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comparison image_math.py @ 2:972d2c365739 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 09:31:44 +0000
parents 644e5e32a83c
children
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1:1fd453cd757b 2:972d2c365739
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 2
3 import argparse 3 import argparse
4 import json 4 import json
5 5
6 from cp_common_functions import build_header 6 from cp_common_functions import (build_header, concat_conditional,
7 from cp_common_functions import concat_conditional 7 get_json_value, get_pipeline_lines,
8 from cp_common_functions import get_json_value 8 get_total_number_of_modules,
9 from cp_common_functions import get_pipeline_lines 9 INDENTATION, update_module_count,
10 from cp_common_functions import get_total_number_of_modules 10 write_pipeline)
11 from cp_common_functions import INDENTATION
12 from cp_common_functions import update_module_count
13 from cp_common_functions import write_pipeline
14 11
15 MODULE_NAME = "ImageMath" 12 MODULE_NAME = "ImageMath"
16 OUTPUT_FILENAME = "output.cppipe" 13 OUTPUT_FILENAME = "output.cppipe"
17 14
18 operator_map = { 15 operator_map = {
27 "log_2": "Log transform (base 2)", 24 "log_2": "Log transform (base 2)",
28 "log_legacy": "Log transform (legacy)", 25 "log_legacy": "Log transform (legacy)",
29 "and": "And", 26 "and": "And",
30 "or": "Or", 27 "or": "Or",
31 "not": "Not", 28 "not": "Not",
32 "equals": "Equals" 29 "equals": "Equals",
33 } 30 }
34 31
35 32
36 def build_main_block(input_params): 33 def build_main_block(input_params):
37 """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices""" 34 """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
38 operation = operator_map[get_json_value( 35 operation = operator_map[get_json_value(input_params, "operation.operation")]
39 input_params, 'operation.operation')] 36 result = INDENTATION.join(
40 result = INDENTATION.join([f"{INDENTATION}Operation:{operation}\n", 37 [
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", 38 f"{INDENTATION}Operation:{operation}\n",
42 f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n", 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",
43 f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n", 40 f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
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", 41 f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n",
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", 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",
46 f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n", 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",
47 f"Name the output image:{get_json_value(input_params,'name_output_image')}" 44 f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
48 ]) 45 f"Name the output image:{get_json_value(input_params,'name_output_image')}",
46 ]
47 )
49 return result 48 return result
50 49
51 50
52 def build_variable_block(inputs_galaxy): 51 def build_variable_block(inputs_galaxy):
53 result = "" 52 result = ""
54 first_image_block = build_first_image_block( 53 first_image_block = build_first_image_block(
55 get_json_value(inputs_galaxy, 'operation.first_image')) 54 get_json_value(inputs_galaxy, "operation.first_image")
55 )
56 result += f"\n{first_image_block}" 56 result += f"\n{first_image_block}"
57 second_image_block = build_second_image_block( 57 second_image_block = build_second_image_block(
58 get_json_value(inputs_galaxy, 'operation.second_image')) 58 get_json_value(inputs_galaxy, "operation.second_image")
59 )
59 result += f"\n{second_image_block}" 60 result += f"\n{second_image_block}"
60 return result 61 return result
61 62
62 63
63 def build_first_image_block(input_params): 64 def build_first_image_block(input_params):
64 """Creates the block of parameters for the first operator in operations""" 65 """Creates the block of parameters for the first operator in operations"""
65 66
66 value_select = get_json_value( 67 value_select = get_json_value(
67 input_params, 'image_or_measurement_first.image_or_measurement_first') 68 input_params, "image_or_measurement_first.image_or_measurement_first"
