Mercurial > repos > bgruening > cp_measure_object_size_shape

comparison tile.py @ 4:79e10d12d90a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:08:15 +0000
parents
children acf3aa487283
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3:5c9549983af8 4:79e10d12d90a
1 #!/usr/bin/env python
2
3 import argparse
4 import json
5
6 from cp_common_functions import get_json_value
7 from cp_common_functions import get_pipeline_lines
8 from cp_common_functions import get_total_number_of_modules
9 from cp_common_functions import INDENTATION
10 from cp_common_functions import update_module_count
11 from cp_common_functions import write_pipeline
12
13
14 MODULE_NAME = "Tile"
15 OUTPUT_FILENAME = "output.cppipe"
16
17
18 def build_header(module_name, module_number):
19 result = "|".join([f"{module_name}:[module_num:{module_number}",
20 "svn_version:\\'Unknown\\'",
21 "variable_revision_number:1",
22 "show_window:True",
23 "notes:\\x5B\\'Tile the original color image, the outlined image and the image of tracked labels together.\\'\\x5D",
24 "batch_state:array(\\x5B\\x5D, dtype=uint8)",
25 "enabled:True",
26 "wants_pause:False]\n"])
27 return result
28
29
30 def build_main_block(input_params):
31 result = INDENTATION.join([f"{INDENTATION}Select an input image:{get_json_value(input_params,'input_image')}\n",
32 f"Name the output image:{get_json_value(input_params,'output_image_name')}\n",
33 f"Tile assembly method:{get_json_value(input_params,'con_assembly_method.assembly_method')}\n"
34 ])
35
36 calc_rows = get_json_value(input_params, 'con_assembly_method.con_calc_no_row.calc_no_row')
37 no_of_rows = 8
38
39 calc_cols = get_json_value(input_params, 'con_assembly_method.con_calc_no_cols.calc_no_cols')
40 no_of_cols = 12
41
42 if calc_rows == "No":
43 no_of_rows = get_json_value(input_params, 'con_assembly_method.con_calc_no_row.no_of_row')
44
45 if calc_cols == "No":
46 no_of_cols = get_json_value(input_params, 'con_assembly_method.con_calc_no_cols.no_of_cols')
47
48 corner_to_begin = get_json_value(input_params, 'con_assembly_method.corner_to_begin')
49 direction_tiling = get_json_value(input_params, 'con_assembly_method.direction')
50 meander = get_json_value(input_params, 'con_assembly_method.meander_mode')
51
52 assembly_method = get_json_value(input_params, 'con_assembly_method.assembly_method')
53
54 result += INDENTATION.join(
55 [f"{INDENTATION}Final number of rows:{str(no_of_rows)}\n",
56 f"Final number of columns:{str(no_of_cols)}\n",
57 f"Image corner to begin tiling:{corner_to_begin}\n",
58 f"Direction to begin tiling:{direction_tiling}\n",
59 f"Use meander mode?:{meander}\n",
60 f"Automatically calculate number of rows?:{calc_rows}\n",
61 f"Automatically calculate number of columns?:{calc_cols}\n"
62 ])
63
64 if assembly_method == "Within cycles":
65 additionals = input_params['con_assembly_method']['rpt_additional_image']
66
67 for img in additionals:
68 result += INDENTATION.join(
69 [f"{INDENTATION}Select an additional image to tile:{get_json_value(img, 'additional_img')}\n"
70 ])
71
72 return result
73
74
75 if __name__ == "__main__":
76 parser = argparse.ArgumentParser()
77 parser.add_argument(
78 '-p', '--pipeline',
79 help='CellProfiler pipeline'
80 )
81 parser.add_argument(
82 '-i', '--inputs',
83 help='JSON inputs from Galaxy'
84 )
85 args = parser.parse_args()
86
87 pipeline_lines = get_pipeline_lines(args.pipeline)
88 inputs_galaxy = json.load(open(args.inputs, "r"))
89
90 current_module_num = get_total_number_of_modules(pipeline_lines)
91 current_module_num += 1
92 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
93
94 header_block = build_header(MODULE_NAME, current_module_num)
95 main_block = build_main_block(inputs_galaxy)
96
97 module_pipeline = f"\n{header_block}{main_block}\n"
98 pipeline_lines.append(module_pipeline)
99
100 write_pipeline(OUTPUT_FILENAME, pipeline_lines)