Mercurial > repos > bgruening > cp_measure_image_intensity

annotate tile.py @ 6:b64af54c5c09 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 09:28:54 +0000
parents 8536b1ae0254
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 = "Tile"
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13 OUTPUT_FILENAME = "output.cppipe"
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16 def build_header(module_name, module_number):
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17 result = "|".join(
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18 [
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19 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 ]
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28 )
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29 return result
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32 def build_main_block(input_params):
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33 result = INDENTATION.join(
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34 [
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35 f"{INDENTATION}Select an input image:{get_json_value(input_params,'input_image')}\n",
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36 f"Name the output image:{get_json_value(input_params,'output_image_name')}\n",
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37 f"Tile assembly method:{get_json_value(input_params,'con_assembly_method.assembly_method')}\n",
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38 ]
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39 )
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41 calc_rows = get_json_value(
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42 input_params, "con_assembly_method.con_calc_no_row.calc_no_row"
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43 )
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44 no_of_rows = 8
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46 calc_cols = get_json_value(
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47 input_params, "con_assembly_method.con_calc_no_cols.calc_no_cols"
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48 )
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49 no_of_cols = 12
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51 if calc_rows == "No":
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52 no_of_rows = get_json_value(
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53 input_params, "con_assembly_method.con_calc_no_row.no_of_row"
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54 )
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56 if calc_cols == "No":
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57 no_of_cols = get_json_value(
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58 input_params, "con_assembly_method.con_calc_no_cols.no_of_cols"
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59 )
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61 corner_to_begin = get_json_value(
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62 input_params, "con_assembly_method.corner_to_begin"
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63 )
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64 direction_tiling = get_json_value(input_params, "con_assembly_method.direction")
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65 meander = get_json_value(input_params, "con_assembly_method.meander_mode")
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66
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67 assembly_method = get_json_value(
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68 input_params, "con_assembly_method.assembly_method"
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69 )
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71 result += INDENTATION.join(
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72 [
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73 f"{INDENTATION}Final number of rows:{str(no_of_rows)}\n",
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74 f"Final number of columns:{str(no_of_cols)}\n",
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75 f"Image corner to begin tiling:{corner_to_begin}\n",
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76 f"Direction to begin tiling:{direction_tiling}\n",
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77 f"Use meander mode?:{meander}\n",
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78 f"Automatically calculate number of rows?:{calc_rows}\n",
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79 f"Automatically calculate number of columns?:{calc_cols}\n",
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80 ]
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81 )
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83 if assembly_method == "Within cycles":
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84 additionals = input_params["con_assembly_method"]["rpt_additional_image"]
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86 for img in additionals:
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87 result += INDENTATION.join(
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88 [
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89 f"{INDENTATION}Select an additional image to tile:{get_json_value(img, 'additional_img')}\n"
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91 )
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92 result = result.rstrip("\n")
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93 return result
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94
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95
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96 if __name__ == "__main__":
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97 parser = argparse.ArgumentParser()
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98 parser.add_argument("-p", "--pipeline", help="CellProfiler pipeline")
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99 parser.add_argument("-i", "--inputs", help="JSON inputs from Galaxy")
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100 args = parser.parse_args()
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101
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102 pipeline_lines = get_pipeline_lines(args.pipeline)
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103 inputs_galaxy = json.load(open(args.inputs, "r"))
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104
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105 current_module_num = get_total_number_of_modules(pipeline_lines)
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106 current_module_num += 1
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107 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
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108
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109 header_block = build_header(MODULE_NAME, current_module_num)
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110 main_block = build_main_block(inputs_galaxy)
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111
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112 module_pipeline = f"\n{header_block}{main_block}\n"
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113 pipeline_lines.append(module_pipeline)
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114
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115 write_pipeline(OUTPUT_FILENAME, pipeline_lines)