<commit_before><?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>TextureAnalysis</category>
  <title>Co-occurrence matrix texture</title>
  <version>1.0.2</version>
  <description>
    CoMatrixTextureTool calculates run length encoding 
  </description>
  <contributor><NAME></contributor>

  <parameters>
    <label>Input parameters</label>
    <description>Input parameters</description>

    <image>
      <name>inputVolume</name>
      <label>Input volume</label>
      <channel>input</channel>
      <description>Input volume to be filtered</description>
      <longflag>i</longflag>
    </image>

    <image>
      <name>inputMask</name>
      <label>Input Mask</label>
      <channel>input</channel>
      <description>Input mask with 0 for background and otherwise for objects.</description>
      <longflag>m</longflag>
    </image>

    <image>
      <name>inputLabelMap</name>
      <label>Input Label map</label>
      <channel>input</channel>
      <description>Label map with 0 for background and non 0 labels elsewhere. The RLE analysis is done separately for each label.</description>
      <longflag>l</longflag>
    </image>

    <double>
      <name>backGroundValue</name>
      <longflag>backGroundValue</longflag>
      <description>Set the background value of the image</description>
      <label>Back ground value</label>
      <default>0</default>
    </double>

    <boolean>
      <name>useMinMaxIntensity</name>
      <longflag>useMinMaxIntensity</longflag>
      <description>Use the min max intensity set by parameter. Defaults to compute the values.</description>
      <label>Use minimum maximum intensity</label>
      <default>0</default>
    </boolean>

    <boolean>
      <name>useFullConnectivity</name>
      <longflag>useFullConnectivity</longflag>
      <description>Use full connectivity to compute the run lenghts</description>
      <label>Use full connectivity to compute the run lenghts</label>
      <default>0</default>
    </boolean>

    <double>
      <name>minIntensity</name>
      <longflag>minIntensity</longflag>
      <description>Minimum intensity to run the RLE</description>
      <label>Min intensity</label>
      <default>1</default>
    </double>

    <double>
      <name>maxIntensity</name>
      <longflag>maxIntensity</longflag>
      <description>Maximum intensity to run the RLE</description>
      <label>Max intensity</label>
      <default>255</default>
    </double>

    <integer>
      <name>numberOfIntensityBins</name>
      <longflag>numberOfIntensityBins</longflag>
      <description>Number of intensity bins to build the histogram</description>
      <label>Intensity Bins</label>
      <default>64</default>
    </integer>

    <boolean>
      <name>useDynamicThreshold</name>
      <longflag>useDynamicThreshold</longflag>
      <description>Compute a dynamic threshold around each pixel, Threshold_i = Pixel_i '+-' BinSize / 2.0 </description>
      <label>Dynamic threshold</label>
      <default>0</default>
    </boolean>

    <boolean>
      <name>useMinMaxSize</name>
      <longflag>useMinMaxSize</longflag>
      <description>Use the minimum and maximum set by parameter. Defaults to compute the minimum and maximum size</description>
      <label>Max intensity</label>
      <default>0</default>
    </boolean>

    <integer>
      <name>minSize</name>
      <longflag>minSize</longflag>
      <description>Minimum size of the connected components in the image to run the RLE</description>
      <label>Min size</label>
      <default>1</default>
    </integer>

    <integer>
      <name>maxSize</name>
      <longflag>maxSize</longflag>
      <description>Maximum size of the connected components to run the RLE. If size is -1, there is no cap for size.</description>
      <label>Max size</label>
      <default>-1</default>
    </integer>

    <integer>
      <name>numberOfSizeBins</name>
      <longflag>numberOfSizeBins</longflag>
      <description>Number of size bins to build the histogram</description>
      <label>Max intensity</label>
      <default>64</default>
    </integer>

    <integer>
      <name>percentile</name>
      <longflag>percentile</longflag>
      <description>Value were the percentage of observations falls in the sample, e.x.: percentile = 5 then histogram window will be [5%, 95%] of observations. Measurements outside of range are not clipped but instead contribute to the closest bin.</description>
      <label>Percentile</label>
      <default>5</default>
    </integer>

