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Calculate Mean, Min and Max for 5D Images
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Statistical tests that calculate the mean, min, and max for N5 files loaded into images.
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@AvocadoMoon
AvocadoMoon committed Jul 26, 2024
1 parent 6a0cf5f commit b20a80e
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Showing 2 changed files with 127 additions and 29 deletions.
31 changes: 26 additions & 5 deletions view-simulation-results/src/test/java/org/vcell/N5/N5DataSetFile.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,8 @@ public class N5DataSetFile {
public final double[][] histMin;
public final double[][] histAverage;
public final double totalArea;
public final double testDomainArea;
public N5DataSetFile(String uri, String[] variables, HashMap<Integer, String> mask, double[][] histMax, double[][] histMin, double[][] histAverage, double totalArea, double testDomainArea){
public final double[] testDomainArea;
public N5DataSetFile(String uri, String[] variables, HashMap<Integer, String> mask, double[][] histMax, double[][] histMin, double[][] histAverage, double totalArea, double[] testDomainArea){
this.uri = uri;
this.histMax = histMax;
this.histMin = histMin;
Expand All @@ -23,7 +23,7 @@ public N5DataSetFile(String uri, String[] variables, HashMap<Integer, String> ma
}

public static N5DataSetFile[] alphaTestFiles(){
N5DataSetFile frapSimulationResultsMasked = new N5DataSetFile("https://vcell-dev.cam.uchc.edu/n5Data/ezequiel23/c607b779af9481f.n5?dataSetName=6262029569",
N5DataSetFile frapSimulationResultsMasked = new N5DataSetFile("https://vcell-dev.cam.uchc.edu/n5Data/ezequiel23/c607b779af9481f.n5?dataSetName=4457702594",
new String[]{"Dex"},
new HashMap<Integer, String>(){{put(1, "Cyt"); put(0, "Ec");}},
new double[][]{{10.0, 9.990392675155721, 9.83580092714469, 9.520539931524715, 9.162150060086567, 8.82335160436397, 8.523689113752786, 8.265381795870683, 8.044751960699015, 7.856809648125466,
Expand All @@ -35,9 +35,30 @@ public static N5DataSetFile[] alphaTestFiles(){
6.728509585652239, 6.7285095856523345, 6.728509585652324, 6.72850958565233, 6.728509585652335, 6.728509585652381, 6.728509585652381, 6.728509585652362, 6.728509585652365,
6.728509585652356, 6.7285095856523185, 6.728509585652278, 6.7285095856522865, 6.728509585652241, 6.728509585652113, 6.728509585652124, 6.7285095856521355, 6.728509585652127, 6.728509585652108}},
484,
314.64);
new double[]{0,314.64});

return new N5DataSetFile[]{frapSimulationResultsMasked};
N5DataSetFile anns5DTIRFSimulation = new N5DataSetFile("https://vcell-dev.cam.uchc.edu/n5Data/ezequiel23/a530ce83268de2a.n5?dataSetName=3340371272",
new String[]{"Dark", "Flour"},
new HashMap<Integer, String>(){{put(0, "ec"); put(1, "cytosol"); put(2, "Nucleus");}},
new double[][]{
{2.2250738585072014E-308, 2.2250738585072014E-308, 2.2250738585072014E-308, 3.52810806343277, 3.67238125879494,
0.37504412562962713, 0.1941393552238283},
{10.0, 10.0, 10.0, 10.0, 10.0, 10.0, 10.0}
},
new double[][]{
{0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{10.0, 10.0, 10.0, 6.471891936567229, 6.32761874120506, 9.624955874370375, 9.805860644776171}
},
new double[][]{
{0.0, 0.0, 0.0, 0.007280282509686344, 0.013997372023832945, 0.013997372023832947, 0.013997372023832949},
{9.999999999999494, 9.999999999999494, 9.999999999999494, 9.992719717489994, 9.986002627975711,
9.98600262797569, 9.986002627975722}
},
143300,
new double[]{0, 14891, 3697}
);

return new N5DataSetFile[]{frapSimulationResultsMasked, anns5DTIRFSimulation};
}

}
125 changes: 101 additions & 24 deletions view-simulation-results/src/test/java/org/vcell/N5/N5ImageHandlerTest.java
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Original file line number Diff line number Diff line change
@@ -1,17 +1,21 @@
package org.vcell.N5;

import com.google.gson.internal.LinkedTreeMap;
import ij.ImagePlus;
import ij.io.Opener;
import ij.plugin.Duplicator;
import ij.plugin.ImageCalculator;
import ij.process.ImageProcessor;
import org.junit.*;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;

import java.io.File;
import java.io.IOException;
import java.net.URISyntaxException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Map;


