org.hkijena.jipipe.plugins.imagejalgorithms.utils

Class ImageJAlgorithmUtils

java.lang.Object

org.hkijena.jipipe.plugins.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.ImagePlus	connectedComponents3D(ij.ImagePlus inputImage, Neighborhood3D connectivity, int bitDepth)
static void	generateROIRelationRowMeasurements(ij.ImagePlus reference, int roi1Index, int roi2Index, int measurements, boolean physicalUnits, ResultsTableData target, ij.gui.Roi roi1, ij.gui.Roi roi2, int row, String columnPrefix)
static void	generateROIRowMeasurements(ij.ImagePlus referenceImage, int index, ij.gui.Roi roi, ImageStatisticsSetParameter measurements, boolean physicalUnits, ResultsTableData target, int targetRow, String columnPrefix)
static ij.process.ByteProcessor	getLabelMask(ij.process.ImageProcessor processor, int label)
static ij.ImagePlus	getMaskFromMaskOrROI(ImageROITargetArea targetArea, JIPipeSingleIterationStep iterationStep, String imageSlotName, JIPipeProgressInfo progressInfo)
static ij.process.ImageProcessor	getMaskProcessorFromMaskOrROI(ImageROITargetArea sourceArea, int width, int height, ROI2DListData rois, ij.ImagePlus mask, ImageSliceIndex sliceIndex)
static ij.process.ImageProcessor	getMaskProcessorFromMaskOrROI(ImageROITargetArea targetArea, JIPipeSingleIterationStep iterationStep, 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	measureROI(ij.ImagePlus referenceImage, ROI2DListData roiList, ImageStatisticsSetParameter measurements, boolean physicalUnits, String columnPrefix, ResultsTableData target, JIPipeProgressInfo progressInfo)
static void	measureROIRelation(ij.ImagePlus referenceImage, ROI2DListData roi1List, ROI2DListData roi2List, int measurements, boolean physicalUnits, boolean requireColocalization, boolean preciseColocalization, String columnPrefix, ResultsTableData target, JIPipeProgressInfo progressInfo)
static void	removeLabelsExcept(ij.process.ImageProcessor processor, int[] labelsToKeep)
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

connectedComponents3D

public static ij.ImagePlus connectedComponents3D(ij.ImagePlus inputImage,
                                                 Neighborhood3D connectivity,
                                                 int bitDepth)

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,
                                                                      ROI2DListData rois,
                                                                      ij.ImagePlus mask,
                                                                      ImageSliceIndex sliceIndex)

updateROIOrMaskSlot

public static void updateROIOrMaskSlot(ImageROITargetArea sourceArea,
                                       JIPipeSlotConfiguration configuration)

getMaskProcessorFromMaskOrROI

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

getMaskFromMaskOrROI

public static ij.ImagePlus getMaskFromMaskOrROI(ImageROITargetArea targetArea,
                                                JIPipeSingleIterationStep iterationStep,
                                                String imageSlotName,
                                                JIPipeProgressInfo progressInfo)

measureROI

public static void measureROI(ij.ImagePlus referenceImage,
                              ROI2DListData roiList,
                              ImageStatisticsSetParameter measurements,
                              boolean physicalUnits,
                              String columnPrefix,
                              ResultsTableData target,
                              JIPipeProgressInfo progressInfo)

measureROIRelation

public static void measureROIRelation(ij.ImagePlus referenceImage,
                                      ROI2DListData roi1List,
                                      ROI2DListData roi2List,
                                      int measurements,
                                      boolean physicalUnits,
                                      boolean requireColocalization,
                                      boolean preciseColocalization,
                                      String columnPrefix,
                                      ResultsTableData target,
                                      JIPipeProgressInfo progressInfo)

generateROIRelationRowMeasurements

public static void generateROIRelationRowMeasurements(ij.ImagePlus reference,
                                                      int roi1Index,
                                                      int roi2Index,
                                                      int measurements,
                                                      boolean physicalUnits,
                                                      ResultsTableData target,
                                                      ij.gui.Roi roi1,
                                                      ij.gui.Roi roi2,
                                                      int row,
                                                      String columnPrefix)

generateROIRowMeasurements

public static void generateROIRowMeasurements(ij.ImagePlus referenceImage,
                                              int index,
                                              ij.gui.Roi roi,
                                              ImageStatisticsSetParameter measurements,
                                              boolean physicalUnits,
                                              ResultsTableData target,
                                              int targetRow,
                                              String columnPrefix)