Mercurial > repos > imgteam > imagej2_enhance_contrast

annotate imagej2_enhance_contrast.xml @ 0:edfc597fb180 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 17:01:04 -0400
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children ef3de3e84817
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edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="imagej2_enhance_contrast" name="Enhance contrast" version="@WRAPPER_VERSION@.0">
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3 <description></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[
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 python $__tool_directory__/imagej2_enhance_contrast.py
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 --input "$input"
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12 --input_datatype $input.ext
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13 --equalize_histogram $equalize_histogram_cond.equalize_histogram
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14 #if $equalize_histogram_cond.equalize_histogram == 'no':
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15 --saturated_pixels $equalize_histogram_cond.saturated_pixels
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16 --normalize $equalize_histogram_cond.normalize
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17 #end if
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18 --jython_script $__tool_directory__/imagej2_enhance_contrast_jython_script.py
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19 --output_datatype $output.ext
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20 --output "$output"
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
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25 <conditional name="equalize_histogram_cond">
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26 <param name="equalize_histogram" type="select" label="Equalize histogram?">
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27 <option value="no" selected="True">No</option>
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28 <option value="yes">Yes</option>
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29 </param>
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30 <when value="no">
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31 <param name="saturated_pixels" type="float" value="0.3" min="0.0" max="100.0" label="Saturated pixels pct" help="Value is percentage of total number of pixels">
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32 <validator type="in_range" min="0" exclude_min="true" max="100" />
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33 </param>
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34 <param name="normalize" type="select" label="Normalize?">
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35 <option value="no" selected="True">No</option>
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36 <option value="yes">Yes</option>
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37 </param>
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38 </when>
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39 <when value="yes"/>
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40 </conditional>
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41 </inputs>
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42 <outputs>
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43 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input" value="blobs.gif" />
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48 <param name="equalize_histogram" value="yes" />
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49 <output name="output" file="blobs_equalize.gif" compare="sim_size" />
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50 </test>
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51 <test>
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52 <param name="input" value="blobs.gif" />
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53 <param name="saturated_pixels" value="6.2" />
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54 <output name="output" file="blobs_saturate.gif" compare="sim_size" />
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55 </test>
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56 <test>
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57 <param name="input" value="blobs.gif" />
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58 <param name="saturated_pixels" value="13.0" />
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59 <param name="normalize" value="yes" />
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60 <output name="output" file="blobs_normalize.gif" compare="sim_size" />
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61 </test>
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62 </tests>
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63 <help>
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64
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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65 **What it does**
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66
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67 <![CDATA[
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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68
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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69 Enhances image contrast by using either normalization (contrast stretching) or histogram
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70 equalization.
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71
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72 Normalization (i.e., contrast stretching) attempts to improve the contrast in an image by
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73 stretching the range of intensity values it contains to span a desired range of values
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74 (e.g. the the full range of pixel values that the image type allows). It differs from the
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75 more sophisticated histogram equalization in that it can only apply a linear scaling function
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76 to the image pixel values. As a result the enhancement is less harsh.
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77
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78 Histogram equalization provides a sophisticated method for modifying the dynamic range and
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79 contrast of an image by altering the image such that its intensity histogram has a desired
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80 shape. Unlike contrast stretching, histogram modeling operators may employ non-linear and
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81 non-monotonic transfer functions to map between pixel intensity values in the input and output
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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82 images. Histogram equalization re-assigns the intensity values of pixels in the input image
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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83 such that the output image contains a uniform distribution of intensities (i.e. a flat histogram).
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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84
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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85 - **Equalize histogram** - Enhances the image using histogram equalization. Choosing this option eliminates the "Saturated pixels pct" and "Normalize" options.
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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86 - **Saturated pixels pct** - Determines the number of pixels in the image that are allowed to become saturated. Increasing this value increases contrast. This value should be greater than zero to prevent a few outlying pixels from causing the histogram stretch to not work as intended.
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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87 - **Normalize** - Recalculates the pixel values of the image so the range is equal to the maximum range for the data type, or 0-1.0 for float images. The maximum range is 0-255 for 8-bit images and 0-65535 for 16-bit images. Normalization of RGB images is not supported, so selecting "yes" is ignored for this image type.
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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88
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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89 ]]>
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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90
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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91 </help>
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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92 <expand macro="fiji_headless_citations" />
edfc597fb180 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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93 </tool>