peak_input_indices]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1228 if return_peak_x_indices:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1229 selected_peaks = peak_x_indices[selected_peak_input_indices]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1230
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1231 if return_sorted:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1232 selected_peaks.sort()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1233
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1234 return(selected_peaks)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1235
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1236 def find_image_files(path, filetype, name=None):
49
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parents:
diff changeset
1237 if isinstance(name, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1238 name = f'{name.strip()} '
49
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rv43
parents:
diff changeset
1239 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1240 name = ''
49
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rv43
parents:
diff changeset
1241 # Find available index range
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1242 if filetype == 'tif':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1243 if not isinstance(path, str) or not os.path.isdir(path):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1244 illegal_value(path, 'path', 'find_image_files')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1245 return(-1, 0, [])
49
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parents:
diff changeset
1246 indexRegex = re.compile(r'\d+')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1247 # At this point only tiffs
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1248 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
1249 f.endswith('.tif') and indexRegex.search(f)])
69
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parents: 68
diff changeset
1250 num_img = len(files)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1251 if num_img < 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1252 logger.warning(f'No available {name}files')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1253 return(-1, 0, [])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1254 first_index = indexRegex.search(files[0]).group()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1255 last_index = indexRegex.search(files[-1]).group()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1256 if first_index is None or last_index is None:
69
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parents: 68
diff changeset
1257 logger.error(f'Unable to find correctly indexed {name}images')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1258 return(-1, 0, [])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1259 first_index = int(first_index)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1260 last_index = int(last_index)
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1261 if num_img != last_index-first_index+1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1262 logger.error(f'Non-consecutive set of indices for {name}images')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1263 return(-1, 0, [])
49
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rv43
parents:
diff changeset
1264 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
1265 elif filetype == 'h5':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1266 if not isinstance(path, str) or not os.path.isfile(path):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1267 illegal_value(path, 'path', 'find_image_files')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1268 return(-1, 0, [])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1269 # 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
1270 first_index = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1271 with h5py.File(path, 'r') as f:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1272 num_img = f['entry/instrument/detector/data'].shape[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1273 last_index = num_img-1
49
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rv43
parents:
diff changeset
1274 paths = [path]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
1275 else:
69
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parents: 68
diff changeset
1276 illegal_value(filetype, 'filetype', 'find_image_files')
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parents: 68
diff changeset
1277 return(-1, 0, [])
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parents: 68
diff changeset
1278 logger.info(f'Number of available {name}images: {num_img}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1279 logger.info(f'Index range of available {name}images: [{first_index}, '+
49
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rv43
parents:
diff changeset
1280 f'{last_index}]')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1281
69
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parents: 68
diff changeset
1282 return(first_index, num_img, paths)
49
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rv43
parents:
diff changeset
1283
69
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parents: 68
diff changeset
1284 def select_image_range(first_index, offset, num_available, num_img=None, name=None,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1285 num_required=None):
49
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rv43
parents:
diff changeset
1286 if isinstance(name, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1287 name = f'{name.strip()} '
49
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parents:
diff changeset
1288 else:
69
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parents: 68
diff changeset
1289 name = ''
49
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rv43
parents:
diff changeset
1290 # Check existing values
69
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parents: 68
diff changeset
1291 if not is_int(num_available, gt=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1292 logger.warning(f'No available {name}images')
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parents: 68
diff changeset
1293 return(0, 0, 0)
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parents: 68
diff changeset
1294 if num_img is not None and not is_int(num_img, ge=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1295 illegal_value(num_img, 'num_img', 'select_image_range')
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parents: 68
diff changeset
1296 return(0, 0, 0)
