Mercurial > repos > bgruening > cp_measure_image_quality
diff measure_image_quality.xml @ 0:26945c55ddff draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
| author | bgruening |
|---|---|
| date | Thu, 26 Mar 2020 16:47:42 -0400 |
| parents | |
| children | 4dcd464c22ff |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/measure_image_quality.xml Thu Mar 26 16:47:42 2020 -0400 @@ -0,0 +1,276 @@ +<tool id="cp_measure_image_quality" name="MeasureImageQuality" version="@CP_VERSION@"> + <description>measures features that indicate image quality</description> + + <macros> + <import>macros.xml</import> + <xml name="macro_calc_threshold"> + <conditional name="con_use_all_methods"> + <param name="use_all_methods" type="select" display="radio" label="Use all thresholding methods?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes" /> + <when value="No"> + <repeat name="rpt_threshold_method" title="Add another threshold method"> + <conditional name="con_threshold_methods"> + <param name="select_threshold_method" type="select" label="Select a thresholding method"> + <option value="Otsu">Otsu</option> + <option value="MoG">MoG</option> + <option value="Background">Background</option> + <option value="RobustBackground">RobustBackground</option> + <option value="RidlerCalvard">RidlerCalvard</option> + <option value="Kapur">Kapur</option> + <option value="MCT">MCT</option> + </param> + <when value="Otsu"> + <expand macro="otsu_method" /> + </when> + <when value="MoG"> + <expand macro="mog_method" /> + </when> + <when value="Background" /> + <when value="RobustBackground" /> + <when value="RidlerCalvard" /> + <when value="Kapur" /> + <when value="MCT" /> + </conditional> + </repeat> + </when> + </conditional> + </xml> + + <xml name="otsu_method"> + <param name="otsu_weighted_entropy" label="Minimize the weighted variance or the entropy?" type="select"> + <option value="Weighted variance">Weighted variance</option> + <option value="Entropy">Entropy</option> + </param> + <conditional name="con_threshold_classes"> + <param name="threshold_classes" label="Two-class or three-class thresholding?" type="select"> + <option value="Two classes">Two classes</option> + <option value="Three classes">Three classes</option> + </param> + <when value="Three classes"> + <param name="pixel_foreground_or_background" label="Assign pixels in the middle intensity class to the foreground or the background?" type="select"> + <option value="Foreground">Foreground</option> + <option value="Background">Background</option> + </param> + </when> + <when value="Two classes" /> + </conditional> + </xml> + + <xml name="mog_method"> + <param name="mog_fraction_cover" label="Typical fraction of the image covered by objects" type="float" value="0.1" min="0.0" max="1.0"/> + </xml> + </macros> + + <expand macro="py_requirements"/> + <expand macro="cmd_modules" /> + + <configfiles> + <inputs name="inputs" /> + + <configfile name="script_file"> +import json +import sys +import os + +FOURSPACES=@SPACES@ + +input_json_path = sys.argv[1] +input_pipeline= sys.argv[2] + +params = json.load(open(input_json_path, "r")) + +def writemiq(): + _str = "\nMeasureImageQuality:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:5|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count + + for_images = params['calc_for_images'] + selected_images = "" + + if for_images == "All loaded images": + _str += FOURSPACES + "Calculate metrics for which images?:%s\n" % for_images + else: + _str += FOURSPACES + "Calculate metrics for which images?:Select...\n" + selected_images = params['calc_for_images'] + + image_count = 1 + _str += FOURSPACES + "Image count:%d\n" % image_count + + if 'rpt_blur_measurements' in params['con_calc_blur_metrics']: + scale_count = len(params['con_calc_blur_metrics']['rpt_blur_measurements']) + else: + scale_count = 1 + + _str += FOURSPACES + "Scale count:%d\n" % scale_count + + calc_threshold = params['con_calc_threshold']['calc_threshold'] + if calc_threshold == "No": + threshold_count = 1 + all_method = "No" + else: + all_method = params['con_calc_threshold']['con_use_all_methods']['use_all_methods'] + if all_method == "No": + threshold_count = 1 + else: + threshold_count = len(params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']) + + _str += FOURSPACES + "Threshold count:%d\n" % threshold_count + + _str += FOURSPACES + "Select the images to measure:%s\n" % selected_images + + include_rescaling = params['include_rescaling_value'] + _str += FOURSPACES + "Include the image rescaling value?:%s\n" % include_rescaling + + calc_blur_metrics = params['con_calc_blur_metrics']['calc_blur_metrics'] + _str += FOURSPACES + "Calculate blur metrics?:%s\n" % calc_blur_metrics + + if calc_blur_metrics == "Yes" and 'rpt_blur_measurements' in params['con_calc_blur_metrics']: + for bm in params['con_calc_blur_metrics']['rpt_blur_measurements']: + _str += FOURSPACES + "Spatial