69 )
68 image_name = get_json_value( 70 image_name = get_json_value(
69 input_params, 'image_or_measurement_first.select_the_first_image') 71 input_params, "image_or_measurement_first.select_the_first_image"
70 value_multiply = get_json_value( 72 )
71 input_params, 'multiply_the_first_image_by') 73 value_multiply = get_json_value(input_params, "multiply_the_first_image_by")
72 category = get_json_value( 74 category = get_json_value(
73 input_params, 'image_or_measurement_first.category_first.category_first') 75 input_params, "image_or_measurement_first.category_first.category_first"
76 )
74 measurement = get_json_value( 77 measurement = get_json_value(
75 input_params, 'image_or_measurement_first.category_first.measurement_first') 78 input_params, "image_or_measurement_first.category_first.measurement_first"
79 )
76 80
77 result = INDENTATION.join( 81 result = INDENTATION.join(
78 [f"{INDENTATION}Image or measurement?:{value_select}\n", 82 [
79 f"Select the first image:{image_name}\n", 83 f"{INDENTATION}Image or measurement?:{value_select}\n",
80 f"Multiply the first image by:{value_multiply}\n", 84 f"Select the first image:{image_name}\n",
81 f"Measurement:{concat_conditional(category, measurement)}" 85 f"Multiply the first image by:{value_multiply}\n",
82 ]) 86 f"Measurement:{concat_conditional(category, measurement)}",
87 ]
88 )
83 return result 89 return result
84 90
85 91
86 def build_second_image_block(input_params): 92 def build_second_image_block(input_params):
87 """Creates the block of parameters for the second operator in binary operations""" 93 """Creates the block of parameters for the second operator in binary operations"""
88 94
89 value_select = get_json_value( 95 value_select = get_json_value(
90 input_params, 'image_or_measurement_second.image_or_measurement_second') 96 input_params, "image_or_measurement_second.image_or_measurement_second"
97 )
91 image_name = get_json_value( 98 image_name = get_json_value(
92 input_params, 'image_or_measurement_second.select_the_second_image') 99 input_params, "image_or_measurement_second.select_the_second_image"
93 value_multiply = get_json_value( 100 )
94 input_params, 'multiply_the_second_image_by') 101 value_multiply = get_json_value(input_params, "multiply_the_second_image_by")
95 category = get_json_value( 102 category = get_json_value(
96 input_params, 'image_or_measurement_second.category_second.category_second') 103 input_params, "image_or_measurement_second.category_second.category_second"
104 )
97 measurement = get_json_value( 105 measurement = get_json_value(
98 input_params, 'image_or_measurement_second.category_second.measurement_second') 106 input_params, "image_or_measurement_second.category_second.measurement_second"
107 )
99 108
100 result = INDENTATION.join( 109 result = INDENTATION.join(
101 [f"{INDENTATION}Image or measurement?:{value_select}\n", 110 [
102 f"Select the second image:{image_name}\n", 111 f"{INDENTATION}Image or measurement?:{value_select}\n",
103 f"Multiply the second image by:{value_multiply}\n", 112 f"Select the second image:{image_name}\n",
104 f"Measurement:{concat_conditional(category, measurement)}" 113 f"Multiply the second image by:{value_multiply}\n",
105 ]) 114 f"Measurement:{concat_conditional(category, measurement)}",
115 ]
116 )
106 return result 117 return result
107 118
108 119
109 if __name__ == "__main__": 120 if __name__ == "__main__":
110 parser = argparse.ArgumentParser() 121 parser = argparse.ArgumentParser()
111 parser.add_argument( 122 parser.add_argument("-p", "--pipeline", help="CellProfiler pipeline")
112 '-p', '--pipeline', 123 parser.add_argument("-i", "--inputs", help="JSON inputs from Galaxy")
113 help='CellProfiler pipeline'
114 )
115 parser.add_argument(
116 '-i', '--inputs',
117 help='JSON inputs from Galaxy'
118 )
119 args = parser.parse_args() 124 args = parser.parse_args()
120 125
121 pipeline_lines = get_pipeline_lines(args.pipeline) 126 pipeline_lines = get_pipeline_lines(args.pipeline)
122 inputs_galaxy = json.load(open(args.inputs, "r")) 127 inputs_galaxy = json.load(open(args.inputs, "r"))
123 128