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parents: 68
diff changeset
1297 if is_int(first_index, ge=0) and is_int(offset, ge=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1298 if num_required is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1299 if input_yesno(f'\nCurrent {name}first image index/offset = {first_index}/{offset},'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1300 'use these values (y/n)?', 'y'):
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diff changeset
1301 if num_img is not None:
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parents: 68
diff changeset
1302 if input_yesno(f'Current number of {name}images = {num_img}, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1303 'use this value (y/n)? ', 'y'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1304 return(first_index, offset, num_img)
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parents: 68
diff changeset
1305 else:
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rv43
parents: 68
diff changeset
1306 if input_yesno(f'Number of available {name}images = {num_available}, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1307 'use all (y/n)? ', 'y'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1308 return(first_index, offset, num_available)
49
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rv43
parents:
diff changeset
1309 else:
69
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parents: 68
diff changeset
1310 if input_yesno(f'\nCurrent {name}first image offset = {offset}, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1311 f'use this values (y/n)?', 'y'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1312 return(first_index, offset, num_required)
49
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rv43
parents:
diff changeset
1313
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1314 # Check range against requirements
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parents:
diff changeset
1315 if num_required is None:
69
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parents: 68
diff changeset
1316 if num_available == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1317 return(first_index, 0, 1)
49
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parents:
diff changeset
1318 else:
69
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parents: 68
diff changeset
1319 if not is_int(num_required, ge=1):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1320 illegal_value(num_required, 'num_required', 'select_image_range')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1321 return(0, 0, 0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1322 if num_available < num_required:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1323 logger.error(f'Unable to find the required {name}images ({num_available} out of '+
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parents: 68
diff changeset
1324 f'{num_required})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1325 return(0, 0, 0)
49
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parents:
diff changeset
1326
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1327 # Select index range
69
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parents: 68
diff changeset
1328 print(f'\nThe number of available {name}images is {num_available}')
49
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parents:
diff changeset
1329 if num_required is None:
69
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parents: 68
diff changeset
1330 last_index = first_index+num_available
49
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parents:
diff changeset
1331 use_all = f'Use all ([{first_index}, {last_index}])'
69
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parents: 68
diff changeset
1332 pick_offset = 'Pick the first image index offset and the number of images'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1333 pick_bounds = 'Pick the first and last image index'
65
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diff changeset
1334 choice = input_menu([use_all, pick_offset, pick_bounds], default=pick_offset)
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
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diff changeset
1335 if not choice:
49
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parents:
diff changeset
1336 offset = 0
69
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diff changeset
1337 num_img = num_available
65
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parents: 63
diff changeset
1338 elif choice == 1:
69
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parents: 68
diff changeset
1339 offset = input_int('Enter the first index offset', ge=0, le=last_index-first_index)
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parents: 68
diff changeset
1340 if first_index+offset == last_index:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1341 num_img = 1
49
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parents:
diff changeset
1342 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1343 num_img = input_int('Enter the number of images', ge=1, le=num_available-offset)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1344 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1345 offset = input_int('Enter the first index', ge=first_index, le=last_index)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1346 num_img = 1-offset+input_int('Enter the last index', ge=offset, le=last_index)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1347 offset -= first_index
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1348 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1349 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
1350 pick_offset = 'Pick the first index offset'
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1351 choice = input_menu([use_all, pick_offset], pick_offset)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1352 offset = 0
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1353 if choice == 1:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1354 offset = input_int('Enter the first index offset', ge=0, le=num_available-num_required)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1355 num_img = num_required
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1356
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1357 return(first_index, offset, num_img)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1358
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1359 def load_image(f, img_x_bounds=None, img_y_bounds=None):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1360 """Load a single image from file.