scale for blur measurements:%d\n" % bm['blur_measurements'] + + calc_saturation = params['calc_saturation_metrics'] + _str += FOURSPACES + "Calculate saturation metrics?:%s\n" % calc_saturation + + calc_intensity = params['calc_intensity_metrics'] + _str += FOURSPACES + "Calculate intensity metrics?:%s\n" % calc_intensity + + calc_threshold = params['con_calc_threshold']['calc_threshold'] + _str += FOURSPACES + "Calculate thresholds?:%s\n" % calc_threshold + _str += FOURSPACES + "Use all thresholding methods?:%s\n" % all_method + + if all_method == "No": + for method in params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']: + _str += FOURSPACES + "Select a thresholding method:%s\n" % method['con_threshold_methods']['select_threshold_method'] + + fraction_cover = method['con_threshold_methods']['mog_fraction_cover'] if 'mog_fraction_cover' in method[ + 'con_threshold_methods'] else 0.1 + + tt_classes = method['con_threshold_methods']['con_threshold_classes'][ + 'threshold_classes'] if 'con_threshold_classes' in method['con_threshold_methods'] else 'Two classes' + + minimize = method['con_threshold_methods']['otsu_weighted_entropy'] if 'otsu_weighted_entropy' in method[ + 'con_threshold_methods'] else 'Entropy' + + if tt_classes == "Three classes": + pixel_intensity = method['con_threshold_methods']['con_threshold_classes'][ + 'pixel_foreground_or_background'] + else: + pixel_intensity = "Foreground" + + _str += FOURSPACES + "Typical fraction of the image covered by objects:%.1f\n" % fraction_cover + + _str += FOURSPACES + "Two-class or three-class thresholding?:%s\n" % tt_classes + + _str += FOURSPACES + "Minimize the weighted variance or the entropy:%s\n" % minimize + + _str += FOURSPACES + "Assign pixels in the middle intensity class to the foreground or the background?:%s\n" % pixel_intensity + + return _str + +with open(input_pipeline) as fin: + lines = fin.readlines() + + k, v = lines[4].strip().split(':') + + module_count = int(v) + new_count = module_count + 1 + lines[4] = k + ":%d\n" % new_count + + with open("output", "w") as f: + f.writelines(lines) + f.write(writemiq()) + +f.close() + </configfile> + </configfiles> + + <inputs> + <expand macro="input_pipeline_macro" /> + <param name="calc_for_images" type="text" label="Calculate metrics for which images?" value="All loaded images"> + <expand macro="text_validator" /> + </param> + <param name="include_rescaling_value" type="select" display="radio" label="Include the image rescaling value?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + + <conditional name="con_calc_blur_metrics"> + <param name="calc_blur_metrics" type="select" display="radio" label="Calculate blur metrics?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes"> + <repeat name="rpt_blur_measurements" title="Add another scale"> + <param name="blur_measurements" label="Spatial scale for blur measurements" type="integer" value="20"/> + </repeat> + </when> + <when value="No" /> + </conditional> + + <param name="calc_intensity_metrics" type="select" display="radio" label="Calculate intensity metrics?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <param name="calc_saturation_metrics" type="select" display="radio" label="Calculate saturation metrics"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + + <conditional name="con_calc_threshold"> + <param name="calc_threshold" type="select" display="radio" label="Calculate thresholds?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes"> + <expand macro="macro_calc_threshold" /> + </when> + <when value="No" /> + </conditional> + + </inputs> + + <outputs> + <expand macro="output_pipeline_macro" /> + </outputs> + + <tests> + <test> + <expand macro="test_input_pipeline_param" /> + + <param name="calc_for_images" value="All loaded images" /> + <param name="include_rescaling_value" value="Yes" /> + + <conditional name="con_calc_blur_metrics"> + <param name="calc_blur_metrics" value="Yes" /> + <repeat name="rpt_blur_measurements"> + <param name="blur_measurements" value="20" /> + </repeat> + </conditional> + + <param name="calc_intensity_metrics" value="Yes" /> + <param name="calc_saturation_metrics" value="Yes" /> + <conditional name="con_calc_threshold"> + <param name="calc_threshold" value="Yes" /> + </conditional> + + <conditional name="con_use_all_methods"> + <param name="use_all_methods" value="No" /> + <repeat name="rpt_threshold_method"> + <conditional name="con_threshold_methods"> + <param name="select_threshold_method" value="Otsu" /> + <param name="otsu_weighted_entropy" value="Weighted variance" /> + <conditional name="con_threshold_classes"> + <param name="threshold_classes" value="Two classes" /> + </conditional> + </conditional> + </repeat> + </conditional> + + <expand macro="test_out_file" file="measure_image_quality.txt" /> + </test> + </tests> + + <expand macro="help" module="MeasureImageQuality" /> + <expand macro="citations" /> +</tool>