/*
Expand Down Expand Up @@ -86,9 +90,13 @@ public void testS3AlphaInstanceLoadedIntoMemory() throws IOException {
SimResultsLoader simResultsLoader = new SimResultsLoader(n5DataSetFile.uri, "");
simResultsLoader.createS3Client();
ImagePlus imagePlus = simResultsLoader.getImgPlusFromN5File();
alphaStatsTest(new Duplicator().run(imagePlus), n5DataSetFile, stats.HISTMAX);
alphaStatsTest(new Duplicator().run(imagePlus), n5DataSetFile, stats.HISTMIN);
alphaStatsTest(new Duplicator().run(imagePlus), n5DataSetFile, stats.HISTAVERAGE);
ImagePlus inMemory = new Duplicator().run(imagePlus);
for (Object property : imagePlus.getProperties().keySet()){
inMemory.setProperty((String) property, imagePlus.getProperty((String) property));
}
alphaStatsTest(inMemory, n5DataSetFile, stats.HISTMAX);
alphaStatsTest(inMemory, n5DataSetFile, stats.HISTMIN);
alphaStatsTest(inMemory, n5DataSetFile, stats.HISTAVERAGE);
}
}

Expand All @@ -105,35 +113,100 @@ public void testUnits() throws IOException {
ImagePlus imagePlus = simResultsLoader.getImgPlusFromN5File();
double areaOfPixel = imagePlus.getCalibration().getX(1) * imagePlus.getCalibration().getY(1);
double totalArea = areaOfPixel * imagePlus.getWidth() * imagePlus.getHeight();

boolean threeD = imagePlus.getNSlices() > 1;
if (threeD){
areaOfPixel *= imagePlus.getCalibration().getZ(1);
totalArea *= imagePlus.getDimensions()[3];
}
Assert.assertEquals(n5DataSetFile.totalArea, totalArea, 0.0000001);

totalArea = 0;
imagePlus.setPosition(imagePlus.getNChannels(), 1, 1);
ImageProcessor imageProcessor = imagePlus.getProcessor();

PixelCalculations pixelCalculations = ((w, h, w1, h1) -> {
int inBounds = (0 <= w1) && (w1 < imagePlus.getWidth()) && (0 <= h1) && (h1 < imagePlus.getHeight()) ? 2 : 1;
if (inBounds == 2 && imageProcessor.getf(w1, h1) != imageProcessor.getf(w, h)){
boolean edgeOfDomain = (inBounds == 2) &&
(imageProcessor.getf(w1, h1) != imageProcessor.getf(w, h));
if (edgeOfDomain){
return inBounds;
}
return 1;
});
for (int h = 0; h < imagePlus.getHeight(); h++){
for (int w = 0; w < imagePlus.getWidth(); w++){
double sum = pixelCalculations.grabEdge(w, h, w, h -1) *

for(int domain: n5DataSetFile.mask.keySet()){
totalArea = 0;
for (int h = 0; h < imagePlus.getHeight(); h++){
for (int w = 0; w < imagePlus.getWidth(); w++){
double sum = pixelCalculations.grabEdge(w, h, w, h -1) *
pixelCalculations.grabEdge(w, h, w, h + 1) *
pixelCalculations.grabEdge(w, h,w + 1, h) *
pixelCalculations.grabEdge(w, h,w -1, h);
if (imageProcessor.getf(w, h) != 1 && sum > 1){
totalArea += (areaOfPixel / sum);
if (imageProcessor.getf(w,h) != domain && sum > 1 && domain != 0){
totalArea += (areaOfPixel / sum);
}
if (imageProcessor.getf(w, h) == domain && domain != 0){
totalArea += areaOfPixel;
}
}
}
Assert.assertEquals(n5DataSetFile.testDomainArea[domain], totalArea, n5DataSetFile.testDomainArea[domain] * 0.013);
}
}
}