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1361 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1362 if not os.path.isfile(f):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1363 logger.error(f'Unable to load {f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1364 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1365 img_read = plt.imread(f)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1366 if not img_x_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1367 img_x_bounds = (0, img_read.shape[0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1368 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1369 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
1370 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= img_read.shape[0])):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1371 logger.error(f'inconsistent row dimension in {f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1372 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1373 if not img_y_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1374 img_y_bounds = (0, img_read.shape[1])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1375 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1376 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
1377 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= img_read.shape[1])):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1378 logger.error(f'inconsistent column dimension in {f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1379 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1380 return(img_read[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1381
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1382 def load_image_stack(files, filetype, img_offset, num_img, num_img_skip=0,
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1383 img_x_bounds=None, img_y_bounds=None):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1384 """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
1385 """
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1386 logger.debug(f'img_offset = {img_offset}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1387 logger.debug(f'num_img = {num_img}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1388 logger.debug(f'num_img_skip = {num_img_skip}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1389 logger.debug(f'\nfiles:\n{files}\n')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1390 img_stack = np.array([])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1391 if filetype == 'tif':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1392 img_read_stack = []
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1393 i = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1394 t0 = time()
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1395 for f in files[img_offset:img_offset+num_img:num_img_skip+1]:
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1396 if not i%20:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1397 logger.info(f' loading {i}/{num_img}: {f}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1398 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1399 logger.debug(f' loading {i}/{num_img}: {f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1400 img_read = load_image(f, img_x_bounds, img_y_bounds)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1401 img_read_stack.append(img_read)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1402 i += num_img_skip+1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1403 img_stack = np.stack([img_read for img_read in img_read_stack])
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1404 logger.info(f'... done in {time()-t0:.2f} seconds!')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1405 logger.debug(f'img_stack shape = {np.shape(img_stack)}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1406 del img_read_stack, img_read
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1407 elif filetype == 'h5':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1408 if not isinstance(files[0], str) and not os.path.isfile(files[0]):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1409 illegal_value(files[0], 'files[0]', 'load_image_stack')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1410 return(img_stack)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1411 t0 = time()
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1412 logger.info(f'Loading {files[0]}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1413 with h5py.File(files[0], 'r') as f:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1414 shape = f['entry/instrument/detector/data'].shape
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1415 if len(shape) != 3:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1416 logger.error(f'inconsistent dimensions in {files[0]}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1417 if not img_x_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1418 img_x_bounds = (0, shape[1])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1419 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1420 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
1421 not (0 <= img_x_bounds[0] < img_x_bounds[1] <= shape[1])):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1422 logger.error(f'inconsistent row dimension in {files[0]} {img_x_bounds} '+
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1423 f'{shape[1]}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1424 if not img_y_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1425 img_y_bounds = (0, shape[2])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1426 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1427 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
1428 not (0 <= img_y_bounds[0] < img_y_bounds[1] <= shape[2])):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1429 logger.error(f'inconsistent column dimension in {files[0]}')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1430 img_stack = f.get('entry/instrument/detector/data')[
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1431 img_offset:img_offset+num_img:num_img_skip+1,
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1432 img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1433 logger.info(f'... done in {time()-t0:.2f} seconds!')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1434 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1435 illegal_value(filetype, 'filetype', 'load_image_stack')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1436 return(img_stack)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1437
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1438 def combine_tiffs_in_h5(files, num_img, h5_filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1439 img_stack = load_image_stack(files, 'tif', 0, num_img)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1440 with h5py.File(h5_filename, 'w') as f:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1441 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
1442 del img_stack
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1443 return([h5_filename])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1444
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1445 def clear_imshow(title=None):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1446 plt.ioff()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1447 if title is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1448 title = 'quick imshow'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1449 elif not isinstance(title, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1450 illegal_value(title, 'title', 'clear_imshow')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1451 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1452 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1453
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1454 def clear_plot(title=None):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1455 plt.ioff()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1456 if title is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1457 title = 'quick plot'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1458 elif not isinstance(title, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1459 illegal_value(title, 'title', 'clear_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1460 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1461 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1462
