Merge pull request #110 from melissalinkert/jzarr-switch

Update to new jzarr 0.4.2
glencoesoftware · Nov 16, 2023 · 51d15e2 · 51d15e2
2 parents 4d2a79f + 6d6c558
commit 51d15e2
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Showing 3 changed files with 23 additions and 15 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -23,7 +23,6 @@ jobs:
         with:
           java-version: ${{ matrix.java }}
           distribution: 'zulu'
-          cache: "gradle"
       - name: Install libraries
         run: |
           sudo apt-get install -y libblosc1

diff --git a/build.gradle b/build.gradle
@@ -23,24 +23,18 @@ repositories {
     maven {
         url 'https://repo.glencoesoftware.com/repository/bioformats2raw2ometiff/'
     }
-    maven {
-        url 'https://nexus.senbox.net/nexus/content/groups/public'
-    }
-    maven {
-        url 'https://repo.glencoesoftware.com/repository/jzarr-snapshots'
-    }
     maven {
         url 'https://maven.scijava.org/content/groups/public'
     }
 }
 
 dependencies {
     implementation 'net.java.dev.jna:jna:5.10.0'
-    implementation 'com.bc.zarr:jzarr:0.3.5'
+    implementation 'dev.zarr:jzarr:0.4.2'
     implementation 'info.picocli:picocli:4.2.0'
     implementation 'me.tongfei:progressbar:0.9.0'
     implementation 'ome:formats-bsd:7.0.0'
-    implementation 'com.glencoesoftware:bioformats2raw:0.7.0'
+    implementation 'com.glencoesoftware:bioformats2raw:0.8.0-rc1'
     implementation 'org.json:json:20230227'
     implementation group: 'ch.qos.logback', name: 'logback-classic', version: '1.3.4'
     implementation group: 'ch.qos.logback', name: 'logback-core', version: '1.3.4'

diff --git a/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java b/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
@@ -1150,20 +1150,35 @@ public void convertToPyramid()
     throws FormatException, IOException,
       InterruptedException, DependencyException
   {
-    for (PyramidSeries s : series) {
-      convertPyramid(s);
+    long tileCount = 0;
+    int[] seriesTileCount = new int[series.size()];
+    for (int s=0; s<series.size(); s++) {
+      PyramidSeries ps = series.get(s);
+      seriesTileCount[s] = 0;
+      for (int resolution=0; resolution<ps.numberOfResolutions; resolution++) {
+        ResolutionDescriptor descriptor = ps.resolutions.get(resolution);
+        int resTiles = descriptor.numberOfTilesY * descriptor.numberOfTilesX;
+        seriesTileCount[s] += resTiles * ps.planeCount;
+      }
+      tileCount += seriesTileCount[s];
+    }
+    getProgressListener().notifyStart(series.size(), tileCount);
+
+    for (int s=0; s<series.size(); s++) {
+      convertPyramid(series.get(s), seriesTileCount[s]);
     }
     StopWatch t0 = new Slf4JStopWatch("writeIFDs");
     writeIFDs();
     t0.stop();
     binaryOnly = null;
   }
 
-  private void convertPyramid(PyramidSeries s)
+  private void convertPyramid(PyramidSeries s, int totalTileCount)
     throws FormatException, IOException,
       InterruptedException, DependencyException
   {
-    getProgressListener().notifySeriesStart(s.index);
+    getProgressListener().notifySeriesStart(
+      s.index, s.numberOfResolutions, totalTileCount);
 
     // convert every resolution in the pyramid
     s.ifds = new IFDList[s.numberOfResolutions];
@@ -1185,9 +1200,9 @@ private void convertPyramid(PyramidSeries s)
         LOG.info("Converting resolution #{}", resolution);
         ResolutionDescriptor descriptor = s.resolutions.get(resolution);
         int tileCount = descriptor.numberOfTilesY * descriptor.numberOfTilesX;
-        int totalTileCount = tileCount * s.planeCount;
+        int resTileCount = tileCount * s.planeCount;
 
-        getProgressListener().notifyResolutionStart(resolution, totalTileCount);
+        getProgressListener().notifyResolutionStart(resolution, resTileCount);
 
         int plane = 0;
         for (int t=0; t<s.t; t++) {