annotate image_math.py @ 5:d0178bdcd00e draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:12:26 +0000
parents f8fa0f6718a3
children
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1 #!/usr/bin/env python
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2
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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
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7 from cp_common_functions import concat_conditional
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8 from cp_common_functions import get_json_value
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9 from cp_common_functions import get_pipeline_lines
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10 from cp_common_functions import get_total_number_of_modules
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11 from cp_common_functions import INDENTATION
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12 from cp_common_functions import update_module_count
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13 from cp_common_functions import write_pipeline
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15 MODULE_NAME = "ImageMath"
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16 OUTPUT_FILENAME = "output.cppipe"
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18 operator_map = {
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19 "add": "Add",
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20 "subtract": "Subtract",
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21 "multiply": "Multiply",
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22 "divide": "Divide",
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23 "average": "Average",
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24 "minimum": "Minimum",
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25 "maximum": "Maximum",
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26 "invert": "Invert",
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27 "log_2": "Log transform (base 2)",
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28 "log_legacy": "Log transform (legacy)",
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29 "and": "And",
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30 "or": "Or",
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31 "not": "Not",
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32 "equals": "Equals"
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33 }
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35
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36 def build_main_block(input_params):
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37 """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
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38 operation = operator_map[get_json_value(
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39 input_params, 'operation.operation')]
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40 result = INDENTATION.join([f"{INDENTATION}Operation:{operation}\n",
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41 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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42 f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
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43 f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n",
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44 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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45 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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46 f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
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47 f"Name the output image:{get_json_value(input_params,'name_output_image')}"
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48 ])
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49 return result
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50
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51
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52 def build_variable_block(inputs_galaxy):
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53 result = ""
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54 first_image_block = build_first_image_block(
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55 get_json_value(inputs_galaxy, 'operation.first_image'))
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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 result += f"\n{second_image_block}"
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60 return result
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62
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63 def build_first_image_block(input_params):
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64 """Creates the block of parameters for the first operator in operations"""
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65
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66 value_select = get_json_value(
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67 input_params, 'image_or_measurement_first.image_or_measurement_first')
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68 image_name = get_json_value(
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69 input_params, 'image_or_measurement_first.select_the_first_image')
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70 value_multiply = get_json_value(
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71 input_params, 'multiply_the_first_image_by')
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72 category = get_json_value(
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73 input_params, 'image_or_measurement_first.category_first.category_first')
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74 measurement = get_json_value(
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75 input_params, 'image_or_measurement_first.category_first.measurement_first')
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76
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77 result = INDENTATION.join(
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78 [f"{INDENTATION}Image or measurement?:{value_select}\n",
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79 f"Select the first image:{image_name}\n",
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80 f"Multiply the first image by:{value_multiply}\n",
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81 f"Measurement:{concat_conditional(category, measurement)}"
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82 ])
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83 return result
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84
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85
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86 def build_second_image_block(input_params):
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87 """Creates the block of parameters for the second operator in binary operations"""
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88
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89 value_select = get_json_value(
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90 input_params, 'image_or_measurement_second.image_or_measurement_second')
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91 image_name = get_json_value(
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92 input_params, 'image_or_measurement_second.select_the_second_image')
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93 value_multiply = get_json_value(
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94 input_params, 'multiply_the_second_image_by')
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95 category = get_json_value(
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96 input_params, 'image_or_measurement_second.category_second.category_second')
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97 measurement = get_json_value(
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98 input_params, 'image_or_measurement_second.category_second.measurement_second')
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99
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100 result = INDENTATION.join(
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101 [f"{INDENTATION}Image or measurement?:{value_select}\n",
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102 f"Select the second image:{image_name}\n",
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103 f"Multiply the second image by:{value_multiply}\n",
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104 f"Measurement:{concat_conditional(category, measurement)}"
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105 ])
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106 return result
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107
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108
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109 if __name__ == "__main__":
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110 parser = argparse.ArgumentParser()
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111 parser.add_argument(
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112 '-p', '--pipeline',
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113 help='CellProfiler pipeline'
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114 )
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115 parser.add_argument(
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116 '-i', '--inputs',
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117 help='JSON inputs from Galaxy'
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118 )
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119 args = parser.parse_args()
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120
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121 pipeline_lines = get_pipeline_lines(args.pipeline)
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122 inputs_galaxy = json.load(open(args.inputs, "r"))
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123
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124 current_module_num = get_total_number_of_modules(pipeline_lines)
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125 current_module_num += 1
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126 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
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127
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128 header_block = build_header(MODULE_NAME, current_module_num)
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129 main_block = build_main_block(inputs_galaxy)
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130 variable_block = build_variable_block(inputs_galaxy)
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131
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132 module_pipeline = f"\n{header_block}{main_block}{variable_block}\n"
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133 pipeline_lines.append(module_pipeline)
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134
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135 write_pipeline(OUTPUT_FILENAME, pipeline_lines)