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1463 def quick_imshow(a, title=None, path=None, name=None, save_fig=False, save_only=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1464 clear=True, extent=None, show_grid=False, grid_color='w', grid_linewidth=1,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1465 block=False, **kwargs):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1466 if title is not None and not isinstance(title, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1467 illegal_value(title, 'title', 'quick_imshow')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1468 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1469 if path is not None and not isinstance(path, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1470 illegal_value(path, 'path', 'quick_imshow')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1471 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1472 if not isinstance(save_fig, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1473 illegal_value(save_fig, 'save_fig', 'quick_imshow')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1474 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1475 if not isinstance(save_only, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1476 illegal_value(save_only, 'save_only', 'quick_imshow')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1477 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1478 if not isinstance(clear, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1479 illegal_value(clear, 'clear', 'quick_imshow')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1480 return
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1481 if not isinstance(block, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1482 illegal_value(block, 'block', 'quick_imshow')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1483 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1484 if not title:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1485 title='quick imshow'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1486 # else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1487 # title = re.sub(r"\s+", '_', title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1488 if name is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1489 ttitle = re.sub(r"\s+", '_', title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1490 if path is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1491 path = f'{ttitle}.png'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1492 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1493 path = f'{path}/{ttitle}.png'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1494 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1495 if path is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1496 path = name
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1497 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1498 path = f'{path}/{name}'
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1499 if 'cmap' in kwargs and a.ndim == 3 and (a.shape[2] == 3 or a.shape[2] == 4):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1500 use_cmap = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1501 if a.shape[2] == 4 and a[:,:,-1].min() != a[:,:,-1].max():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1502 use_cmap = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1503 if any(True if a[i,j,0] != a[i,j,1] and a[i,j,0] != a[i,j,2] else False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1504 for i in range(a.shape[0]) for j in range(a.shape[1])):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1505 use_cmap = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1506 if use_cmap:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1507 a = a[:,:,0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1508 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1509 logger.warning('Image incompatible with cmap option, ignore cmap')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1510 kwargs.pop('cmap')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1511 if extent is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1512 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
1513 if clear:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1514 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1515 plt.close(fig=title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1516 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1517 pass
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1518 if not save_only:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1519 if block:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1520 plt.ioff()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1521 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1522 plt.ion()
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1523 plt.figure(title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1524 plt.imshow(a, extent=extent, **kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1525 if show_grid:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1526 ax = plt.gca()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1527 ax.grid(color=grid_color, linewidth=grid_linewidth)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1528 # if title != 'quick imshow':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1529 # plt.title = title
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1530 if save_only:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1531 plt.savefig(path)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1532 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1533 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1534 if save_fig:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1535 plt.savefig(path)
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1536 if block:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1537 plt.show(block=block)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1538
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1539 def quick_plot(*args, xerr=None, yerr=None, vlines=None, title=None, xlim=None, ylim=None,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1540 xlabel=None, ylabel=None, legend=None, path=None, name=None, show_grid=False,
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1541 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
1542 if title is not None and not isinstance(title, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1543 illegal_value(title, 'title', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1544 title = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1545 if xlim is not None and not isinstance(xlim, (tuple, list)) and len(xlim) != 2:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1546 illegal_value(xlim, 'xlim', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1547 xlim = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1548 if ylim is not None and not isinstance(ylim, (tuple, list)) and len(ylim) != 2:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1549 illegal_value(ylim, 'ylim', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1550 ylim = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1551 if xlabel is not None and not isinstance(xlabel, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1552 illegal_value(xlabel, 'xlabel', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1553 xlabel = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1554 if ylabel is not None and not isinstance(ylabel, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1555 illegal_value(ylabel, 'ylabel', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1556 ylabel = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1557 if legend is not None and not isinstance(legend, (tuple, list)):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1558 illegal_value(legend, 'legend', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1559 legend = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1560 if path is not None and not isinstance(path, str):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1561 illegal_value(path, 'path', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1562 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1563 if not isinstance(show_grid, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1564 illegal_value(show_grid, 'show_grid', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1565 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1566 if not isinstance(save_fig, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1567 illegal_value(save_fig, 'save_fig', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1568 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1569 if not isinstance(save_only, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1570 illegal_value(save_only, 'save_only', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1571 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1572 if not isinstance(clear, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1573 illegal_value(clear, 'clear', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1574 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1575 if not isinstance(block, bool):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1576 illegal_value(block, 'block', 'quick_plot')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1577 return
