Mercurial > repos > bgruening > cp_identify_primary_objects

comparison overlay_outlines.py @ 4:993faa34333b 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 09:57:35 +0000
parents
children 87d4d92d7487
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3:52c01fb29b2a 4:993faa34333b
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 MODULE_NAME = "OverlayOutlines"
14 OUTPUT_FILENAME = "output.cppipe"
15
16
17 def build_ctg_header(module_name, module_number):
18 """Creates the first line of a module given the name and module number"""
19 result = "|".join([f"{module_name}:[module_num:{module_number}",
20 "svn_version:\\'Unknown\\'",
21 "variable_revision_number:4",
22 "show_window:True",
23 "notes:\\x5B\\'Overlay the embryo outlines on the grayscale image.\\'\\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 = f"{INDENTATION}Display outlines on a blank image?:{get_json_value(input_params,'con_blank_img.blank_img')}\n"
32
33 on_blank = get_json_value(input_params, 'con_blank_img.blank_img')
34 # defaults
35 img_to_display = "None"
36 display_mode = get_json_value(input_params, 'con_blank_img.con_display_mode.display_mode')
37 method_brightness = "Max of image"
38 howto = get_json_value(input_params, 'howto_outline')
39 outline_color = "#FF0000"
40 obj_to_display = "None"
41
42 name_output_img = get_json_value(input_params, 'name_output_image')
43
44 if on_blank == "No":
45 img_to_display = get_json_value(input_params, 'con_blank_img.image_to_outline')
46
47 result += INDENTATION.join(
48 [f"{INDENTATION}Select image on which to display outlines:{img_to_display}\n",
49 f"Name the output image:{name_output_img}\n",
50 f"Outline display mode:{display_mode}\n"
51 ])
52
53 if on_blank == "No" and display_mode == "Grayscale":
54 method_brightness = get_json_value(input_params, 'con_blank_img.con_display_mode.method_brightness')
55
56 result += INDENTATION.join(
57 [f"{INDENTATION}Select method to determine brightness of outlines:{method_brightness}\n",
58 f"How to outline:{howto}\n"
59 ])
60
61 obj_outline_str = ""
62
63 if display_mode == "Color":
64 for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
65 outline_color = get_json_value(obj, 'outline_color')
66 obj_to_display = get_json_value(obj, 'obj_to_display')
67 obj_outline_str += INDENTATION.join(
68 [f"{INDENTATION}Select outline color:{outline_color}\n",
69 f"Select objects to display:{obj_to_display}\n"
70 ])
71 else: # grayscale
72 for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
73 obj_to_display = get_json_value(obj, 'obj_to_display')
74 obj_outline_str += INDENTATION.join(
75 [f"{INDENTATION}Select outline color:{outline_color}\n",
76 f"Select objects to display:{obj_to_display}\n"
77 ])
78 obj_outline_str = obj_outline_str.rstrip("\n")
79 result += f"{obj_outline_str}"
80
81 return result
82
83
84 if __name__ == "__main__":
85 parser = argparse.ArgumentParser()
86 parser.add_argument(
87 '-p', '--pipeline',
88 help='CellProfiler pipeline'
89 )
90 parser.add_argument(
91 '-i', '--inputs',
92 help='JSON inputs from Galaxy'
93 )
94 args = parser.parse_args()
95
96 pipeline_lines = get_pipeline_lines(args.pipeline)
97 inputs_galaxy = json.load(open(args.inputs, "r"))
98
99 current_module_num = get_total_number_of_modules(pipeline_lines)
100 current_module_num += 1
101 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
102
103 header_block = build_ctg_header(MODULE_NAME, current_module_num)
104 main_block = build_main_block(inputs_galaxy)
105
106 module_pipeline = f"\n{header_block}{main_block}\n"
107 pipeline_lines.append(module_pipeline)
108
109 write_pipeline(OUTPUT_FILENAME, pipeline_lines)