From 8bc606c0f55fd1d54a8fc3ab07d8c43eef6e0978 Mon Sep 17 00:00:00 2001
From: Gabor Kovacs <gabor.kovacs@alleninstitute.org>
Date: Fri, 10 May 2024 16:51:37 -0700
Subject: [PATCH] Add scaling rounded by default to 4 decimal places in
 determining mipmaptransforms and mipmapresolutions.

---
 .../bdv/img/omezarr/XmlIoZarrImageLoader.java |  9 ++++---
 .../java/bdv/img/omezarr/ZarrImageLoader.java | 24 +++++++++++++++----
 2 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/src/main/java/bdv/img/omezarr/XmlIoZarrImageLoader.java b/src/main/java/bdv/img/omezarr/XmlIoZarrImageLoader.java
index f9dfcd4..a49961f 100644
--- a/src/main/java/bdv/img/omezarr/XmlIoZarrImageLoader.java
+++ b/src/main/java/bdv/img/omezarr/XmlIoZarrImageLoader.java
@@ -35,6 +35,7 @@
 import bdv.spimdata.XmlIoSpimDataMinimal;
 
 import java.io.File;
+import java.util.Arrays;
 import java.util.Map;
 import java.util.TreeMap;
 
@@ -110,15 +111,13 @@ public ZarrImageLoader fromXml(final Element elem, final File basePath,
     }
 
     public static void main(String[] args) throws SpimDataException {
-//        final String fn = "/home/gkovacs/data/davidf_zarr_dataset.xml";
-        final String fn = "/home/gabor.kovacs/data/davidf_zarr_dataset.xml";
-//        final String fn = "/home/gabor.kovacs/data/zarr_reader_test_2022-11-16/bdv_zarr_test3.xml";
-//        final String fn = "/Users/kgabor/data/davidf_zarr_dataset.xml";
+        final String fn = "/home/gkovacs/data/davidf_sample_dataset/davidf_zarr_dataset.xml";
+//        final String fn = "/home/gabor.kovacs/data/davidf_zarr_dataset.xml";
         final SpimDataMinimal spimData = new XmlIoSpimDataMinimal().load(fn);
         final ViewerImgLoader imgLoader = (ViewerImgLoader) spimData.getSequenceDescription().getImgLoader();
         final ViewerSetupImgLoader<?, ?> setupImgLoader = imgLoader.getSetupImgLoader(0);
         int d = setupImgLoader.getImage(0).numDimensions();
-        setupImgLoader.getMipmapResolutions();
+        System.out.println(Arrays.toString(setupImgLoader.getMipmapTransforms()));
 //        BigDataViewer.open(spimData, "BigDataViewer Zarr Example", new ProgressWriterConsole(), ViewerOptions.options());
         System.out.println("imgLoader = " + imgLoader);
         System.out.println("setupimgLoader = " + setupImgLoader);
diff --git a/src/main/java/bdv/img/omezarr/ZarrImageLoader.java b/src/main/java/bdv/img/omezarr/ZarrImageLoader.java
index 0c94a1a..388d411 100644
--- a/src/main/java/bdv/img/omezarr/ZarrImageLoader.java
+++ b/src/main/java/bdv/img/omezarr/ZarrImageLoader.java
@@ -69,6 +69,8 @@
  */
 public class ZarrImageLoader implements ViewerImgLoader, MultiResolutionImgLoader, Closeable {
 //    private final String zpath;
+    private static final int[] POWERS_OF_10 = {1, 10, 100, 1000, 10000, 100000,
+        1000000, 10000000, 100000000, 1000000000};
     private final SortedMap<ViewId, String> zgroups;
     private final AbstractSequenceDescription<?, ?, ?> seq;
     private final MultiscaleImage.ZarrKeyValueReaderBuilder zarrKeyValueReaderBuilder;
@@ -83,6 +85,13 @@ public class ZarrImageLoader implements ViewerImgLoader, MultiResolutionImgLoade
 
     private SortedMap<Integer, SetupImgLoader> setupImgLoaders;
 
+    public static double roundDouble(double s, int decimals) {
+        if (decimals < 0)
+            return s;
+        if (decimals >= POWERS_OF_10.length)
+            throw new IllegalArgumentException("Decimals out of range");
+        return Math.rint(s * POWERS_OF_10[decimals]) / (double) POWERS_OF_10[decimals];
+    }
 
     public ZarrImageLoader(final MultiscaleImage.ZarrKeyValueReaderBuilder zarrKeyValueReaderBuilder, final SortedMap<ViewId, String> zgroups, final AbstractSequenceDescription<?, ?, ?> sequenceDescription) {
         this.zgroups = zgroups;
@@ -296,6 +305,10 @@ private AffineTransform3D concatenateOMETransforms(final Multiscales mscales,
             return affT;
         }
 
+
+        private void calculateMipmapTransforms() {
+            calculateMipmapTransforms(4);
+        }
         /**
          * Create the 3D affine transformations and calculate the resolution factors
          * for the multi resolution display relative to the first resolution.
@@ -315,7 +328,7 @@ private AffineTransform3D concatenateOMETransforms(final Multiscales mscales,
          *
          * <p>Set "mipmaptransforms" and "mipmapresolutions".</p>
          */
-        private void calculateMipmapTransforms() {
+        private void calculateMipmapTransforms(int decimals) {
             // Assume everything is the same in case there are multiple timepoints
             final Multiscales mscale = tpMmultiscaleImages.get(0).getMultiscales();
             final int numResolutions = tpMmultiscaleImages.get(0).numResolutions();
@@ -335,15 +348,19 @@ private void calculateMipmapTransforms() {
             for (int j = 1; j < numResolutions; ++j) {
                 final AffineTransform3D affT = T0inv.copy();
                 affT.concatenate(mipmaptransforms[j]);
+                affT.set(roundDouble(affT.get(0, 0), decimals),0,0);
+                affT.set(roundDouble(affT.get(1, 1), decimals),1,1);
+                affT.set(roundDouble(affT.get(2, 2), decimals),2,2);
                 mipmaptransforms[j] = affT;
             }
 
             // Copy out the scaling from the transformations to the mipmapresolutions
             mipmapresolutions = new double[numResolutions][];
             for (int j = 0; j < numResolutions; ++j) {
-                mipmapresolutions[j] = new double[]{mipmaptransforms[j].get(0, 0),
+                mipmapresolutions[j] = new double[]{
+                        mipmaptransforms[j].get(0, 0),
                         mipmaptransforms[j].get(1, 1),
-                        mipmaptransforms[j].get(2, 2)};
+                        mipmaptransforms[j].get(2, 2) };
             }
 
             // Add pixel center correction
@@ -353,7 +370,6 @@ private void calculateMipmapTransforms() {
                         0.5 * (mipmapresolutions[j][1] - 1.),
                         0.5 * (mipmapresolutions[j][2] - 1.));
             }
-
         }
 
         @Override