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1578 if title is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1579 title = 'quick plot'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1580 # else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1581 # title = re.sub(r"\s+", '_', title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1582 if name is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1583 ttitle = re.sub(r"\s+", '_', title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1584 if path is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1585 path = f'{ttitle}.png'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1586 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1587 path = f'{path}/{ttitle}.png'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1588 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1589 if path is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1590 path = name
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1591 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1592 path = f'{path}/{name}'
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1593 if clear:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1594 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1595 plt.close(fig=title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1596 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1597 pass
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1598 args = unwrap_tuple(args)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1599 if depth_tuple(args) > 1 and (xerr is not None or yerr is not None):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1600 logger.warning('Error bars ignored form multiple curves')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1601 if not save_only:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1602 if block:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1603 plt.ioff()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1604 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1605 plt.ion()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1606 plt.figure(title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1607 if depth_tuple(args) > 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1608 for y in args:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1609 plt.plot(*y, **kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1610 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1611 if xerr is None and yerr is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1612 plt.plot(*args, **kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1613 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1614 plt.errorbar(*args, xerr=xerr, yerr=yerr, **kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1615 if vlines is not None:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1616 if isinstance(vlines, (int, float)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1617 vlines = [vlines]
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1618 for v in vlines:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1619 plt.axvline(v, color='r', linestyle='--', **kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1620 # if vlines is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1621 # 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
1622 # plt.plot(*s, color='red', **kwargs)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1623 if xlim is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1624 plt.xlim(xlim)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1625 if ylim is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1626 plt.ylim(ylim)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1627 if xlabel is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1628 plt.xlabel(xlabel)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1629 if ylabel is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1630 plt.ylabel(ylabel)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1631 if show_grid:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1632 ax = plt.gca()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1633 ax.grid(color='k')#, linewidth=1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1634 if legend is not None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1635 plt.legend(legend)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1636 if save_only:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1637 plt.savefig(path)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1638 plt.close(fig=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1639 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1640 if save_fig:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1641 plt.savefig(path)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1642 if block:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1643 plt.show(block=block)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1644
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1645 def select_array_bounds(a, x_low=None, x_upp=None, num_x_min=None, ask_bounds=False,
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1646 title='select array bounds'):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1647 """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
1648 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1649 if isinstance(a, (tuple, list)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1650 a = np.array(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1651 if not isinstance(a, np.ndarray) or a.ndim != 1:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1652 illegal_value(a.ndim, 'array type or dimension', 'select_array_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1653 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1654 len_a = len(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1655 if num_x_min is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1656 num_x_min = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1657 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1658 if num_x_min < 2 or num_x_min > len_a:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1659 logger.warning('Invalid value for num_x_min in select_array_bounds, input ignored')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1660 num_x_min = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1661
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1662 # Ask to use current bounds
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1663 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
1664 if x_low is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1665 x_low = 0
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1666 if not is_int(x_low, ge=0, le=len_a-num_x_min):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1667 illegal_value(x_low, 'x_low', 'select_array_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1668 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1669 if x_upp is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1670 x_upp = len_a
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1671 if not is_int(x_upp, ge=x_low+num_x_min, le=len_a):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1672 illegal_value(x_upp, 'x_upp', 'select_array_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1673 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1674 quick_plot((range(len_a), a), vlines=(x_low,x_upp), title=title)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1675 if not input_yesno(f'\nCurrent array bounds: [{x_low}, {x_upp}] '+
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1676 'use these values (y/n)?', 'y'):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1677 x_low = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1678 x_upp = None
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1679 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1680 clear_plot(title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1681 return(x_low, x_upp)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1682
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1683 if x_low is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1684 x_min = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1685 x_max = len_a
