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OpsLabelAnalyser.java
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OpsLabelAnalyser.java
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package de.mpicbg.scf.labelhandling;
import de.mpicbg.scf.labelhandling.data.Feature;
import de.mpicbg.scf.labelhandling.data.Measurement;
import de.mpicbg.scf.labelhandling.data.Utilities;
import java.util.*;
import de.mpicbg.scf.imgtools.ui.DebugHelper;
import net.imagej.mesh.Mesh;
import net.imagej.ops.image.cooccurrenceMatrix.MatrixOrientation2D;
import net.imagej.ops.image.cooccurrenceMatrix.MatrixOrientation3D;
import net.imglib2.*;
import net.imglib2.roi.IterableRegion;
import net.imglib2.roi.geom.real.Polygon2D;
import net.imglib2.type.BooleanType;
import net.imglib2.type.numeric.integer.ByteType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.Intervals;
import net.imglib2.util.Pair;
import net.imglib2.view.Views;
import org.scijava.Context;
import net.imagej.ops.OpMatchingService;
import net.imagej.ops.OpService;
import net.imglib2.img.Img;
import net.imglib2.roi.Regions;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.DoubleType;
/**
* This class allows to measure features (volume/area, aspect ratio, average signal value, ...) of labels in a label map in a generic way. Only features which
* have been handed over to the constructor will be determined.
*
* Example code can be found in LabelParticleAnalyserTest
*
*
*
* @author Robert Haase, Scientific Computing Facility, MPI-CBG, rhaase@mpi-cbg.de
* @version 1.0.2 Jul, 2016
* @param <F> Type of the image where signal measures are performed on.
* @param <B> Boolean Type of the binary regions of interest, which should be analysed
*/
public class OpsLabelAnalyser<F extends RealType<F>, B extends BooleanType<B>> {
// Input:
ArrayList<Feature> whatToMeasure = new ArrayList<Feature>();
int numberNOfClosestNeighbors = 5;
double closeNeighborDistanceD = 100;
private ArrayList<RandomAccessibleInterval<B>> labelMap;
private Img<F> signalMap;
private double[] voxelSize;
private double[] origin;
// State:
boolean resultsValid = false;
// Output:
int numLabels = 0;
Hashtable<Feature, Measurement> results;
public OpsLabelAnalyser(RandomAccessibleInterval<B> singleLabel, Feature[] featuresToExtract) {
this.labelMap = new ArrayList<RandomAccessibleInterval<B>>();
this.labelMap.add(singleLabel);
this.whatToMeasure.addAll(Arrays.asList(featuresToExtract));
}
public OpsLabelAnalyser(ArrayList<RandomAccessibleInterval<B>> labelMap, Feature[] featuresToExtract) {
this.labelMap = labelMap;
this.whatToMeasure.addAll(Arrays.asList(featuresToExtract));
}
/*
public OpsLabelAnalyser(ArrayList<RandomAccessibleInterval<B>> labelMap, double[] voxelSize, Feature[] featuresToExtract) {
this.labelMap = labelMap;
this.whatToMeasure.addAll(Arrays.asList(featuresToExtract));
this.voxelSize = voxelSize;
}
public OpsLabelAnalyser(ArrayList<RandomAccessibleInterval<B>> labelMap, Img<F> signalMap, double[] voxelSize, Feature[] featuresToExtract) {
this.labelMap = labelMap;
this.whatToMeasure.addAll(Arrays.asList(featuresToExtract));
this.voxelSize = voxelSize;
this.signalMap = signalMap;
}
public OpsLabelAnalyser(ArrayList<RandomAccessibleInterval<B>> labelMap, Img<F> signalMap, double[] voxelSize, EnumSet<Feature> featuresToExtract) {
this.labelMap = labelMap;
this.whatToMeasure.addAll(featuresToExtract);
this.voxelSize = voxelSize;
this.signalMap = signalMap;
}*/
public void setSignalImage(Img<F> signalImage) {
if (signalImage == null)
{
return;
}
this.signalMap = signalImage;
resultsValid = false;
