Mercurial > repos > bgruening > cp_measure_image_intensity

annotate tile.py @ 5:bd0a391f8545 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 13:48:59 +0000
parents 5832468d6e1d
children
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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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5
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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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14 MODULE_NAME = "Tile"
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15 OUTPUT_FILENAME = "output.cppipe"
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18 def build_header(module_name, 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:1",
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22 "show_window:True",
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23 "notes:\\x5B\\'Tile the original color image, the outlined image and the image of tracked labels together.\\'\\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 = INDENTATION.join([f"{INDENTATION}Select an input image:{get_json_value(input_params,'input_image')}\n",
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32 f"Name the output image:{get_json_value(input_params,'output_image_name')}\n",
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33 f"Tile assembly method:{get_json_value(input_params,'con_assembly_method.assembly_method')}\n"
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34 ])
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36 calc_rows = get_json_value(input_params, 'con_assembly_method.con_calc_no_row.calc_no_row')
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37 no_of_rows = 8
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39 calc_cols = get_json_value(input_params, 'con_assembly_method.con_calc_no_cols.calc_no_cols')
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40 no_of_cols = 12
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42 if calc_rows == "No":
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43 no_of_rows = get_json_value(input_params, 'con_assembly_method.con_calc_no_row.no_of_row')
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45 if calc_cols == "No":
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46 no_of_cols = get_json_value(input_params, 'con_assembly_method.con_calc_no_cols.no_of_cols')
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48 corner_to_begin = get_json_value(input_params, 'con_assembly_method.corner_to_begin')
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49 direction_tiling = get_json_value(input_params, 'con_assembly_method.direction')
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50 meander = get_json_value(input_params, 'con_assembly_method.meander_mode')
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51
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52 assembly_method = get_json_value(input_params, 'con_assembly_method.assembly_method')
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53
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54 result += INDENTATION.join(
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55 [f"{INDENTATION}Final number of rows:{str(no_of_rows)}\n",
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56 f"Final number of columns:{str(no_of_cols)}\n",
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57 f"Image corner to begin tiling:{corner_to_begin}\n",
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58 f"Direction to begin tiling:{direction_tiling}\n",
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59 f"Use meander mode?:{meander}\n",
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60 f"Automatically calculate number of rows?:{calc_rows}\n",
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61 f"Automatically calculate number of columns?:{calc_cols}\n"
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62 ])
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63
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64 if assembly_method == "Within cycles":
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65 additionals = input_params['con_assembly_method']['rpt_additional_image']
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67 for img in additionals:
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68 result += INDENTATION.join(
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69 [f"{INDENTATION}Select an additional image to tile:{get_json_value(img, 'additional_img')}\n"
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70 ])
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71 result = result.rstrip("\n")
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72 return result
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75 if __name__ == "__main__":
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76 parser = argparse.ArgumentParser()
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77 parser.add_argument(
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78 '-p', '--pipeline',
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79 help='CellProfiler pipeline'
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80 )
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81 parser.add_argument(
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82 '-i', '--inputs',
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83 help='JSON inputs from Galaxy'
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84 )
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85 args = parser.parse_args()
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86
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87 pipeline_lines = get_pipeline_lines(args.pipeline)
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88 inputs_galaxy = json.load(open(args.inputs, "r"))
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89
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90 current_module_num = get_total_number_of_modules(pipeline_lines)
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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91 current_module_num += 1
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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92 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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93
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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94 header_block = build_header(MODULE_NAME, current_module_num)
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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95 main_block = build_main_block(inputs_galaxy)
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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96
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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97 module_pipeline = f"\n{header_block}{main_block}\n"
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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98 pipeline_lines.append(module_pipeline)
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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99
5832468d6e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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100 write_pipeline(OUTPUT_FILENAME, pipeline_lines)