Mercurial > repos > bgruening > cp_measure_image_area_occupied

annotate measure_image_area_occupied.xml @ 3:3e6774b33ece draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 11:42:28 +0000
parents 757857ea192d
children 8f8c4561fffb
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1 <tool id="cp_measure_image_area_occupied" name="MeasureImageAreaOccupied" version="@CP_VERSION@">
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2 <description>measure the area in an image occupied by objects</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="py_requirements"/>
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9 <expand macro="cmd_modules" />
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11 <configfiles>
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12 <inputs name="inputs" />
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13 <configfile name="script_file">
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14 import json
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15 import sys
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16 import os
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18 FOURSPACES=@SPACES@
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20 input_json_path = sys.argv[1]
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21 input_pipeline= sys.argv[2]
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23 params = json.load(open(input_json_path, "r"))
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25 def writemiao():
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26 _str = "\nMeasureImageAreaOccupied:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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28 hidden = len(params['rpt_area'])
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30 _str += FOURSPACES + "Hidden:%d\n" % hidden
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32 for area in params['rpt_area']:
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33 _str += FOURSPACES + "Measure the area occupied in a binary image, or in objects?:%s\n" % area['con_area']['objects_or_image']
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35 obj_flag = area['con_area']['objects_or_image']
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37 if obj_flag == "Objects":
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38 _str += FOURSPACES + "Select objects to measure:%s\n" % area['con_area']['objects_to_measure']
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39 _str += FOURSPACES + "Select a binary image to measure:None\n"
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40 else:
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41 _str += FOURSPACES + "Select objects to measure:None\n"
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42 _str += FOURSPACES + "Select a binary image to measure:%s\n" % area['con_area']['image_to_measure']
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43
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44 return _str
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47 with open(input_pipeline) as fin:
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48 lines = fin.readlines()
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50 k, v = lines[4].strip().split(':')
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52 module_count = int(v)
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53 new_count = module_count + 1
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54 lines[4] = k + ":%d\n" % new_count
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55 with open("output.cppipe", "w") as f:
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56 f.writelines(lines)
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57 f.write(writemiao())
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58
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59 f.close()
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60 </configfile>
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61 </configfiles>
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63 <inputs>
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64 <expand macro="input_pipeline_param" />
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65 <repeat name="rpt_area" title="new area" min="1">
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66 <conditional name="con_area">
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67 <param name="objects_or_image" label="Measure the area occupied in a binary image, or in objects?" type="select">
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68 <help>
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69 <![CDATA[
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70 The area can be measured in two ways:
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71 <br> - Binary Image: The area occupied by the foreground in a binary (black and white) image.
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72 <br> - Objects: The area occupied by previously-identified objects.
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73 ]]>
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74 </help>
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75 <option value="Binary image">Binary image</option>
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76 <option value="Objects">Objects</option>
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77 </param>
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78 <when value="Objects">
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79 <param name="objects_to_measure" label="Enter the name of the objects to measure" type="text">
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80 <expand macro="text_validator" />
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81 </param>
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82 </when>
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83 <when value="Binary image">
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84 <param name="image_to_measure" label="Enter the name of a binary image to measure" type="text">
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85 <expand macro="text_validator" />
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86 </param>
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87 </when>
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88 </conditional>
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89 </repeat>
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90 </inputs>
0
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91
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92 <outputs>
3
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93 <expand macro="output_pipeline_param" />
0
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94 </outputs>
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95
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96 <tests>
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97 <test>
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98 <expand macro="test_input_pipeline_param" />
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99 <repeat name="rpt_area">
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100 <conditional name="con_area">
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101 <param name="objects_or_image" value="Objects" />
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102 <param name="objects_to_measure" value="Nuclei" />
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103 </conditional>
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104 </repeat>
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105 <repeat name="rpt_area">
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106 <conditional name="con_area">
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107 <param name="objects_or_image" value="Objects" />
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108 <param name="objects_to_measure" value="Nucleoli" />
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109 </conditional>
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110 </repeat>
3
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111 <expand macro="test_out_file" file="measure_image_area_occupied.cppipe" />
0
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112 </test>
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113 </tests>
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114
3
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115 <help>
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116 <![CDATA[
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117
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118 .. class:: infomark
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119
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120 **What it does**
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121 This tool reports the sum of the areas and perimeters of the objects defined by one of the Identify modules, or the area of the foreground in a binary image.
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122 If the input image has a mask (for example, created by the MaskImage module), the measurements made by this module will take the mask into account by ignoring the pixels outside the mask.
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123 You can use this tool to measure the number of pixels above a given threshold if you precede it with thresholding performed by Threshold, and then select the binary image output by Threshold to be measured by this module.
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124
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125 @COMMON_HELP@
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126 ]]>
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127 </help>
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128
0
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129 <expand macro="citations" />
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130 </tool>