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annotate image_math.py @ 6:6070780813d9 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:36:34 +0000
parents e7273daa5ae2
children
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1 #!/usr/bin/env python
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3 import argparse
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4 import json
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5
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6 from cp_common_functions import (build_header, concat_conditional,
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7 get_json_value, get_pipeline_lines,
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8 get_total_number_of_modules,
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9 INDENTATION, update_module_count,
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10 write_pipeline)
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12 MODULE_NAME = "ImageMath"
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13 OUTPUT_FILENAME = "output.cppipe"
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15 operator_map = {
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16 "add": "Add",
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17 "subtract": "Subtract",
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18 "multiply": "Multiply",
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19 "divide": "Divide",
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20 "average": "Average",
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21 "minimum": "Minimum",
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22 "maximum": "Maximum",
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23 "invert": "Invert",
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24 "log_2": "Log transform (base 2)",
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25 "log_legacy": "Log transform (legacy)",
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26 "and": "And",
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27 "or": "Or",
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28 "not": "Not",
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29 "equals": "Equals",
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30 }
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33 def build_main_block(input_params):
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34 """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
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35 operation = operator_map[get_json_value(input_params, "operation.operation")]
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36 result = INDENTATION.join(
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37 [
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38 f"{INDENTATION}Operation:{operation}\n",
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39 f"Raise the power of the result by:{get_json_value(input_params,'operation.op_results.raise_the_power_of_the_result_by')}\n",
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40 f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
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41 f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n",
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42 f"Set values less than 0 equal to 0?:{get_json_value(input_params,'operation.op_results.set_values_less_than_0_equal_to_0')}\n",
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43 f"Set values greater than 1 equal to 1?:{get_json_value(input_params,'operation.op_results.set_values_greater_than_1_equal_to_1')}\n",
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44 f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
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45 f"Name the output image:{get_json_value(input_params,'name_output_image')}",
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46 ]
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47 )
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48 return result
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51 def build_variable_block(inputs_galaxy):
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52 result = ""
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53 first_image_block = build_first_image_block(
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54 get_json_value(inputs_galaxy, "operation.first_image")
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55 )
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56 result += f"\n{first_image_block}"
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57 second_image_block = build_second_image_block(
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58 get_json_value(inputs_galaxy, "operation.second_image")
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59 )
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60 result += f"\n{second_image_block}"
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61 return result
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64 def build_first_image_block(input_params):
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65 """Creates the block of parameters for the first operator in operations"""
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67 value_select = get_json_value(
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68 input_params, "image_or_measurement_first.image_or_measurement_first"
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69 )
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70 image_name = get_json_value(
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71 input_params, "image_or_measurement_first.select_the_first_image"
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72 )
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73 value_multiply = get_json_value(input_params, "multiply_the_first_image_by")
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74 category = get_json_value(
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75 input_params, "image_or_measurement_first.category_first.category_first"
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76 )
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77 measurement = get_json_value(
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78 input_params, "image_or_measurement_first.category_first.measurement_first"
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79 )
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80
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81 result = INDENTATION.join(
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82 [
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83 f"{INDENTATION}Image or measurement?:{value_select}\n",
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84 f"Select the first image:{image_name}\n",
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85 f"Multiply the first image by:{value_multiply}\n",
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86 f"Measurement:{concat_conditional(category, measurement)}",
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87 ]
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88 )
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89 return result
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90
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91
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92 def build_second_image_block(input_params):
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93 """Creates the block of parameters for the second operator in binary operations"""
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94
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95 value_select = get_json_value(
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96 input_params, "image_or_measurement_second.image_or_measurement_second"
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97 )
2
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98 image_name = get_json_value(
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99 input_params, "image_or_measurement_second.select_the_second_image"
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100 )
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101 value_multiply = get_json_value(input_params, "multiply_the_second_image_by")
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102 category = get_json_value(
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103 input_params, "image_or_measurement_second.category_second.category_second"
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104 )
2
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105 measurement = get_json_value(
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106 input_params, "image_or_measurement_second.category_second.measurement_second"
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107 )
2
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108
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109 result = INDENTATION.join(
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110 [
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111 f"{INDENTATION}Image or measurement?:{value_select}\n",
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112 f"Select the second image:{image_name}\n",
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113 f"Multiply the second image by:{value_multiply}\n",
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114 f"Measurement:{concat_conditional(category, measurement)}",
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115 ]
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116 )
2
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117 return result
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118
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119
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120 if __name__ == "__main__":
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121 parser = argparse.ArgumentParser()
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122 parser.add_argument("-p", "--pipeline", help="CellProfiler pipeline")
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123 parser.add_argument("-i", "--inputs", help="JSON inputs from Galaxy")
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124 args = parser.parse_args()
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125
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126 pipeline_lines = get_pipeline_lines(args.pipeline)
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127 inputs_galaxy = json.load(open(args.inputs, "r"))
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128
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129 current_module_num = get_total_number_of_modules(pipeline_lines)
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130 current_module_num += 1
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131 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
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132
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133 header_block = build_header(MODULE_NAME, current_module_num)
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134 main_block = build_main_block(inputs_galaxy)
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135 variable_block = build_variable_block(inputs_galaxy)
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136
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137 module_pipeline = f"\n{header_block}{main_block}{variable_block}\n"
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138 pipeline_lines.append(module_pipeline)
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139
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140 write_pipeline(OUTPUT_FILENAME, pipeline_lines)