}
public void setVoxelSize(double[] voxelSize)
{
this.voxelSize = voxelSize;
resultsValid = false;
}
public void setOrigin(double[] origin)
{
this.origin = origin;
resultsValid = false;
}
public void addMeasurement(Feature feature) {
whatToMeasure.add(feature);
resultsValid = false;
}
private void doFeatureExtaction() {
if (resultsValid) {
return;
}
if (labelMap.size() == 0)
{
return;
}
int numDimensions = labelMap.get(0).numDimensions();
results = new Hashtable<Feature, Measurement>();
//Iterator<Feature> iter = whatToMeasure.iterator();
//while(iter.hasNext())
//{
// Feature feature = iter.next();
for (Feature feature : whatToMeasure)
{
results.put(feature, new Measurement(feature, numDimensions, labelMap.size()));
}
// ------------------------
// reset
Interval[] boundingIntervals = OpsLabelAnalyser.getLabelsBoundingIntervals(labelMap);
numLabels = boundingIntervals.length;
double pixelArea = 1;
if (voxelSize != null && voxelSize.length > 1) {
pixelArea = voxelSize[0] * voxelSize[1];
}
double voxelVolume = 1;
if (voxelSize != null && voxelSize.length > 2) {
voxelVolume = voxelSize[0] * voxelSize[1] * voxelSize[2]; //(voxelSize.length > 2 ? voxelSize[2] : 1.0);
}
OpService ops = new Context(OpService.class, OpMatchingService.class).getService(OpService.class);
// Check Features for applicability
//iter = whatToMeasure.iterator();
//while(iter.hasNext())
//{
// Feature feature = iter.next();
for (Feature feature : whatToMeasure)
{
if (feature.getPreferredDimensionality() != numDimensions && feature.getPreferredDimensionality() > -1)
{
DebugHelper.print(this, "Warning: The feature \"" + feature.toString() + "\" is only applicable to images with " + feature.getPreferredDimensionality() + " dimensions. The given image has " + numDimensions + " dimensions!");
}
if (feature.needsSignalImage() && signalMap == null)
{
DebugHelper.print(this, "Warning: The feature \"" + feature.toString() + "\" is only applicable if a grey value image is given, but there is none! Use setSignalImage()!");
}
}
long meshGenerationDurationInMilliseconds = 0;
long polygonGenerationDurationInMilliseconds = 0;
long samplingDurationInMilliseconds = 0;
// ---------------------------------------------------------------------------------------
// Go through all labels and determine parameters (which were not determined so far)
for (int i = 0; i < numLabels; i++) {
//Regions.sample(region, img)
//RandomAccessibleInterval<? extends BooleanType<?>> map = labelMap.get(i);
IterableRegion<B> map = Regions.iterable(labelMap.get(i));
IterableInterval<F> sampledRegion = null;
Polygon2D polygon = null;
Mesh mesh = null;
long pixelCount = -1;
for (Feature feature : whatToMeasure)
{
DoubleType measure = new DoubleType();
//Feature feature = iter.next();
Measurement measurement = ((Measurement)results.get(feature));
long timeStamp;
if (feature.needsPolygon() && polygon == null)
{
timeStamp = System.currentTimeMillis();
polygon = ops.geom().contour(map, true);
polygon = transformPolygonInPhysicalSpace(polygon);
polygonGenerationDurationInMilliseconds += System.currentTimeMillis() - timeStamp;
//DebugHelper.print(this, "Polygon initialized");
}
if (feature.needsMesh() && mesh == null)
{
timeStamp = System.currentTimeMillis();
mesh = ops.geom().marchingCubes(map);
//mesh = transformMeshInPhysicalSpace(mesh);
meshGenerationDurationInMilliseconds += System.currentTimeMillis() - timeStamp;
//DebugHelper.print(this, "Mesh initialized");
}
if (feature.needsSignalImage() && signalMap != null && sampledRegion == null ) {
timeStamp = System.currentTimeMillis();