  </parameters>

  <parameters>
    <label>Ouput parameters</label>
    <description>Output parameters</description>

    <string>
      <name>outputHistogram</name>
      <longflag>outputHistogram</longflag>
      <description>Filename to store the histogram in CSV format</description>
      <label>OutputHistogramCSV</label>
      <default></default>
    </string>

    <boolean>
      <name>outputHistogramPrint</name>
      <longflag>outputHistogramPrint</longflag>
      <description>Print the histogram to console</description>
      <label>OutputHistogramPrint</label>
      <default>0</default>
    </boolean>

    <string>
      <name>outputRLE</name>
      <longflag>outputRLE</longflag>
      <description>Filename to store the RLE analysis values</description>
      <label>OutputRLEValues</label>
      <default></default>
    </string>

    <integer>
      <name>outputHistogramVar</name>
      <longflag>outputHistogramVar</longflag>
      <description>Javascript variable name to store the output histogram string in CSV format in Module.variable[outputHistogramVar], the variable should be given as a pointer.</description>
      <label>OutputHistogramCSV</label>
      <default>0</default>
    </integer>

    <integer>
      <name>outputRLEVar</name>
      <longflag>outputRLEVar</longflag>
      <description>Javascript variable name to store the output string int Module.variable[outputRLEVar], the variable should be given as a pointer.</description>
      <label>OutputRLEValues</label>
      <default>0</default>
    </integer>

    <image>
      <name>outputEntropyImageFilename</name>
      <label>Output entropy image</label>
      <channel>output</channel>
      <description>Write the output entropy image computed from the histogram</description>
      <longflag>entropyImageFilename</longflag>
      <default>""</default>
    </image>

  </parameters>
</executable><commit_msg>STYLE: Update package version<commit_after><?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>TextureAnalysis</category>
  <title>Co-occurrence matrix texture</title>
  <version>1.0.3</version>
  <description>
    CoMatrixTextureTool calculates run length encoding 
  </description>
  <contributor><NAME></contributor>

  <parameters>
    <label>Input parameters</label>
    <description>Input parameters</description>

    <image>
      <name>inputVolume</name>
      <label>Input volume</label>
      <channel>input</channel>
      <description>Input volume to be filtered</description>
      <longflag>i</longflag>
    </image>

    <image>
      <name>inputMask</name>
      <label>Input Mask</label>
      <channel>input</channel>
      <description>Input mask with 0 for background and otherwise for objects.</description>
      <longflag>m</longflag>
    </image>

    <image>
      <name>inputLabelMap</name>
      <label>Input Label map</label>
      <channel>input</channel>
      <description>Label map with 0 for background and non 0 labels elsewhere. The RLE analysis is done separately for each label.</description>
      <longflag>l</longflag>
    </image>

    <double>
      <name>backGroundValue</name>
      <longflag>backGroundValue</longflag>
      <description>Set the background value of the image</description>
      <label>Back ground value</label>
      <default>0</default>
    </double>

    <boolean>
      <name>useMinMaxIntensity</name>
      <longflag>useMinMaxIntensity</longflag>
      <description>Use the min max intensity set by parameter. Defaults to compute the values.</description>
      <label>Use minimum maximum intensity</label>
      <default>0</default>
    </boolean>

    <boolean>
      <name>useFullConnectivity</name>
      <longflag>useFullConnectivity</longflag>
      <description>Use full connectivity to compute the run lenghts</description>
      <label>Use full connectivity to compute the run lenghts</label>
      <default>0</default>
    </boolean>

    <double>
      <name>minIntensity</name>
      <longflag>minIntensity</longflag>
      <description>Minimum intensity to run the RLE</description>
      <label>Min intensity</label>
      <default>1</default>
    </double>

