Mercurial > repos > bgruening > cp_identify_primary_objects

annotate overlay_outlines.py @ 6:87d4d92d7487 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 09:32:24 +0000
parents 993faa34333b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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3 import argparse
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4 import json
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6 from cp_common_functions import (get_json_value,
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7 get_pipeline_lines,
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8 get_total_number_of_modules,
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9 INDENTATION, update_module_count,
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10 write_pipeline)
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12 MODULE_NAME = "OverlayOutlines"
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13 OUTPUT_FILENAME = "output.cppipe"
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16 def build_ctg_header(module_name, module_number):
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17 """Creates the first line of a module given the name and module number"""
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18 result = "|".join(
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19 [
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20 f"{module_name}:[module_num:{module_number}",
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21 "svn_version:\\'Unknown\\'",
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22 "variable_revision_number:4",
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23 "show_window:True",
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24 "notes:\\x5B\\'Overlay the embryo outlines on the grayscale image.\\'\\x5D",
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25 "batch_state:array(\\x5B\\x5D, dtype=uint8)",
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26 "enabled:True",
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27 "wants_pause:False]\n",
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28 ]
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29 )
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30 return result
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33 def build_main_block(input_params):
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34 result = f"{INDENTATION}Display outlines on a blank image?:{get_json_value(input_params,'con_blank_img.blank_img')}\n"
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36 on_blank = get_json_value(input_params, "con_blank_img.blank_img")
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37 # defaults
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38 img_to_display = "None"
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39 display_mode = get_json_value(
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40 input_params, "con_blank_img.con_display_mode.display_mode"
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41 )
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42 method_brightness = "Max of image"
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43 howto = get_json_value(input_params, "howto_outline")
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44 outline_color = "#FF0000"
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45 obj_to_display = "None"
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46
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47 name_output_img = get_json_value(input_params, "name_output_image")
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49 if on_blank == "No":
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50 img_to_display = get_json_value(input_params, "con_blank_img.image_to_outline")
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52 result += INDENTATION.join(
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53 [
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54 f"{INDENTATION}Select image on which to display outlines:{img_to_display}\n",
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55 f"Name the output image:{name_output_img}\n",
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56 f"Outline display mode:{display_mode}\n",
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57 ]
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58 )
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60 if on_blank == "No" and display_mode == "Grayscale":
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61 method_brightness = get_json_value(
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62 input_params, "con_blank_img.con_display_mode.method_brightness"
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63 )
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65 result += INDENTATION.join(
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66 [
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67 f"{INDENTATION}Select method to determine brightness of outlines:{method_brightness}\n",
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68 f"How to outline:{howto}\n",
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69 ]
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70 )
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72 obj_outline_str = ""
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74 if display_mode == "Color":
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75 for obj in input_params["con_blank_img"]["con_display_mode"][
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76 "rpt_obj_to_display"
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77 ]:
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78 outline_color = get_json_value(obj, "outline_color")
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79 obj_to_display = get_json_value(obj, "obj_to_display")
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80 obj_outline_str += INDENTATION.join(
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81 [
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82 f"{INDENTATION}Select outline color:{outline_color}\n",
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83 f"Select objects to display:{obj_to_display}\n",
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84 ]
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85 )
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86 else: # grayscale
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87 for obj in input_params["con_blank_img"]["con_display_mode"][
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88 "rpt_obj_to_display"
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89 ]:
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90 obj_to_display = get_json_value(obj, "obj_to_display")
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91 obj_outline_str += INDENTATION.join(
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92 [
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93 f"{INDENTATION}Select outline color:{outline_color}\n",
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94 f"Select objects to display:{obj_to_display}\n",
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95 ]
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96 )
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97 obj_outline_str = obj_outline_str.rstrip("\n")
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98 result += f"{obj_outline_str}"
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99
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100 return result
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101
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102
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103 if __name__ == "__main__":
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104 parser = argparse.ArgumentParser()
6
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105 parser.add_argument("-p", "--pipeline", help="CellProfiler pipeline")
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106 parser.add_argument("-i", "--inputs", help="JSON inputs from Galaxy")
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107 args = parser.parse_args()
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108
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109 pipeline_lines = get_pipeline_lines(args.pipeline)
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110 inputs_galaxy = json.load(open(args.inputs, "r"))
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111
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112 current_module_num = get_total_number_of_modules(pipeline_lines)
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113 current_module_num += 1
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114 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
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115
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116 header_block = build_ctg_header(MODULE_NAME, current_module_num)
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117 main_block = build_main_block(inputs_galaxy)
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118
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119 module_pipeline = f"\n{header_block}{main_block}\n"
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120 pipeline_lines.append(module_pipeline)
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121
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122 write_pipeline(OUTPUT_FILENAME, pipeline_lines)