sampledRegion = Regions.sample(map, signalMap);
samplingDurationInMilliseconds += System.currentTimeMillis() - timeStamp;
}
if ((pixelCount == -1) && (feature == Feature.PIXELCOUNT || feature == Feature.AREA || feature == Feature.VOLUME))
{
pixelCount = (long)ops.geom().size(Regions.iterable(map)).get();
}
timeStamp = System.currentTimeMillis();
switch (feature)
{
case MEAN:
ops.stats().mean(measure, sampledRegion);
measurement.setValue(measure.get(), 0, i);
break;
case MIN:
F val = ops.stats().min(sampledRegion);
measurement.setValue(val.getRealDouble(), 0, i);
break;
case MAX:
F val1 = ops.stats().max(sampledRegion);
measurement.setValue(val1.getRealDouble(), 0, i);
break;
case MEDIAN:
ops.stats().median(measure, sampledRegion);
measurement.setValue(measure.get(), 0, i);
break;
case STD_DEV:
ops.stats().stdDev(measure, sampledRegion);
measurement.setValue(measure.get(), 0, i);
break;
case SUM:
ops.stats().sum(measure, sampledRegion);
measurement.setValue(measure.get(), 0, i);
break;
case CENTROID:
RealLocalizable point = ops.geom().centroid(Regions.iterable(map));
for (int d = 0; d < point.numDimensions(); d++)
{
measurement.setValue(point.getDoublePosition(d), d, i);
}
break;
case CENTROID_2D:
RealLocalizable point2 = ops.geom().centroid(polygon);
for (int d = 0; d < point2.numDimensions(); d++)
{
measurement.setValue(point2.getDoublePosition(d), d, i);
}
break;
//case CENTROID_3D:
// RealLocalizable point3 = ops.geom().centroid(mesh);
// for (int d = 0; d < point3.numDimensions(); d++)
// {
// measurement.setValue(point3.getDoublePosition(d), d, i);
// }
// break;
case BOUNDARY_SIZE_2D:
ops.geom().boundarySize(measure, polygon);
measurement.setValue(measure.get(), 0, i);
break;
//case BOUNDARY_SIZE_3D:
// ops.geom().boundarySize(measure, mesh);
// measurement.setValue(measure.get(), 0, i);
// break;
case SKEWNESS:
ops.stats().skewness(measure, sampledRegion);
measurement.setValue(measure.get(), 0, i);
break;
case KURTOSIS:
ops.stats().kurtosis(measure, sampledRegion);
measurement.setValue(measure.get(), 0, i);
break;
case PIXELCOUNT:
measurement.setValue(pixelCount, 0, i);
break;
case AREA:
measurement.setValue(pixelArea * pixelCount, 0, i) ;
break;
case VOLUME:
measurement.setValue(voxelVolume * pixelCount, 0, i);
break;
case CENTER_OF_MASS:
RealLocalizable position = ops.geom().centerOfGravity(sampledRegion);
for (int d = 0; d < position.numDimensions(); d++)
{
measurement.setValue(position.getDoublePosition(d), d, i);
}
break;
//case SURFACE_AREA:
// measurement.setValue(mesh.getSurfaceArea(), 0, i );
// break;
case MAJOR_AXIS2D:
ops.geom().majorAxis(measure, polygon);
measurement.setValue(measure.get(), 0, i);
break;
case MINOR_AXIS2D:
ops.geom().minorAxis(measure, polygon);
measurement.setValue(measure.get(), 0, i);
break;
//case BOUNDARY_PIXEL_COUNT3D:
// ops.geom().boundaryPixelCount(measure, mesh);
// measurement.setValue(measure.get(), 0, i);
// break;
//case COMPACTNESS_3D:
// ops.geom().compactness(measure, mesh);
// measurement.setValue(measure.get(), 0, i);
// break;
/*case ASPECT_RATIO2D:
DebugHelper.print(this, "Aspect ratio not implemented yet.");
break;
case EIGENVALUES2D:
cov = 20 11 / 00 00
11 02 00 00
lambda1/2 = (20 + 02) / 2 + (!) - sqrt((pow(4*11,2) + pow(20 - 02,2))/2)
https://de.wikipedia.org/wiki/Moment_(Bildverarbeitung)
case EIGENVALUES3D:
DoubleType moment00 = ops.imagemoments().moment00(sampledRegion);
DoubleType moment01 = ops.imagemoments().moment01(sampledRegion);
DoubleType moment10 = ops.imagemoments().moment10(sampledRegion);
DoubleType moment11 = ops.imagemoments().moment11(sampledRegion);
ops.imagemoments().
