Mercurial > repos > bgruening > cp_common
diff color_to_gray.py @ 6:6070780813d9 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
| author | bgruening |
|---|---|
| date | Sun, 05 Nov 2023 09:36:34 +0000 |
| parents | 670975e92458 |
| children |
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--- a/color_to_gray.py Fri Feb 26 14:09:20 2021 +0000 +++ b/color_to_gray.py Sun Nov 05 09:36:34 2023 +0000 @@ -3,12 +3,11 @@ import argparse import json -from cp_common_functions import get_json_value -from cp_common_functions import get_pipeline_lines -from cp_common_functions import get_total_number_of_modules -from cp_common_functions import INDENTATION -from cp_common_functions import update_module_count -from cp_common_functions import write_pipeline +from cp_common_functions import (get_json_value, + get_pipeline_lines, + get_total_number_of_modules, + INDENTATION, update_module_count, + write_pipeline) MODULE_NAME = "ColorToGray" OUTPUT_FILENAME = "output.cppipe" @@ -16,27 +15,38 @@ def build_ctg_header(module_name, module_number): """Creates the first line of a module given the name and module number""" - result = "|".join([f"{module_name}:[module_num:{module_number}", - "svn_version:\\'Unknown\\'", - "variable_revision_number:4", - "show_window:True", - "notes:\\x5B\\'Convert the color image to grayscale.\\'\\x5D", - "batch_state:array(\\x5B\\x5D, dtype=uint8)", - "enabled:True", - "wants_pause:False]\n"]) + result = "|".join( + [ + f"{module_name}:[module_num:{module_number}", + "svn_version:\\'Unknown\\'", + "variable_revision_number:4", + "show_window:True", + "notes:\\x5B\\'Convert the color image to grayscale.\\'\\x5D", + "batch_state:array(\\x5B\\x5D, dtype=uint8)", + "enabled:True", + "wants_pause:False]\n", + ] + ) return result def build_main_block(input_params): """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices""" - result = INDENTATION.join([f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n", - f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n", - f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n", - ]) + result = INDENTATION.join( + [ + f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n", + f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n", + f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n", + ] + ) - conversion_method = get_json_value(input_params, 'con_conversion_method.conversion_method') + conversion_method = get_json_value( + input_params, "con_conversion_method.conversion_method" + ) - image_type = get_json_value(input_params, 'con_conversion_method.con_image_type.image_type') + image_type = get_json_value( + input_params, "con_conversion_method.con_image_type.image_type" + ) rgb_comb_name_out = "OrigGray" combine_w_red = 1.0 combine_w_green = 1.0 @@ -59,88 +69,131 @@ channel_count = 1 if conversion_method == "Combine": if image_type == "RGB" or image_type == "HSV": - rgb_comb_name_out = get_json_value(input_params, 'con_conversion_method.name_output_image') - combine_w_red = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_red_channel') - combine_w_green = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_green_channel') - combine_w_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_blue_channel') + rgb_comb_name_out = get_json_value( + input_params, "con_conversion_method.name_output_image" + ) + combine_w_red = get_json_value( + input_params, "con_conversion_method.con_image_type.weight_red_channel" + ) + combine_w_green = get_json_value( + input_params, + "con_conversion_method.con_image_type.weight_green_channel", + ) + combine_w_blue = get_json_value( + input_params, "con_conversion_method.con_image_type.weight_blue_channel" + ) elif conversion_method == "Split": if image_type == "RGB": - split_red = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.yes_no') - red_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.name_output_image') - split_green = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.yes_no') - green_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.name_output_image') - split_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.yes_no') - blue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.name_output_image') + split_red = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_red.yes_no", + ) + red_output_name = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_red.name_output_image", + ) + split_green = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_green.yes_no", + ) + green_output_name = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_green.name_output_image", + ) + split_blue = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_blue.yes_no", + ) + blue_output_name = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_blue.name_output_image", + ) elif