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1686 x_low_max = len_a-num_x_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1687 while True:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1688 quick_plot(range(x_min, x_max), a[x_min:x_max], title=title)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1689 zoom_flag = input_yesno('Set lower data bound (y) or zoom in (n)?', 'y')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1690 if zoom_flag:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1691 x_low = input_int(' Set lower data bound', ge=0, le=x_low_max)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1692 break
63
98a83f03d91b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877"
rv43
parents: 56
diff changeset
1693 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1694 x_min = input_int(' Set lower zoom index', ge=0, le=x_low_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1695 x_max = input_int(' Set upper zoom index', ge=x_min+1, le=x_low_max+1)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1696 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1697 if not is_int(x_low, ge=0, le=len_a-num_x_min):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1698 illegal_value(x_low, 'x_low', 'select_array_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1699 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1700 if x_upp is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1701 x_min = x_low+num_x_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1702 x_max = len_a
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1703 x_upp_min = x_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1704 while True:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1705 quick_plot(range(x_min, x_max), a[x_min:x_max], title=title)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1706 zoom_flag = input_yesno('Set upper data bound (y) or zoom in (n)?', 'y')
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1707 if zoom_flag:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1708 x_upp = input_int(' Set upper data bound', ge=x_upp_min, le=len_a)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1709 break
63
98a83f03d91b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877"
rv43
parents: 56
diff changeset
1710 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1711 x_min = input_int(' Set upper zoom index', ge=x_upp_min, le=len_a-1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1712 x_max = input_int(' Set upper zoom index', ge=x_min+1, le=len_a)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1713 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1714 if not is_int(x_upp, ge=x_low+num_x_min, le=len_a):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1715 illegal_value(x_upp, 'x_upp', 'select_array_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1716 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1717 print(f'lower bound = {x_low} (inclusive)\nupper bound = {x_upp} (exclusive)]')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1718 quick_plot((range(len_a), a), vlines=(x_low,x_upp), title=title)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1719 if not input_yesno('Accept these bounds (y/n)?', 'y'):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1720 x_low, x_upp = select_array_bounds(a, None, None, num_x_min, title=title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1721 clear_plot(title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1722 return(x_low, x_upp)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1723
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1724 def select_image_bounds(a, axis, low=None, upp=None, num_min=None, title='select array bounds',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1725 raise_error=False):
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1726 """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
1727 """
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1728 a = np.asarray(a)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1729 if a.ndim != 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1730 illegal_value(a.ndim, 'array dimension', location='select_image_bounds',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1731 raise_error=raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1732 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1733 if axis < 0 or axis >= a.ndim:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1734 illegal_value(axis, 'axis', location='select_image_bounds', raise_error=raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1735 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1736 low_save = low
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1737 upp_save = upp
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1738 num_min_save = num_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1739 if num_min is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1740 num_min = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1741 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1742 if num_min < 2 or num_min > a.shape[axis]:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1743 logger.warning('Invalid input for num_min in select_image_bounds, input ignored')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1744 num_min = 1
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1745 if low is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1746 min_ = 0
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1747 max_ = a.shape[axis]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1748 low_max = a.shape[axis]-num_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1749 while True:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1750 if axis:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1751 quick_imshow(a[:,min_:max_], title=title, aspect='auto',
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1752 extent=[min_,max_,a.shape[0],0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1753 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1754 quick_imshow(a[min_:max_,:], title=title, aspect='auto',
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1755 extent=[0,a.shape[1], max_,min_])
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1756 zoom_flag = input_yesno('Set lower data bound (y) or zoom in (n)?', 'y')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1757 if zoom_flag:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1758 low = input_int(' Set lower data bound', ge=0, le=low_max)
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1759 break
63
98a83f03d91b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877"
rv43
parents: 56
diff changeset
1760 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1761 min_ = input_int(' Set lower zoom index', ge=0, le=low_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1762 max_ = input_int(' Set upper zoom index', ge=min_+1, le=low_max+1)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1763 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1764 if not is_int(low, ge=0, le=a.shape[axis]-num_min):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1765 illegal_value(low, 'low', location='select_image_bounds', raise_error=raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1766 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1767 if upp is None:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1768 min_ = low+num_min
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1769 max_ = a.shape[axis]
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1770 upp_min = min_
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1771 while True:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1772 if axis:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1773 quick_imshow(a[:,min_:max_], title=title, aspect='auto',
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1774 extent=[min_,max_,a.shape[0],0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1775 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1776 quick_imshow(a[min_:max_,:], title=title, aspect='auto',
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1777 extent=[0,a.shape[1], max_,min_])
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1778 zoom_flag = input_yesno('Set upper data bound (y) or zoom in (n)?', 'y')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1779 if zoom_flag:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1780 upp = input_int(' Set upper data bound', ge=upp_min, le=a.shape[axis])
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1781 break
63
98a83f03d91b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877"
rv43
parents: 56
diff changeset
1782 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1783 min_ = input_int(' Set upper zoom index', ge=upp_min, le=a.shape[axis]-1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1784 max_ = input_int(' Set upper zoom index', ge=min_+1, le=a.shape[axis])