double[][] covXY = {
};
//ops.imagemoments().
//
//double[][] covXYZ = { { tim[2][0][0] / tim[0][0][0], tim[1][1][0] / tim[0][0][0], tim[1][0][1] / tim[0][0][0] },
// { tim[1][1][0] / tim[0][0][0], tim[0][2][0] / tim[0][0][0], tim[0][1][1] / tim[0][0][0] },
// { tim[1][0][1] / tim[0][0][0], tim[0][1][1] / tim[0][0][0], tim[0][0][2] / tim[0][0][0] } };
//Matrix covXYZMatrix = new Matrix(covXYZ);
//// DebugHelper.print(this, "mat:" + ArrayUtilities.toString(covXYZ));
//// DebugHelper.print(this, "EigenvalueDecomposition");
//EigenvalueDecomposition eigenvalueDecomposition = new EigenvalueDecomposition(covXYZMatrix);
//double[] eigenvalues = eigenvalueDecomposition.getRealEigenvalues();
//DebugHelper.print(this, "Eigen values not implemented yet.");
break;*/
case BOXIVITY2D:
measure = ops.geom().boxivity(polygon);
measurement.setValue(measure.get(), 0, i);
break;
case SOLIDITY2D:
measure = ops.geom().solidity(polygon);
measurement.setValue(measure.get(), 0, i);
break;
case ROUNDNESS2D:
measure = ops.geom().roundness(polygon);
measurement.setValue(measure.get(), 0, i);
break;
case BOUNDING_BOX2D:
RealInterval interval = getBoundingBox(polygon);
for (int d = 0; d < interval.numDimensions(); d++) {
measurement.setValue(interval.realMin(d), d, i);
measurement.setValue(interval.realMax(d), d + interval.numDimensions(), i);
}
break;
//case BOUNDING_BOX3D:
// RealInterval interval2 = getBoundingBox(mesh);
// for (int d = 0; d < interval2.numDimensions(); d++) {
// measurement.setValue(interval2.realMin(d), d, i);
// measurement.setValue(interval2.realMax(d), d + interval2.numDimensions(), i);
// }
// break;
/*
Polygon bb = ops.geom().boundingBox(polygon);
//.boundingbox(polygon);
@SuppressWarnings("unchecked")
List<RealLocalizable> vertices = (List<RealLocalizable>) bb.getVertices();
int count = 0;
for (int p = 0; p < vertices.size(); p++)
{
for (int d = 0; d < vertices.get(p).numDimensions(); d++)
{
measurement.setValue(vertices.get(p).getDoublePosition(d), d, count);
}
count++;
}
break;
*/
//case SPHERICITY:
// measure = ops.geom().sphericity(mesh);
// measurement.setValue(measure.get(), 0, i);
// break;
//case BOXIVITY3D:
// ops.geom().boxivity(measure, mesh);
// measurement.setValue(measure.get(), 0, i);
// break;
//case SOLIDITY3D:
// measure = ops.geom().solidity(mesh);
// measurement.setValue(measure.get(), 0, i);
// break;
case COARSENESS:
ops.tamura().coarseness(measure, map);
measurement.setValue(measure.get(), 0, i);
break;
case FERET:
Pair<RealLocalizable, RealLocalizable> minFeret = ops.geom().minimumFeret(polygon);
measurement.setValue(minFeret.getA().getDoublePosition(0), 0, i);
measurement.setValue(minFeret.getA().getDoublePosition(1), 1, i);
measurement.setValue(minFeret.getB().getDoublePosition(0), 2, i);
