Mercurial > repos > bgruening > cp_tile

annotate color_to_gray.py @ 0:33bf7aa4e684 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 10:00:59 +0000
parents
children 878bafb411dd
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33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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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 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 = "ColorToGray"
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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\\'Convert the color image to grayscale.\\'\\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 """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
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32 result = INDENTATION.join([f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n",
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33 f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n",
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34 f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n",
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35 ])
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37 conversion_method = get_json_value(input_params, 'con_conversion_method.conversion_method')
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38
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39 image_type = get_json_value(input_params, 'con_conversion_method.con_image_type.image_type')
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40 rgb_comb_name_out = "OrigGray"
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41 combine_w_red = 1.0
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42 combine_w_green = 1.0
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43 combine_w_blue = 1.0
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45 split_red = "Yes"
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46 split_green = "Yes"
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47 split_blue = "Yes"
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48 red_output_name = "OrigRed"
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49 green_output_name = "OrigGreen"
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50 blue_output_name = "OrigBlue"
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52 split_hue = "Yes"
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53 split_saturation = "Yes"
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54 split_value = "Yes"
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55 hue_output_name = "OrigHue"
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56 saturation_output_name = "OrigSaturation"
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57 value_output_name = "OrigValue"
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58
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59 channel_count = 1
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60 if conversion_method == "Combine":
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61 if image_type == "RGB" or image_type == "HSV":
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62 rgb_comb_name_out = get_json_value(input_params, 'con_conversion_method.name_output_image')
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63 combine_w_red = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_red_channel')
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64 combine_w_green = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_green_channel')
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65 combine_w_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_blue_channel')
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66 elif conversion_method == "Split":
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67 if image_type == "RGB":
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68 split_red = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.yes_no')
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69 red_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.name_output_image')
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70 split_green = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.yes_no')
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71 green_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.name_output_image')
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72 split_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.yes_no')
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73 blue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.name_output_image')
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74 elif image_type == "HSV":
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75 split_hue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.yes_no')
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76 hue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.name_output_image')
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77 split_saturation = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.yes_no')
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78 saturation_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.name_output_image')
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79 split_value = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.yes_no')
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80 value_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.name_output_image')
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81
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82 result += INDENTATION.join(
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83 [f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n",
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84 f"Relative weight of the red channel:{str(combine_w_red)}\n",
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85 f"Relative weight of the green channel:{str(combine_w_green)}\n",
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86 f"Relative weight of the blue channel:{str(combine_w_blue)}\n",
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87
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88 f"Convert red to gray?:{split_red}\n",
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89 f"Name the output image:{red_output_name}\n",
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90 f"Convert green to gray?:{split_green}\n",
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91 f"Name the output image:{green_output_name}\n",
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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92 f"Convert blue to gray?:{split_blue}\n",
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93 f"Name the output image:{blue_output_name}\n",
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94
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95 f"Convert hue to gray?:{split_hue}\n",
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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96 f"Name the output image:{hue_output_name}\n",
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97 f"Convert saturation to gray?:{split_saturation}\n",
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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98 f"Name the output image:{saturation_output_name}\n",
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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99 f"Convert value to gray?:{split_value}\n",
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100 f"Name the output image:{value_output_name}\n"
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101 ])
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102
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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103 channel_count = 1
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104 if image_type == "Channels":
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105 channels = input_params['con_conversion_method']['con_image_type']['rpt_channel']
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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106 channel_count = len(channels)
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107 result += INDENTATION.join(
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108 [f"{INDENTATION}Channel count:{channel_count}\n"
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109 ])
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110
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111 for ch in channels:
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112 rel_weight_ch = 1.0
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113 image_name = "Channel1"
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114 if conversion_method == "Combine":
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115 rel_weight_ch = get_json_value(ch, 'weight_of_channel')
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116 else:
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117 image_name = get_json_value(ch, 'image_name')
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118 result += INDENTATION.join(
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119 [f"{INDENTATION}Channel number:{get_json_value(ch,'channel_no')}\n",
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120 f"Relative weight of the channel:{str(rel_weight_ch)}\n",
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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121 f"Image name:{image_name}\n"
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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122 ])
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123 else:
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124 result += INDENTATION.join(
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125 [f"{INDENTATION}Channel count:{channel_count}\n",
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126 "Channel number:Red\\x3A 1\n",
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127 "Relative weight of the channel:1.0\n",
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128 "Image name:Channel1\n"
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129 ])
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130
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131 return result
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132
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133
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134 if __name__ == "__main__":
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135 parser = argparse.ArgumentParser()
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136 parser.add_argument(
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137 '-p', '--pipeline',
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138 help='CellProfiler pipeline'
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139 )
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140 parser.add_argument(
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141 '-i', '--inputs',
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142 help='JSON inputs from Galaxy'
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143 )
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144 args = parser.parse_args()
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145
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146 pipeline_lines = get_pipeline_lines(args.pipeline)
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147 inputs_galaxy = json.load(open(args.inputs, "r"))
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148
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149 current_module_num = get_total_number_of_modules(pipeline_lines)
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150 current_module_num += 1
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151 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
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152
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153 header_block = build_ctg_header(MODULE_NAME, current_module_num)
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154 main_block = build_main_block(inputs_galaxy)
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155
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156 module_pipeline = f"\n{header_block}{main_block}\n"
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157 pipeline_lines.append(module_pipeline)
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158
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159 write_pipeline(OUTPUT_FILENAME, pipeline_lines)