annotate overlay_outlines.py @ 0:4395ea2a01f4 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:00:10 +0000
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1 #!/usr/bin/env python
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2
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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 from cp_common_functions import get_pipeline_lines
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8 from cp_common_functions import get_total_number_of_modules
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9 from cp_common_functions import INDENTATION
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10 from cp_common_functions import update_module_count
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11 from cp_common_functions import write_pipeline
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13 MODULE_NAME = "OverlayOutlines"
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14 OUTPUT_FILENAME = "output.cppipe"
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17 def build_ctg_header(module_name, module_number):
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18 """Creates the first line of a module given the name and module number"""
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19 result = "|".join([f"{module_name}:[module_num:{module_number}",
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20 "svn_version:\\'Unknown\\'",
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21 "variable_revision_number:4",
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22 "show_window:True",
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23 "notes:\\x5B\\'Overlay the embryo outlines on the grayscale image.\\'\\x5D",
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24 "batch_state:array(\\x5B\\x5D, dtype=uint8)",
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25 "enabled:True",
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26 "wants_pause:False]\n"])
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27 return result
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30 def build_main_block(input_params):
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31 result = f"{INDENTATION}Display outlines on a blank image?:{get_json_value(input_params,'con_blank_img.blank_img')}\n"
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33 on_blank = get_json_value(input_params, 'con_blank_img.blank_img')
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34 # defaults
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35 img_to_display = "None"
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36 display_mode = get_json_value(input_params, 'con_blank_img.con_display_mode.display_mode')
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37 method_brightness = "Max of image"
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38 howto = get_json_value(input_params, 'howto_outline')
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39 outline_color = "#FF0000"
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40 obj_to_display = "None"
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41
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42 name_output_img = get_json_value(input_params, 'name_output_image')
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43
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44 if on_blank == "No":
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45 img_to_display = get_json_value(input_params, 'con_blank_img.image_to_outline')
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46
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47 result += INDENTATION.join(
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48 [f"{INDENTATION}Select image on which to display outlines:{img_to_display}\n",
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49 f"Name the output image:{name_output_img}\n",
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50 f"Outline display mode:{display_mode}\n"
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51 ])
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52
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53 if on_blank == "No" and display_mode == "Grayscale":
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54 method_brightness = get_json_value(input_params, 'con_blank_img.con_display_mode.method_brightness')
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55
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56 result += INDENTATION.join(
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57 [f"{INDENTATION}Select method to determine brightness of outlines:{method_brightness}\n",
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58 f"How to outline:{howto}\n"
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59 ])
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61 obj_outline_str = ""
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62
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63 if display_mode == "Color":
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64 for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
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65 outline_color = get_json_value(obj, 'outline_color')
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66 obj_to_display = get_json_value(obj, 'obj_to_display')
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67 obj_outline_str += INDENTATION.join(
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68 [f"{INDENTATION}Select outline color:{outline_color}\n",
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69 f"Select objects to display:{obj_to_display}\n"
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70 ])
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71 else: # grayscale
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72 for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
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73 obj_to_display = get_json_value(obj, 'obj_to_display')
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74 obj_outline_str += INDENTATION.join(
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75 [f"{INDENTATION}Select outline color:{outline_color}\n",
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76 f"Select objects to display:{obj_to_display}\n"
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77 ])
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78 obj_outline_str = obj_outline_str.rstrip("\n")
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79 result += f"{obj_outline_str}"
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80
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81 return result
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82
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83
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84 if __name__ == "__main__":
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85 parser = argparse.ArgumentParser()
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86 parser.add_argument(
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87 '-p', '--pipeline',
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88 help='CellProfiler pipeline'
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89 )
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90 parser.add_argument(
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91 '-i', '--inputs',
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92 help='JSON inputs from Galaxy'
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93 )
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94 args = parser.parse_args()
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95
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96 pipeline_lines = get_pipeline_lines(args.pipeline)
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97 inputs_galaxy = json.load(open(args.inputs, "r"))
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98
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99 current_module_num = get_total_number_of_modules(pipeline_lines)
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100 current_module_num += 1
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101 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
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102
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103 header_block = build_ctg_header(MODULE_NAME, current_module_num)
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104 main_block = build_main_block(inputs_galaxy)
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105
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106 module_pipeline = f"\n{header_block}{main_block}\n"
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107 pipeline_lines.append(module_pipeline)
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108
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109 write_pipeline(OUTPUT_FILENAME, pipeline_lines)