measurement.setValue(minFeret.getB().getDoublePosition(1), 3, i);
Pair<RealLocalizable, RealLocalizable> maxFeret = ops.geom().maximumFeret(polygon);
measurement.setValue(maxFeret.getA().getDoublePosition(0), 4, i);
measurement.setValue(maxFeret.getA().getDoublePosition(1), 5, i);
measurement.setValue(maxFeret.getB().getDoublePosition(0), 5, i);
measurement.setValue(maxFeret.getB().getDoublePosition(1), 7, i);
break;
//case FERET_ANGLE:
// ops.geom().feretsAngle(measure, polygon);
// measurement.setValue(measure.get(), 0, i);
// break;
case MAIN_ELONGATION_2D:
ops.geom().mainElongation(measure, polygon);
measurement.setValue(measure.get(), 0, i);
break;
case HARALICK_TEXTURE_ORIENTATION_2D:
measure = ops.haralick().textureHomogeneity(sampledRegion, 255, 2, MatrixOrientation2D.ANTIDIAGONAL);
measurement.setValue(measure.get(), 0, i);
break;
case HARALICK_TEXTURE_ORIENTATION_3D:
measure = ops.haralick().textureHomogeneity(sampledRegion, 255, 2, MatrixOrientation3D.ANTIDIAGONAL);
measurement.setValue(measure.get(), 0, i);
break;
default:
for (int d = 0; d < measurement.getColumnCount(); d++)
{
measurement.setValue(Double.NaN, d, i);
}
break;
}
measurement.timeTakenInMilliseconds += System.currentTimeMillis() - timeStamp;
}
/*
if (boundingBoxPosition != null) {
for (int d = 0; d < numDimensions; d++) {
boundingBoxPosition[d][i] = boundingIntervals[i].min(d);
boundingBoxPosition[d + numDimensions][i] = boundingIntervals[i].max(d);
}
}
*/
}
DebugHelper.print(this, "Generating polygons took " + polygonGenerationDurationInMilliseconds + " ms");
DebugHelper.print(this, "Generating meshes took " + meshGenerationDurationInMilliseconds + " ms");
DebugHelper.print(this, "Sampling the image took " + samplingDurationInMilliseconds + " ms");
for (Feature feature : results.keySet()) {
Measurement measurement = results.get(feature);
DebugHelper.print(this, "Measuring " + feature.toString() + " took " + measurement.timeTakenInMilliseconds + " ms");
}
resultsValid = true;
}
public double[] getFeatures(Feature measurement) {
return getFeatures(measurement, 0);
}
public int getFeaturesNumDimensions(Feature measurement) {
doFeatureExtaction();
return measurement.getSubParameterCount(labelMap.get(0).numDimensions());
}
public double[] getFeatures(Feature measurement, int dimension) {
doFeatureExtaction();
return results.get(measurement).getValues(dimension);
}
public int getNumLabels() {
doFeatureExtaction();
return numLabels;
}
/**
* Returns a histogram of all pixels in the image. In fact, the indexes of
* the histogram are the rounded (rather floored) pixel signal values.
*
* @param img
* ImgLib2 Img to be processed.
* @return returns an array containing (int)max grey value elements.
