Mercurial > repos > bgruening > cp_display_data_on_image
diff display_data_on_image.xml @ 0:c49a557b4e3e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
| author | bgruening |
|---|---|
| date | Thu, 26 Mar 2020 17:45:44 -0400 |
| parents | |
| children | 7c70e5268acd |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/display_data_on_image.xml Thu Mar 26 17:45:44 2020 -0400 @@ -0,0 +1,277 @@ +<tool id="cp_display_data_on_image" name="DisplayDataOnImage" version="@CP_VERSION@"> + <description>produces an image with measured data on top of identified objects</description> + <macros> + <import>macros.xml</import> + <xml name="display_object"> + <param name="select_input_obj" label="Select the input objects" type="text" /> + <conditional name="con_obj_measurement_category"> + <param name="measurement_category" label="Measurement category" type="select"> + <option value="Location">Location</option> + <option value="Number">Number</option> + </param> + <when value="Number"> + <param name="measurement" label="Measurement" type="select"> + <option value="Object_Number">Object_Number</option> + </param> + </when> + <when value="Location"> + <param name="obj_measurement" label="Measurement" type="select"> + <option value="Center_X">Center_X</option> + <option value="Center_Y">Center_Y</option> + <option value="Center_Z">Center_Z</option> + </param> + </when> + </conditional> + </xml> + <xml name="display_image"> + <conditional name="con_obj_measurement_category"> + <param name="measurement_category" label="Measurement category" type="select"> + <option value="Count">Count</option> + <option value="FileName">FileName</option> + <option value="Frame">Frame</option> + <option value="Height">Height</option> + <option value="MD5Digest">MD5Digest</option> + <option value="Metadata">Metadata</option> + <option value="PathName">PathName</option> + <option value="Scaling">Scaling</option> + <option value="Series">Series</option> + <option value="PathName">PathName</option> + <option value="Threshold">Threshold</option> + <option value="URL">URL</option> + <option value="Width">Width</option> + </param> + <when value="Count"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="FileName"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="Frame"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="Height"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="MD5Digest"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="Metadata"> + <param name="measurement" label="Measurement" type="select"> + <option value="FileLocation">FileLocation</option> + <option value="Frame">Frame</option> + <option value="ImageId">ImageId</option> + <option value="Screen">Screen</option> + <option value="Series">Series</option> + </param> + </when> + <when value="PathName"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="Scaling"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="Series"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="PathName"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="Threshold"> + <param name="measurement" label="Measurement" type="text" /> + <param name="image_thresh_objects" label="Objects" type="text"/> + </when> + <when value="URL"> + <param name="measurement" label="Measurement" type="text" /> + </when> + <when value="Width"> + <param name="measurement" label="Measurement" type="text" /> + </when> + </conditional> + </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 writemi(): + _str = "\nDisplayDataOnImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:6|show_window:False|notes:\\x5B\\'Add nuclei id as label\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count + + obj_img_params = params['con_display_obj_image'] + display_mode_params = params['con_display_mode'] + + _str += FOURSPACES + "Display object or image measurements?:%s\n" % obj_img_params['display_obj_image'] + + input_obj = obj_img_params['select_input_obj'] if obj_img_params['display_obj_image'] == "Object" else "None" + + _str += FOURSPACES + "Select the input objects:%s\n" % input_obj + _str += FOURSPACES + "Measurement to display:%s_%s\n" % (obj_img_params['con_obj_measurement_category'][ + 'measurement_category'],obj_img_params['con_obj_measurement_category']['measurement']) + _str += FOURSPACES + "Select the image on which to display the measurements:%s\n" % params[ + 'image_to_display_measurements'] + + display_mode = display_mode_params['display_mode'] + + if display_mode == "Text": + text_color = display_mode_params['text_color'] + font_size = display_mode_params['font_size'] + no_of_decimals = display_mode_params['number_of_decimals'] + annotation_offset = display_mode_params['annotation_offset'] + color_map = "Default" + color_map_scale = "Use this image's measurement range" + color_map_range = "0.0,1.0" + else: + text_color = "#ff0000" + font_size = 11 + no_of_decimals = 0 + annotation_offset = 0 + color_map = display_mode_params['color_map'] + color_map_scale = display_mode_params['con_color_map_scale']['color_map_scale'] + if color_map_scale == "Manual": + color_map_range ="%.1f,%.1f" % (display_mode_params['con_color_map_scale']['min_color_map_range'], display_mode_params['con_color_map_scale']['max_color_map_range']) + else: + color_map_range = "0.0,1.0" + + _str += FOURSPACES + "Text color:%s\n" % text_color + _str += FOURSPACES + "Name the output image that has the measurements