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1785 else:
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1786 if not is_int(upp, ge=low+num_min, le=a.shape[axis]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1787 illegal_value(upp, 'upp', location='select_image_bounds', raise_error=raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1788 return(None)
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1789 bounds = (low, upp)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1790 a_tmp = np.copy(a)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1791 a_tmp_max = a.max()
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1792 if axis:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1793 a_tmp[:,bounds[0]] = a_tmp_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1794 a_tmp[:,bounds[1]-1] = a_tmp_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1795 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1796 a_tmp[bounds[0],:] = a_tmp_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1797 a_tmp[bounds[1]-1,:] = a_tmp_max
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1798 print(f'lower bound = {low} (inclusive)\nupper bound = {upp} (exclusive)')
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1799 quick_imshow(a_tmp, title=title, aspect='auto')
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1800 del a_tmp
65
f31ef7bfb430 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit d55db09b45d0b542f966cef17892858bb55d94f7"
rv43
parents: 63
diff changeset
1801 if not input_yesno('Accept these bounds (y/n)?', 'y'):
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1802 bounds = select_image_bounds(a, axis, low=low_save, upp=upp_save, num_min=num_min_save,
49
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1803 title=title)
69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1804 return(bounds)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1805
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1806 def select_one_image_bound(a, axis, bound=None, bound_name=None, title='select array bounds',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1807 default='y', raise_error=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1808 """Interactively select a data boundary for a 2D numpy array.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1809 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1810 a = np.asarray(a)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1811 if a.ndim != 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1812 illegal_value(a.ndim, 'array dimension', location='select_one_image_bound',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1813 raise_error=raise_error)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1814 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1815 if axis < 0 or axis >= a.ndim:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1816 illegal_value(axis, 'axis', location='select_one_image_bound', raise_error=raise_error)
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diff changeset
1817 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1818 if bound_name is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1819 bound_name = 'data bound'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1820 if bound is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1821 min_ = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents: 68
diff changeset
1822 max_ = a.shape[axis]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1823 bound_max = a.shape[axis]-1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1824 while True:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1825 if axis:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1826 quick_imshow(a[:,min_:max_], title=title, aspect='auto',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1827 extent=[min_,max_,a.shape[0],0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1828 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1829 quick_imshow(a[min_:max_,:], title=title, aspect='auto',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1830 extent=[0,a.shape[1], max_,min_])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1831 zoom_flag = input_yesno(f'Set {bound_name} (y) or zoom in (n)?', 'y')
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diff changeset
1832 if zoom_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1833 bound = input_int(f' Set {bound_name}', ge=0, le=bound_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1834 clear_imshow(title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1835 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1836 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents: 68
diff changeset
1837 min_ = input_int(' Set lower zoom index', ge=0, le=bound_max)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1838 max_ = input_int(' Set upper zoom index', ge=min_+1, le=bound_max+1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1839
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1840 elif not is_int(bound, ge=0, le=a.shape[axis]-1):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1841 illegal_value(bound, 'bound', location='select_one_image_bound', raise_error=raise_error)
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diff changeset
1842 return(None)
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diff changeset
1843 else:
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diff changeset
1844 print(f'Current {bound_name} = {bound}')
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diff changeset
1845 a_tmp = np.copy(a)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1846 a_tmp_max = a.max()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1847 if axis:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1848 a_tmp[:,bound] = a_tmp_max
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diff changeset
1849 else:
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diff changeset
1850 a_tmp[bound,:] = a_tmp_max
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diff changeset
1851 quick_imshow(a_tmp, title=title, aspect='auto')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1852 del a_tmp
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diff changeset
1853 if not input_yesno(f'Accept this {bound_name} (y/n)?', default):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1854 bound = select_one_image_bound(a, axis, bound_name=bound_name, title=title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1855 clear_imshow(title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
1856 return(bound)
49
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parents:
diff changeset
1857
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rv43
parents:
diff changeset
1858
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rv43
parents:
diff changeset
1859 class Config:
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diff changeset
1860 """Base class for processing a config file or dictionary.
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diff changeset
1861 """
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parents:
diff changeset
1862 def __init__(self, config_file=None, config_dict=None):
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parents:
diff changeset
1863 self.config = {}
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parents:
diff changeset
1864 self.load_flag = False
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parents:
diff changeset
1865 self.suffix = None
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parents:
diff changeset
1866
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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parents:
diff changeset
1867 # Load config file
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parents:
diff changeset
1868 if config_file is not None and config_dict is not None:
69
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diff changeset
1869 logger.warning('Ignoring config_dict (both config_file and config_dict are specified)')
49
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diff changeset
1870 if config_file is not None:
69
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diff changeset
1871 self.load_file(config_file)
49
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diff changeset
1872 elif config_dict is not None:
69
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diff changeset
1873 self.load_dict(config_dict)
49
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rv43
parents:
diff changeset
1874
69
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diff changeset
1875 def load_file(self, config_file):
49
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diff changeset
1876 """Load a config file.
