diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 737e5e8..30e4922 100644 --- 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 index 9aef7e0..a423416 100644 --- a/build.gradle +++ b/build.gradle @@ -23,12 +23,6 @@ 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' } @@ -36,11 +30,11 @@ repositories { 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 index 9665304..4099124 100755 --- a/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java +++ b/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java @@ -1150,8 +1150,22 @@ 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