private double alphaStatsThreeD(ImagePlus imagePlus, stats testType, int channel, int frame){
double experimentValue = Double.NaN;
for (int z = 1; z <= imagePlus.getNSlices(); z++){
imagePlus.setPosition(channel, z, frame);
double currentValue;
switch (testType){
case HISTMAX:
setImageMask(imagePlus);
currentValue = imagePlus.getStatistics().max;
if (currentValue == -Double.MAX_VALUE){
currentValue = 0;
}
if (imageProcessor.getf(w, h) == 1){
totalArea += areaOfPixel;
if (Double.isNaN(experimentValue) || experimentValue < currentValue){
experimentValue = currentValue;
}
break;
case HISTMIN:
setImageMask(imagePlus);
currentValue = imagePlus.getStatistics().min;
if (Double.isNaN(experimentValue) || experimentValue > currentValue){
experimentValue = currentValue;
}
break;
case HISTAVERAGE:
experimentValue = average3D(imagePlus);
}
if (testType.equals(stats.HISTAVERAGE)){
break;
}
}
return experimentValue;
}

private double average3D(ImagePlus imagePlus){
double total = 0;
double voxelVolume = imagePlus.getCalibration().pixelHeight * imagePlus.getCalibration().pixelWidth * imagePlus.getCalibration().pixelDepth;
double totalVolume = 0;
for (int z = 1; z < imagePlus.getNSlices(); z++){
imagePlus.setPosition(imagePlus.getChannel(), z, imagePlus.getFrame());
setImageMask(imagePlus);
ImageProcessor imageProcessor = imagePlus.getProcessor();
for (int x = 0; x < imagePlus.getWidth(); x++){
for (int y = 0; y < imagePlus.getHeight(); y++){
double pixelValue = imageProcessor.getValue(x, y);
if (!Double.isNaN(pixelValue)){
total += (pixelValue * voxelVolume);
totalVolume += voxelVolume;
}
}
}
Assert.assertEquals(n5DataSetFile.testDomainArea, totalArea, n5DataSetFile.testDomainArea * 0.013);

}
return (total / totalVolume );
}

public void alphaStatsTest(ImagePlus imagePlus, N5DataSetFile n5DataSetFile, stats testType){
Expand All @@ -148,25 +221,29 @@ public void alphaStatsTest(ImagePlus imagePlus, N5DataSetFile n5DataSetFile, sta
case HISTAVERAGE:
controlData = n5DataSetFile.histAverage;
}
for(int k = 0; k < controlData.length; k++){
for (int i = 0; i < controlData[k].length; i++){
imagePlus.setPosition(k + 1, 1, i + 1); //frame position seems to start at 1
boolean threeD = imagePlus.getNSlices() > 1;
for(int channel = 1; channel <= controlData.length; channel++){
for (int frame = 1; frame <= controlData[channel - 1].length; frame++){
imagePlus.setPosition(channel, 1, frame); //frame position seems to start at 1
double experimentalData = 0;
switch (testType){
case HISTMAX:
experimentalData = imagePlus.getStatistics().histMax;
experimentalData = threeD ? alphaStatsThreeD(imagePlus, testType, channel, frame) :
imagePlus.getStatistics().max;
break;
case HISTMIN:
setImageMask(imagePlus);
experimentalData = imagePlus.getStatistics().min;
experimentalData = threeD ? alphaStatsThreeD(imagePlus, testType, channel, frame) :
imagePlus.getStatistics().min;
break;
case HISTAVERAGE:
setImageMask(imagePlus);
experimentalData = imagePlus.getStatistics().mean;
experimentalData = threeD ? alphaStatsThreeD(imagePlus, testType, channel, frame) :
imagePlus.getStatistics().mean;
}
Assert.assertEquals("Channel: " + k + " Time: " + i + " Stat: " + testType +
"\n Experiment Value: " + experimentalData + " Control Value: " + controlData[k][i]
,0.0, experimentalData - controlData[k][i], 0.000001);
Assert.assertEquals("Channel: " + channel + " Time: " + frame + " Stat: " + testType +
"\n Experiment Value: " + experimentalData + " Control Value: " + controlData[channel - 1][frame - 1]
,0.0, experimentalData - controlData[channel - 1][frame - 1], 0.0001);
}
}
}
Expand Down

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