displayed:%s\n" % params['name_output_image'] + _str += FOURSPACES + "Font size (points):%d\n" % font_size + _str += FOURSPACES + "Number of decimals:%d\n" % no_of_decimals + _str += FOURSPACES + "Image elements to save:%s\n" % params['element_to_save'] + _str += FOURSPACES + "Annotation offset (in pixels):%d\n" % annotation_offset + _str += FOURSPACES + "Display mode:%s\n" % display_mode + _str += FOURSPACES + "Color map:%s\n" % color_map + _str += FOURSPACES + "Display background image?:%s\n" % params['display_background_image'] + _str += FOURSPACES + "Color map scale:%s\n" % color_map_scale + _str += FOURSPACES + "Color map range:%s\n" % color_map_range + + 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(writemi()) + +f.close() + </configfile> + </configfiles> + + <inputs> + <expand macro="input_pipeline_macro" /> + <conditional name="con_display_obj_image"> + <param name="display_obj_image" type="select" label="Display object or image measurements?"> + <option value="Object">Object</option> + <option value="Image">Image</option> + </param> + <when value="Object"> + <expand macro="display_object" /> + </when> + <when value="Image"> + <expand macro="display_image" /> + </when> + </conditional> + + <param name="display_background_image" label="Display background image?" type="select" display="radio"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + + <param name="image_to_display_measurements" label="Select the image on which to display the measurements" type="text"> + <expand macro="text_validator" /> + </param> + + <conditional name="con_display_mode"> + <param name="display_mode" type="select" label="Display mode"> + <option value="Text">Text</option> + <option value="Color">Color</option> + </param> + <when value="Text"> + <param name="text_color" type="color" label="Text color" /> + <param name="font_size" type="integer" label="Font size(points)" value="11" min="8"> + </param> + <param name="number_of_decimals" type="integer" label="Number of decimals" value="0"/> + <param name="annotation_offset" type="integer" label="Annotation offset (in pixels)" value="0" /> + </when> + <when value="Color"> + <param name="color_map" label="Color map" type="select" help="DisplayDataOnImage assigns a color to each object’s measurement value from a colormap when in colormap-mode, mapping the value to a color along the colormap’s continuum. This mapping has implicit upper and lower bounds to its range which are the extremes of the colormap. This setting determines whether the extremes are the minimum and maximum "> + <option value="Default">Default</option> + </param> + <conditional name="con_color_map_scale"> + <param name="color_map_scale" label="Color map scale" type="select" help="assigns a color to each object’s measurement value from a colormap when in colormap-mode, mapping the value to a color along the colormap’s continuum. This mapping has implicit upper and lower bounds to its range which are the extremes of the colormap. This setting determines whether the extremes are the minimum and maximum values of the measurement from among the objects in the current image or manually-entered extremes"> + <option value="Use this image's measurement range">Use this image's measurement range</option> + <option value="Manual">Manual</option> + <sanitizer sanitize="false"/> + </param> + <when value="Manual"> + <param name="min_color_map_range" label="Min. color map range" type="float" help="This setting determines the lower bounds of the values for the color map" value="0.0" min="0.0" /> + <param name="max_color_map_range" label="Max. color map range" type="float" help="This setting determines the upper bounds of the values for the color map" value="1.0" max="1.0" /> + </when> + <when value="Use this image's measurement range" /> + </conditional> + </when> + </conditional> + + <param name="name_output_image" label="Name the output image that has the measurements displayed" type="text"> + <expand macro="text_validator" /> + </param> + <param name="element_to_save" type="select" label="Image elements to save"> + <option value="Image">Image</option> + <option value="Figure">Figure</option> + <option value="Axes">Axes</option> + </param> + </inputs> + + <outputs> + <expand macro="output_pipeline_macro" /> + </outputs> + + <tests> + <test> + <expand macro="test_input_pipeline_param" /> + <conditional name="con_display_obj_image"> + <param name="display_obj_image" value="Object" /> + <param name="select_input_obj" value="Nuclei" /> + <conditional name="con_obj_measurement_category"> + <param name="measurement_category" value="Number" /> + <param name="measurement" value="Object_Number" /> + </conditional> + </conditional> + <param name="display_background_image" value="Yes" /> + <param name="image_to_display_measurements" value="DNA" /> + <conditional name="con_display_mode"> + <param name="display_mode" value="Text" /> + <param name="text_color" value="#ff0000"/> + <param name="font_size" value="11" /> + <param name="number_of_decimals" value="0" /> + <param name="annotation_offset" value="0" /> + </conditional> + <param name="name_output_image" value="ImageDisplay" /> + <param name="element_to_save" value="Image" /> + + <expand macro="test_out_file" file="display_data_on_image.txt" /> + </test> + </tests> + <expand macro="help" module="DisplayDataOnImage"/> + <expand macro="citations" /> +</tool>