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diff changeset
1877 """
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
1878 if self.load_flag:
69
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diff changeset
1879 logger.warning('Overwriting any previously loaded config file')
49
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parents:
diff changeset
1880 self.config = {}
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
rv43
parents:
diff changeset
1881
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parents:
diff changeset
1882 # Ensure config file exists
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diff changeset
1883 if not os.path.isfile(config_file):
69
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diff changeset
1884 logger.error(f'Unable to load {config_file}')
49
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rv43
parents:
diff changeset
1885 return
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rv43
parents:
diff changeset
1886
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rv43
parents:
diff changeset
1887 # Load config file (for now for Galaxy, allow .dat extension)
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parents:
diff changeset
1888 self.suffix = os.path.splitext(config_file)[1]
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parents:
diff changeset
1889 if self.suffix == '.yml' or self.suffix == '.yaml' or self.suffix == '.dat':
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
1890 with open(config_file, 'r') as f:
69
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diff changeset
1891 self.config = safe_load(f)
49
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diff changeset
1892 elif self.suffix == '.txt':
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parents:
diff changeset
1893 with open(config_file, 'r') as f:
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parents:
diff changeset
1894 lines = f.read().splitlines()
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diff changeset
1895 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"
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diff changeset
1896 [line.split('#')[0].split('=') for line in lines if '=' in line.split('#')[0]]}
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diff changeset
1897 else:
69
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diff changeset
1898 illegal_value(self.suffix, 'config file extension', 'Config.load_file')
49
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diff changeset
1899
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diff changeset
1900 # Make sure config file was correctly loaded
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diff changeset
1901 if isinstance(self.config, dict):
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parents:
diff changeset
1902 self.load_flag = True
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
1903 else:
69
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diff changeset
1904 logger.error(f'Unable to load dictionary from config file: {config_file}')
49
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diff changeset
1905 self.config = {}
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diff changeset
1906
69
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diff changeset
1907 def load_dict(self, config_dict):
49
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diff changeset
1908 """Takes a dictionary and places it into self.config.
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diff changeset
1909 """
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diff changeset
1910 if self.load_flag:
69
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1911 logger.warning('Overwriting the previously loaded config file')
49
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diff changeset
1912
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1913 if isinstance(config_dict, dict):
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1914 self.config = config_dict
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1915 self.load_flag = True
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1916 else:
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1917 illegal_value(config_dict, 'dictionary config object', 'Config.load_dict')
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1918 self.config = {}
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1919
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1920 def save_file(self, config_file):
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1921 """Save the config file (as a yaml file only right now).
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1922 """
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1923 suffix = os.path.splitext(config_file)[1]
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1924 if suffix != '.yml' and suffix != '.yaml':
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1925 illegal_value(suffix, 'config file extension', 'Config.save_file')
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1926
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1927 # Check if config file exists
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1928 if os.path.isfile(config_file):
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1929 logger.info(f'Updating {config_file}')
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1930 else:
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1931 logger.info(f'Saving {config_file}')
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1932
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1933 # Save config file
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1934 with open(config_file, 'w') as f:
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1935 safe_dump(self.config, f)
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1936
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1937 def validate(self, pars_required, pars_missing=None):
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1938 """Returns False if any required keys are missing.
49
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1939 """
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1940 if not self.load_flag:
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1941 logger.error('Load a config file prior to calling Config.validate')
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1942
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diff changeset
1943 def validate_nested_pars(config, par):
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1944 par_levels = par.split(':')
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1945 first_level_par = par_levels[0]
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diff changeset
1946 try:
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1947 first_level_par = int(first_level_par)
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1948 except:
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1949 pass
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1950 try:
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1951 next_level_config = config[first_level_par]
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1952 if len(par_levels) > 1:
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1953 next_level_par = ':'.join(par_levels[1:])
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1954 return(validate_nested_pars(next_level_config, next_level_par))
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1955 else:
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1956 return(True)
65
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diff changeset
1957 except:
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diff changeset
1958 return(False)
65
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diff changeset
1959
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diff changeset
1960 pars_missing = [p for p in pars_required if not validate_nested_pars(self.config, p)]
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diff changeset
1961 if len(pars_missing) > 0:
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diff changeset
1962 logger.error(f'Missing item(s) in configuration: {", ".join(pars_missing)}')
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diff changeset
1963 return(False)
65
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diff changeset
1964 else:
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1965 return(True)