Mercurial > repos > bgruening > cp_track_objects

comparison image_math.py @ 0:644e5e32a83c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:03:00 +0000
parents
children 972d2c365739
comparison
equal deleted inserted replaced
-1:000000000000 0:644e5e32a83c
1 #!/usr/bin/env python
2
3 import argparse
4 import json
5
6 from cp_common_functions import build_header
7 from cp_common_functions import concat_conditional
8 from cp_common_functions import get_json_value
9 from cp_common_functions import get_pipeline_lines
10 from cp_common_functions import get_total_number_of_modules
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
15 MODULE_NAME = "ImageMath"
16 OUTPUT_FILENAME = "output.cppipe"
17
18 operator_map = {
19 "add": "Add",
20 "subtract": "Subtract",
21 "multiply": "Multiply",
22 "divide": "Divide",
23 "average": "Average",
24 "minimum": "Minimum",
25 "maximum": "Maximum",
26 "invert": "Invert",
27 "log_2": "Log transform (base 2)",
28 "log_legacy": "Log transform (legacy)",
29 "and": "And",
30 "or": "Or",
31 "not": "Not",
32 "equals": "Equals"
33 }
34
35
36 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"""
38 operation = operator_map[get_json_value(
39 input_params, 'operation.operation')]
40 result = INDENTATION.join([f"{INDENTATION}Operation:{operation}\n",
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",
42 f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
43 f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\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",
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",
46 f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
47 f"Name the output image:{get_json_value(input_params,'name_output_image')}"
48 ])
49 return result
50
51
52 def build_variable_block(inputs_galaxy):
53 result = ""
54 first_image_block = build_first_image_block(
55 get_json_value(inputs_galaxy, 'operation.first_image'))
56 result += f"\n{first_image_block}"
57 second_image_block = build_second_image_block(
58 get_json_value(inputs_galaxy, 'operation.second_image'))
59 result += f"\n{second_image_block}"
60 return result
61
62
63 def build_first_image_block(input_params):
64 """Creates the block of parameters for the first operator in operations"""
65
66 value_select = get_json_value(
67 input_params, 'image_or_measurement_first.image_or_measurement_first')
68 image_name = get_json_value(
69 input_params, 'image_or_measurement_first.select_the_first_image')
70 value_multiply = get_json_value(
71 input_params, 'multiply_the_first_image_by')
72 category = get_json_value(
73 input_params, 'image_or_measurement_first.category_first.category_first')
74 measurement = get_json_value(
75 input_params, 'image_or_measurement_first.category_first.measurement_first')
76
77 result = INDENTATION.join(
78 [f"{INDENTATION}Image or measurement?:{value_select}\n",
79 f"Select the first image:{image_name}\n",
80 f"Multiply the first image by:{value_multiply}\n",
81 f"Measurement:{concat_conditional(category, measurement)}"
82 ])
83 return result
84
85
86 def build_second_image_block(input_params):
87 """Creates the block of parameters for the second operator in binary operations"""
88
89 value_select = get_json_value(
90 input_params, 'image_or_measurement_second.image_or_measurement_second')
91 image_name = get_json_value(
92 input_params, 'image_or_measurement_second.select_the_second_image')
93 value_multiply = get_json_value(
94 input_params, 'multiply_the_second_image_by')
95 category = get_json_value(
96 input_params, 'image_or_measurement_second.category_second.category_second')
97 measurement = get_json_value(
98 input_params, 'image_or_measurement_second.category_second.measurement_second')
99
100 result = INDENTATION.join(
101 [f"{INDENTATION}Image or measurement?:{value_select}\n",
102 f"Select the second image:{image_name}\n",
103 f"Multiply the second image by:{value_multiply}\n",
104 f"Measurement:{concat_conditional(category, measurement)}"
105 ])
106 return result
107
108
109 if __name__ == "__main__":
110 parser = argparse.ArgumentParser()
111 parser.add_argument(
112 '-p', '--pipeline',
113 help='CellProfiler pipeline'
114 )
115 parser.add_argument(
116 '-i', '--inputs',
117 help='JSON inputs from Galaxy'
118 )
119 args = parser.parse_args()
120
121 pipeline_lines = get_pipeline_lines(args.pipeline)
122 inputs_galaxy = json.load(open(args.inputs, "r"))
123
124 current_module_num = get_total_number_of_modules(pipeline_lines)
125 current_module_num += 1
126 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
127
128 header_block = build_header(MODULE_NAME, current_module_num)
129 main_block = build_main_block(inputs_galaxy)
130 variable_block = build_variable_block(inputs_galaxy)
131
132 module_pipeline = f"\n{header_block}{main_block}{variable_block}\n"
133 pipeline_lines.append(module_pipeline)
134
135 write_pipeline(OUTPUT_FILENAME, pipeline_lines)