Test Normalization of 2D Images

virtualcell · Nov 1, 2024 · 115fecf · 115fecf
1 parent 5ce1235
commit 115fecf
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Showing 2 changed files with 27 additions and 2 deletions.
diff --git a/view-simulation-results/src/main/java/org/vcell/N5/analysis/DataReduction.java b/view-simulation-results/src/main/java/org/vcell/N5/analysis/DataReduction.java
@@ -129,7 +129,7 @@ private void addValuesToCSVMatrix(ReducedData reducedData){
                 imagePlus.setT(k);
                 normal += imagePlus.getProcessor().getStatistics().mean;
             }
-            normal = normal / (endT - startT);
+            normal = normal / (endT - startT + 1); // inclusive of final point
             return normal;
         } else {
             return Double.MIN_NORMAL;

diff --git a/view-simulation-results/src/test/java/org/vcell/N5/analysis/DataReductionTest.java b/view-simulation-results/src/test/java/org/vcell/N5/analysis/DataReductionTest.java
@@ -44,10 +44,15 @@ public static void init(){
     private void compareExpectedCalculations(ImagePlus imagePlus, ArrayList<Roi> roiList, double[][] expectedResults){
         DataReductionGUI.DataReductionSubmission dataReductionSubmission = new DataReductionGUI.DataReductionSubmission(
                 false, roiList, roiList, imagePlus,4, null);
+        compareExpectedCalculations(imagePlus, roiList, expectedResults, dataReductionSubmission, Double.MIN_VALUE);
+    }
+
+    private void compareExpectedCalculations(ImagePlus imagePlus, ArrayList<Roi> roiList, double[][] expectedResults,
+                                             DataReductionGUI.DataReductionSubmission dataReductionSubmission, double normValue){
         DataReduction dataReduction = new DataReduction(dataReductionSubmission);
         DataReduction.ReducedData reducedData = new DataReduction.ReducedData(imagePlus.getNFrames() * imagePlus.getNSlices(),
                 imagePlus.getNChannels() * roiList.size(), DataReductionGUI.AvailableMeasurements.AVERAGE);
-        DataReduction.ReducedData result = dataReduction.calculateMean(imagePlus, roiList, Double.MIN_VALUE, reducedData);
+        DataReduction.ReducedData result = dataReduction.calculateMean(imagePlus, roiList, normValue, reducedData);
         for (int r = 0; r < expectedResults.length; r++){
             for (int c = 0; c < expectedResults[r].length; c++){
                 Assert.assertEquals(expectedResults[r][c], result.data[r][c], 0.0009);
@@ -74,4 +79,24 @@ public void testMean3DCalculation(){
         ArrayList<Roi> roiList = new ArrayList<Roi>(){{add(mitosisROI);}};
         compareExpectedCalculations(mitosis, roiList, threeDMeans);
     }
+
+    @Test
+    public void testMeanAndNormalization2DCalculation(){
+        SimResultsLoader simResultsLoader = new SimResultsLoader("https://vcell.cam.uchc.edu/n5Data/ezequiel23/ddf7f4f0c77dffd.n5?dataSetName=4864003788", "test1");
+        ImagePlus labResultImage2D = simResultsLoader.getImagePlus();
+        double mean = labResultImage2D.getStatistics().mean; // the normal for a single frame normalization
+        double[][] normalizedValues = new double[labMeans2D.length][labMeans2D[0].length];
+        for (int r = 0; r < labMeans2D.length; r++){
+            for (int c =0; c < labMeans2D[0].length; c++){
+                normalizedValues[r][c] = labMeans2D[r][c] / mean;
+            }
+        }
+        Roi labRoi = RoiDecoder.open(getTestResourceFiles("ROIs/Lab ROI.roi").getAbsolutePath());
+        Roi simROI = RoiDecoder.open(getTestResourceFiles("ROIs/Sim ROI.roi").getAbsolutePath());
+        ArrayList<Roi> roiList = new ArrayList<Roi>(){{add(labRoi); add(simROI);}};
+        DataReductionGUI.DataReductionSubmission dataReductionSubmission = new DataReductionGUI.DataReductionSubmission(
+                true, roiList, roiList, labResultImage2D, 1, 1, 1, 1,4, null);
+
+        compareExpectedCalculations(labResultImage2D, roiList, normalizedValues, dataReductionSubmission, mean);
+    }
 }