image_type == "HSV": - split_hue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.yes_no') - hue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.name_output_image') - split_saturation = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.yes_no') - saturation_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.name_output_image') - split_value = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.yes_no') - value_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.name_output_image') + split_hue = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_hue.yes_no", + ) + hue_output_name = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_hue.name_output_image", + ) + split_saturation = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_saturation.yes_no", + ) + saturation_output_name = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_saturation.name_output_image", + ) + split_value = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_value.yes_no", + ) + value_output_name = get_json_value( + input_params, + "con_conversion_method.con_image_type.con_convert_value.name_output_image", + ) result += INDENTATION.join( - [f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n", - f"Relative weight of the red channel:{str(combine_w_red)}\n", - f"Relative weight of the green channel:{str(combine_w_green)}\n", - f"Relative weight of the blue channel:{str(combine_w_blue)}\n", - - f"Convert red to gray?:{split_red}\n", - f"Name the output image:{red_output_name}\n", - f"Convert green to gray?:{split_green}\n", - f"Name the output image:{green_output_name}\n", - f"Convert blue to gray?:{split_blue}\n", - f"Name the output image:{blue_output_name}\n", - - f"Convert hue to gray?:{split_hue}\n", - f"Name the output image:{hue_output_name}\n", - f"Convert saturation to gray?:{split_saturation}\n", - f"Name the output image:{saturation_output_name}\n", - f"Convert value to gray?:{split_value}\n", - f"Name the output image:{value_output_name}\n" - ]) + [ + f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n", + f"Relative weight of the red channel:{str(combine_w_red)}\n", + f"Relative weight of the green channel:{str(combine_w_green)}\n", + f"Relative weight of the blue channel:{str(combine_w_blue)}\n", + f"Convert red to gray?:{split_red}\n", + f"Name the output image:{red_output_name}\n", + f"Convert green to gray?:{split_green}\n", + f"Name the output image:{green_output_name}\n", + f"Convert blue to gray?:{split_blue}\n", + f"Name the output image:{blue_output_name}\n", + f"Convert hue to gray?:{split_hue}\n", + f"Name the output image:{hue_output_name}\n", + f"Convert saturation to gray?:{split_saturation}\n", + f"Name the output image:{saturation_output_name}\n", + f"Convert value to gray?:{split_value}\n", + f"Name the output image:{value_output_name}\n", + ] + ) channel_count = 1 if image_type == "Channels": - channels = input_params['con_conversion_method']['con_image_type']['rpt_channel'] + channels = input_params["con_conversion_method"]["con_image_type"][ + "rpt_channel" + ] channel_count = len(channels) - result += INDENTATION.join( - [f"{INDENTATION}Channel count:{channel_count}\n" - ]) + result += INDENTATION.join([f"{INDENTATION}Channel count:{channel_count}\n"]) for ch in channels: rel_weight_ch = 1.0 image_name = "Channel1" if conversion_method == "Combine": - rel_weight_ch = get_json_value(ch, 'weight_of_channel') + rel_weight_ch = get_json_value(ch, "weight_of_channel") else: - image_name = get_json_value(ch, 'image_name') + image_name = get_json_value(ch, "image_name") result += INDENTATION.join( - [f"{INDENTATION}Channel number:{get_json_value(ch,'channel_no')}\n", - f"Relative weight of the channel:{str(rel_weight_ch)}\n", - f"Image name:{image_name}\n" - ]) + [ + f"{INDENTATION}Channel number:{get_json_value(ch,'channel_no')}\n", + f"Relative weight of the channel:{str(rel_weight_ch)}\n", + f"Image name:{image_name}\n", + ] + ) else: result += INDENTATION.join( - [f"{INDENTATION}Channel count:{channel_count}\n", - "Channel number:Red\\x3A 1\n", - "Relative weight of the channel:1.0\n", - "Image name:Channel1\n" - ]) + [ + f"{INDENTATION}Channel count:{channel_count}\n", + "Channel number:Red\\x3A 1\n", + "Relative weight of the channel:1.0\n", + "Image name:Channel1\n", + ] + ) result = result.rstrip("\n") return result if __name__ == "__main__": parser = argparse.ArgumentParser() - parser.add_argument( - '-p', '--pipeline', - help='CellProfiler pipeline' - ) - parser.add_argument( - '-i', '--inputs', - help='JSON inputs from Galaxy' - ) + parser.add_argument("-p", "--pipeline", help="CellProfiler pipeline") + parser.add_argument("-i", "--inputs", help="JSON inputs from Galaxy") args = parser.parse_args() pipeline_lines = get_pipeline_lines(args.pipeline)