*/
public static <T extends RealType<T>> long[] getLabelsPixelCount(Img<T> img) {
Cursor<T> cursor = img.cursor();
int max = 0;
while (cursor.hasNext()) {
int val = (int) cursor.next().getRealFloat();
if (val > max) {
max = val;
}
}
long[] volumes = new long[max];
cursor.reset();
while (cursor.hasNext()) {
int val = (int) cursor.next().getRealFloat();
if (val > 0) {
volumes[val - 1]++;
}
}
return volumes;
}
/**
* give the center of mass of each labeled region the input image
*
* @param img
* a labeled image (e.g. pixel belonging to the same region have
* the same integer value)
* @return an array of the center of mass of each labeled region, the
* coordinate have 0 value if the region with a particular index is
* empty
*/
public static <T extends RealType<T>> float[][] getLabelsCenterOfMass(Img<T> img) {
Cursor<T> cursor = img.cursor();
// get the value of the maximum label
int max = 0;
while (cursor.hasNext()) {
int val = (int) cursor.next().getRealFloat();
if (val > max) {
max = val;
}
}
// sum the pixels per coordinates per label, also count the number of
// pixels per label
int nD = img.numDimensions();
float[][] posList = new float[nD][];
for (int i = 0; i < nD; i++) {
posList[i] = new float[max];
}
float[] volumes = new float[max];
cursor.reset();
while (cursor.hasNext()) {
int val = (int) cursor.next().getRealFloat();
if (val > 0) {
for (int i = 0; i < nD; i++) {
posList[i][val - 1] += cursor.getFloatPosition(i);
}
volumes[val - 1] += 1;
}
}
// average the pixel position per label
for (int i = 0; i < nD; i++) {
for (int j = 0; j < max; j++) {
posList[i][j] /= volumes[j];
}
}
return posList;
}
public static <T extends RealType<T>, B extends BooleanType<B>> Interval[] getLabelsBoundingIntervals(ArrayList<RandomAccessibleInterval<B>> labelMap) {
Interval[] intervals = new Interval[labelMap.size()];
for (int i = 0; i < intervals.length; i++)
{
intervals[i] = labelMap.get(i);
}
return intervals;
}
private RealInterval getBoundingBox(final Collection<? extends RealLocalizable> input) {
RealLocalizable[] arr = new RealLocalizable[input.size()];
input.toArray(arr);
return getBoundingBox(arr);
}
private RealInterval getBoundingBox(Polygon2D polygon2D) {
return Utilities.transformPolygon(polygon2D, new double[]{0,0}, new double[]{1,1});
}
private RealInterval getBoundingBox(final RealLocalizable[] input) {
if (input.length == 0)
{
return null;
}
int numDimensions = input[0].numDimensions();
double[] mins = new double[numDimensions];
double[] maxs = new double[numDimensions];
for (int d = 0; d < numDimensions; d++)
{
mins[d] = Double.POSITIVE_INFINITY;
maxs[d] = Double.NEGATIVE_INFINITY;
}
for (RealLocalizable rl : input) {
for (int d = 0; d < numDimensions; d++) {
if (rl.getDoublePosition(d) < mins[d]) {
mins[d] = rl.getDoublePosition(d);
}
if (rl.getDoublePosition(d) > maxs[d]) {
maxs[d] = rl.getDoublePosition(d);
}
}
}
double[] minmaxD = new double[numDimensions * 2];
for (int d = 0; d < numDimensions; d++)
{
minmaxD[d] = mins[d];
minmaxD[d + numDimensions] = maxs[d];
}
return Intervals.createMinMaxReal(minmaxD);
}
/*
private Mesh transformMeshInPhysicalSpace(Mesh mesh)
{
return Utilities.transformMesh(mesh, origin, voxelSize);
}
*/
private Polygon2D transformPolygonInPhysicalSpace(Polygon2D polygon)
{
return Utilities.transformPolygon(polygon, origin, voxelSize);
}
public Hashtable<Feature, Measurement> getResults() {
doFeatureExtaction();
return results;
}
}