Mercurial > repos > iuc > imagej2_adjust_threshold_binary

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
author iuc
date Fri, 22 Jul 2016 23:26:55 -0400
parents 8f7beef4f1f3
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="imagej2_adjust_threshold_binary" name="Adjust threshold" version="@WRAPPER_VERSION@.0">
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3 <description>of binary image</description>
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4 <macros>
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5 <import>imagej2_macros.xml</import>
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6 </macros>
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7 <expand macro="fiji_requirements" />
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8 <command>
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9 <![CDATA[
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10 python $__tool_directory__/imagej2_adjust_threshold_binary.py
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11 --input "$input"
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12 --input_datatype $input.ext
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13 --threshold_min $threshold_min
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14 --threshold_max $threshold_max
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15 --method $method
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16 --display $display
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17 --black_background $black_background
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18 --stack_histogram $stack_histogram
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c05d862ac753 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
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19 --jython_script $__tool_directory__/imagej2_adjust_threshold_binary_jython_script.py
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20 --output_datatype $output.ext
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21 --output "$output"
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
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26 <param name="threshold_min" type="float" value="0" min="0" max="255" label="Minimum threshold value" />
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27 <param name="threshold_max" type="float" value="0" min="0" max="255" label="Maximum threshold value" />
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28 <param name="method" type="select" label="Method" help="The Default method is the modified IsoData algorithm.">
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29 <option value="Default" selected="True">Default</option>
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30 <option value="Huang">Huang</option>
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31 <option value="Intermodes">Intermodes</option>
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32 <option value="IsoData">IsoData</option>
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33 <option value="IJ_IsoData">IJ_IsoData</option>
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34 <option value="Li">Li</option>
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35 <option value="MaxEntropy">MaxEntropy</option>
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36 <option value="Mean">Mean</option>
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37 <option value="MinError">MinError</option>
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38 <option value="Minimum">Minimum</option>
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39 <option value="Moments">Moments</option>
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40 <option value="Otsu">Otsu</option>
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41 <option value="RenyiEntropy">RenyiEntropy</option>
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42 <option value="Shanbhag">Shanbhag</option>
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43 <option value="Triangle">Triangle</option>
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44 <option value="Yen">Yen</option>
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45 </param>
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46 <param name="display" type="select" label="Display">
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47 <option value="red" selected="True">Red</option>
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48 <option value="bw">Black and White</option>
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49 <option value="over_under">Over/Under</option>
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50 </param>
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51 <param name="black_background" type="select" label="Black background" help="Select yes if features are lighter than the background.">
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52 <option value="no" selected="True">No</option>
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53 <option value="yes">Yes</option>
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54 </param>
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55 <param name="stack_histogram" type="select" label="Stack histogram" help="Select yes to first compute the histogram of the whole stack (or hyperstack) and then compute the threshold based on that histogram.">
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56 <option value="no" selected="True">No</option>
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57 <option value="yes">Yes</option>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="input" value="blobs.gif" />
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66 <param name="output_datatype" value="gif" />
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67 <param name="threshold_min" value="0.0" />
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68 <param name="threshold_max" value="129.0" />
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69 <param name="method" value="Default" />
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70 <param name="display" value="red" />
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71 <param name="black_background" value="no" />
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72 <param name="stack_histogram" value="no" />
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73 <output name="output" file="blobs_threshold_default.gif" compare="sim_size" />
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74 </test>
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75 <test>
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76 <param name="input" value="blobs.gif" />
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77 <param name="output_datatype" value="gif" />
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78 <param name="threshold_min" value="118.0" />
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79 <param name="threshold_max" value="255.0" />
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80 <param name="method" value="IJ_IsoData" />
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81 <param name="display" value="over_under" />
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82 <param name="black_background" value="no" />
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83 <param name="stack_histogram" value="no" />
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84 <output name="output" file="blobs_threshold_ijiso.gif" compare="sim_size" />
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85 </test>
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86 <test>
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87 <param name="input" value="blobs.gif" />
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88 <param name="output_datatype" value="gif" />
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89 <param name="threshold_min" value="72.0" />
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90 <param name="threshold_max" value="255.0" />
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91 <param name="method" value="Huang" />
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92 <param name="display" value="bw" />
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93 <param name="black_background" value="yes" />
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94 <param name="stack_histogram" value="no" />
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95 <output name="output" file="blobs_threshold_huang_dark.gif" compare="sim_size" />
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96 </test>
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97 </tests>
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98 <help>
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99
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100 @requires_binary_input@
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101
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102 **What it does**
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103
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104 <![CDATA[
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105 Sets lower and upper threshold values, segmenting grayscale images into features of interest and background
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106
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107 - **Minimum threshold value** - Adjusts the minimum threshold value.
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108 - **Maximum threshold value** - Adjusts the maximum threshold value.
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109 - **Method** - Allows any of the 16 different automatic thresholding methods to be selected. These are global thresholding methods that typically cannot deal with unevenly illuminated images (such as in brightfield microscopy)."
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110 - **Display** - Selects one of three display mode: **Red** displays the thresholded values in red, **Black and White** features are displayed in black and background in white, **Over/Under** displays pixels below the lower threshold value in blue, thresholded pixels in grayscale, and pixels above the upper threshold value in green.
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111 - **Black background** - Select **yes** when features are lighter than the background.
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112 - **Stack histogram**  Select **yes** to first compute the histogram of the whole stack (or hyperstack) and then compute the threshold based on that histogram. As such, all slices are binarized using the single computed value. If unchecked, the threshold of each slice is computed separately.
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113 ]]>
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114
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115 </help>
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116 <expand macro="fiji_headless_citations" />
91d82f24657a planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
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117 </tool>