    <double>
      <name>maxIntensity</name>
      <longflag>maxIntensity</longflag>
      <description>Maximum intensity to run the RLE</description>
      <label>Max intensity</label>
      <default>255</default>
    </double>

    <integer>
      <name>numberOfIntensityBins</name>
      <longflag>numberOfIntensityBins</longflag>
      <description>Number of intensity bins to build the histogram</description>
      <label>Intensity Bins</label>
      <default>64</default>
    </integer>

    <boolean>
      <name>useDynamicThreshold</name>
      <longflag>useDynamicThreshold</longflag>
      <description>Compute a dynamic threshold around each pixel, Threshold_i = Pixel_i '+-' BinSize / 2.0 </description>
      <label>Dynamic threshold</label>
      <default>0</default>
    </boolean>

    <boolean>
      <name>useMinMaxSize</name>
      <longflag>useMinMaxSize</longflag>
      <description>Use the minimum and maximum set by parameter. Defaults to compute the minimum and maximum size</description>
      <label>Max intensity</label>
      <default>0</default>
    </boolean>

    <integer>
      <name>minSize</name>
      <longflag>minSize</longflag>
      <description>Minimum size of the connected components in the image to run the RLE</description>
      <label>Min size</label>
      <default>1</default>
    </integer>

    <integer>
      <name>maxSize</name>
      <longflag>maxSize</longflag>
      <description>Maximum size of the connected components to run the RLE. If size is -1, there is no cap for size.</description>
      <label>Max size</label>
      <default>-1</default>
    </integer>

    <integer>
      <name>numberOfSizeBins</name>
      <longflag>numberOfSizeBins</longflag>
      <description>Number of size bins to build the histogram</description>
      <label>Max intensity</label>
      <default>64</default>
    </integer>

    <integer>
      <name>percentile</name>
      <longflag>percentile</longflag>
      <description>Value were the percentage of observations falls in the sample, e.x.: percentile = 5 then histogram window will be [5%, 95%] of observations. Measurements outside of range are not clipped but instead contribute to the closest bin.</description>
      <label>Percentile</label>
      <default>5</default>
    </integer>

  </parameters>

  <parameters>
    <label>Ouput parameters</label>
    <description>Output parameters</description>

    <string>
      <name>outputHistogram</name>
      <longflag>outputHistogram</longflag>
      <description>Filename to store the histogram in CSV format</description>
      <label>OutputHistogramCSV</label>
      <default></default>
    </string>

    <boolean>
      <name>outputHistogramPrint</name>
      <longflag>outputHistogramPrint</longflag>
      <description>Print the histogram to console</description>
      <label>OutputHistogramPrint</label>
      <default>0</default>
    </boolean>

    <string>
      <name>outputRLE</name>
      <longflag>outputRLE</longflag>
      <description>Filename to store the RLE analysis values</description>
      <label>OutputRLEValues</label>
      <default></default>
    </string>

    <integer>
      <name>outputHistogramVar</name>
      <longflag>outputHistogramVar</longflag>
      <description>Javascript variable name to store the output histogram string in CSV format in Module.variable[outputHistogramVar], the variable should be given as a pointer.</description>
      <label>OutputHistogramCSV</label>
      <default>0</default>
    </integer>

    <integer>
      <name>outputRLEVar</name>
      <longflag>outputRLEVar</longflag>
      <description>Javascript variable name to store the output string int Module.variable[outputRLEVar], the variable should be given as a pointer.</description>
      <label>OutputRLEValues</label>
      <default>0</default>
    </integer>

    <image>
      <name>outputEntropyImageFilename</name>
      <label>Output entropy image</label>
      <channel>output</channel>
      <description>Write the output entropy image computed from the histogram</description>
      <longflag>entropyImageFilename</longflag>
    </image>

  </parameters>
</executable>
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{'dir': 'git-commits-cleaned', 'id': '1054059', 'n_tokens_mistral': 3741, 'n_tokens_neox': 3607, 'n_words': 881}