org.hkijena.jipipe.extensions.imagejalgorithms.utils

Class ImageJAlgorithmUtils

java.lang.Object

org.hkijena.jipipe.extensions.imagejalgorithms.utils.ImageJAlgorithmUtils

public class ImageJAlgorithmUtils
extends Object

Constructor Summary

Constructors

Constructor and Description
ImageJAlgorithmUtils()

Method Summary

Modifier and Type	Method and Description
static ij.process.ByteProcessor	getLabelMask(ij.process.ImageProcessor processor, int label)
static ij.ImagePlus	getMaskFromMaskOrROI(ImageROITargetArea targetArea, JIPipeDataBatch dataBatch, String imageSlotName, JIPipeProgressInfo progressInfo)
static ij.process.ImageProcessor	getMaskProcessorFromMaskOrROI(ImageROITargetArea sourceArea, int width, int height, ROIListData rois, ij.ImagePlus mask, ImageSliceIndex sliceIndex)
static ij.process.ImageProcessor	getMaskProcessorFromMaskOrROI(ImageROITargetArea targetArea, JIPipeDataBatch dataBatch, ImageSliceIndex sliceIndex, JIPipeProgressInfo progressInfo)
static ij.process.ByteProcessor	getThresholdMask(ij.process.ImageProcessor processor, float minThreshold)
static ResultsTableData	measureLabels(ij.process.ImageProcessor label, ij.process.ImageProcessor image, ImageStatisticsSetParameter measurements, ImageSliceIndex index, ij.measure.Calibration calibration, JIPipeProgressInfo progressInfo) Measures properties of a label image
static void	removeLabelsExcept(ij.process.ImageProcessor processor, int[] labelsToKeep)
static void	setLut(ij.ImagePlus image, ij.process.LUT lut, boolean applyToAllPlanes)
static void	setLutFromColorMap(ij.ImagePlus image, ColorMap colorMap, boolean applyToAllPlanes)
static void	updateROIOrMaskSlot(ImageROITargetArea sourceArea, JIPipeSlotConfiguration configuration)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ImageJAlgorithmUtils

public ImageJAlgorithmUtils()

Method Detail

getLabelMask

public static ij.process.ByteProcessor getLabelMask(ij.process.ImageProcessor processor,
                                                    int label)

getThresholdMask

public static ij.process.ByteProcessor getThresholdMask(ij.process.ImageProcessor processor,
                                                        float minThreshold)

removeLabelsExcept

public static void removeLabelsExcept(ij.process.ImageProcessor processor,
                                      int[] labelsToKeep)

measureLabels

public static ResultsTableData measureLabels(ij.process.ImageProcessor label,
                                             ij.process.ImageProcessor image,
                                             ImageStatisticsSetParameter measurements,
                                             ImageSliceIndex index,
                                             ij.measure.Calibration calibration,
                                             JIPipeProgressInfo progressInfo)

Measures properties of a label image

Parameters:

label - the label

image - the reference image

measurements - the measurements

index - the current image index (zero-based)

calibration - the calibration (can be null to disable measurements with calibrations)

progressInfo - the progress info

Returns:

the measurements

getMaskProcessorFromMaskOrROI

public static ij.process.ImageProcessor getMaskProcessorFromMaskOrROI(ImageROITargetArea sourceArea,
                                                                      int width,
                                                                      int height,
                                                                      ROIListData rois,
                                                                      ij.ImagePlus mask,
                                                                      ImageSliceIndex sliceIndex)

updateROIOrMaskSlot

public static void updateROIOrMaskSlot(ImageROITargetArea sourceArea,
                                       JIPipeSlotConfiguration configuration)

getMaskProcessorFromMaskOrROI

public static ij.process.ImageProcessor getMaskProcessorFromMaskOrROI(ImageROITargetArea targetArea,
                                                                      JIPipeDataBatch dataBatch,
                                                                      ImageSliceIndex sliceIndex,
                                                                      JIPipeProgressInfo progressInfo)

getMaskFromMaskOrROI

public static ij.ImagePlus getMaskFromMaskOrROI(ImageROITargetArea targetArea,
                                                JIPipeDataBatch dataBatch,
                                                String imageSlotName,
                                                JIPipeProgressInfo progressInfo)

setLutFromColorMap

public static void setLutFromColorMap(ij.ImagePlus image,
                                      ColorMap colorMap,
                                      boolean applyToAllPlanes)

setLut

public static void setLut(ij.ImagePlus image,
                          ij.process.LUT lut,
                          boolean applyToAllPlanes)