Test The Units/Pixel

There is a 1.3% error because of the way VCell handles the "atomic" unit of pixels (in VCell they aren't exactly atomic). It can be calculated to 0%, but this is an initial start.

view-simulation-results/src/main/java/org/vcell/N5/SimResultsLoader.java

@@ -11,13 +11,15 @@
 import com.amazonaws.services.s3.AmazonS3URI;
 import com.google.gson.GsonBuilder;
 import ij.ImagePlus;
+import ij.measure.Calibration;
 import ij.plugin.Duplicator;
 import net.imglib2.cache.img.CachedCellImg;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.type.numeric.real.DoubleType;
 import org.apache.http.conn.socket.ConnectionSocketFactory;
 import org.apache.http.conn.ssl.TrustSelfSignedStrategy;
 import org.apache.http.ssl.SSLContexts;
+import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.N5FSReader;
 import org.janelia.saalfeldlab.n5.N5KeyValueReader;
 import org.janelia.saalfeldlab.n5.N5Reader;
@@ -174,6 +176,7 @@ public ImagePlus getImgPlusFromN5File() throws IOException {
         ImagePlus imagePlus = ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>) N5Utils.open(n5AmazonS3Reader, dataSetChosen), userSetFileName);
         long end = System.currentTimeMillis();
         logger.debug("Read N5 File " + userSetFileName + " Into ImageJ taking: " + ((end - start) / 1000) + "s");
+        setUnits(n5AmazonS3Reader, imagePlus);
         return imagePlus;
     }
 
@@ -189,6 +192,20 @@ public void setURI(URI uri){
         }
     }
 
+    private void setUnits(N5Reader n5Reader, ImagePlus imagePlus){
+        try{
+            double pixelWidth = n5Reader.getAttribute(dataSetChosen, "pixelWidth", double.class);
+            double pixelHeight = n5Reader.getAttribute(dataSetChosen, "pixelHeight", double.class);
+            String unit = n5Reader.getAttribute(dataSetChosen, "unit", String.class);
+            imagePlus.getCalibration().setUnit(unit);
+            imagePlus.getCalibration().pixelHeight = pixelHeight;
+            imagePlus.getCalibration().pixelWidth = pixelWidth;
+        }
+        catch (N5Exception n5Exception){
+            logger.error("Can't read units.");
+        }
+    }
+
     public void setDataSetChosen(String dataSetChosen) {
         this.dataSetChosen = dataSetChosen;
     }

view-simulation-results/src/test/java/org/vcell/N5/N5DataSetFile.java

@@ -3,19 +3,23 @@
 import java.util.HashMap;
 
 public class N5DataSetFile {
-    public String uri;
-    public String[] variables;
-    public HashMap<Integer, String> mask;
-    public double[][] histMax; //channel(variable), frame for [][]
-    public double[][] histMin;
-    public double[][] histAverage;
-    public N5DataSetFile(String uri, String[] variables, HashMap<Integer, String> mask, double[][] histMax, double[][] histMin, double[][] histAverage){
+    public final String uri;
+    public final String[] variables;
+    public final HashMap<Integer, String> mask;
+    public final double[][] histMax; //channel(variable), frame for [][]
+    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){
         this.uri = uri;
         this.histMax = histMax;
         this.histMin = histMin;
         this.histAverage = histAverage;
         this.variables = variables;
         this.mask = mask;
+        this.totalArea = totalArea;
+        this.testDomainArea = testDomainArea;
     }
 
     public static N5DataSetFile[] alphaTestFiles(){
@@ -29,7 +33,9 @@ public static N5DataSetFile[] alphaTestFiles(){
                         4.441933641025697, 4.752525652114409, 5.021489447662615, 5.25417298783172, 5.4553370523518065, 5.62917275251317, 5.7793451286004585, 5.909046810912881, 6.0210510711120975}},
                 new double[][]{{
                         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}});
+                        6.728509585652356, 6.7285095856523185, 6.728509585652278, 6.7285095856522865, 6.728509585652241, 6.728509585652113, 6.728509585652124, 6.7285095856521355, 6.728509585652127, 6.728509585652108}},
+                484,
+                314.64);
 
         return new N5DataSetFile[]{frapSimulationResultsMasked};
     }

view-simulation-results/src/test/java/org/vcell/N5/N5ImageHandlerTest.java

@@ -1,13 +1,9 @@
 package org.vcell.N5;
 
-import com.amazonaws.regions.Regions;
 import ij.ImagePlus;
 import ij.io.Opener;
 import ij.plugin.Duplicator;
 import ij.plugin.ImageCalculator;
-import ij.plugin.Thresholder;
-import ij.process.Blitter;
-import ij.process.ByteProcessor;
 import ij.process.ImageProcessor;
 import org.junit.*;
 
@@ -16,7 +12,6 @@
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.HashMap;
 
 
 /*
@@ -128,6 +123,50 @@ public void testS3AlphaInstanceLoadedIntoMemory() throws IOException {
         }
     }
 
+    interface PixelCalculations {
+        int grabEdge(int w, int h, int w1, int h1);
+    }
+
+    @Test
+    public void testUnits() throws IOException {
+        N5DataSetFile[] n5DataSetFiles = N5DataSetFile.alphaTestFiles();
+        for (N5DataSetFile n5DataSetFile: n5DataSetFiles){
+            SimResultsLoader simResultsLoader = new SimResultsLoader(n5DataSetFile.uri, "");
+            simResultsLoader.createS3Client();
+            ImagePlus imagePlus = simResultsLoader.getImgPlusFromN5File();
+            double areaOfPixel = imagePlus.getCalibration().getX(1) * imagePlus.getCalibration().getY(1);
+            double totalArea = areaOfPixel * imagePlus.getWidth() * imagePlus.getHeight();
+            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)){
+                    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) *
+                                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) == 1){
+                        totalArea += areaOfPixel;
+                    }
+                }
+            }
+            Assert.assertEquals(n5DataSetFile.testDomainArea, totalArea, n5DataSetFile.testDomainArea * 0.013);
+        }
+    }
+
     public void alphaStatsTest(ImagePlus imagePlus, N5DataSetFile n5DataSetFile, stats testType){
         double[][] controlData = {{}};
         switch (testType){