Merge pull request #199 from melissalinkert/opencv-type-error

Throw an informative exception if OpenCV is used to downsample int8/int32
glencoesoftware · May 19, 2023 · 63bae15 · 63bae15
2 parents 637808c + 39fffc4
commit 63bae15
Show file tree

Hide file tree

Showing 2 changed files with 41 additions and 0 deletions.
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -1883,6 +1883,15 @@ public void saveResolutions(int series)
       readers.put(workingReader);
     }
 
+    if ((pixelType == FormatTools.INT8 || pixelType == FormatTools.INT32) &&
+      getDownsampling() != Downsampling.SIMPLE && resolutions > 0)
+    {
+      String type = FormatTools.getPixelTypeString(pixelType);
+      throw new UnsupportedOperationException(
+        "OpenCV does not support downsampling " + type + " data. " +
+        "See https://github.com/opencv/opencv/issues/7862");
+    }
+
     LOGGER.info(
       "Preparing to write pyramid sizeX {} (tileWidth: {}) " +
       "sizeY {} (tileWidth: {}) sizeZ {} (tileDepth: {}) imageCount {}",

diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -972,6 +972,38 @@ public void testDownsampleTypes(Downsampling type) throws IOException {
     }
   }
 
+  /**
+   * Make sure an informative exception is thrown when trying to use
+   * OpenCV to downsample int8 data.
+   * See https://github.com/opencv/opencv/issues/7862
+   */
+  @Test
+  public void testUnsupportedOpenCVType() throws Exception {
+    input = fake("pixelType", "int8");
+    assertThrows(ExecutionException.class, () -> {
+      assertTool("--downsample-type", "LINEAR");
+    });
+  }
+
+  /**
+   * Make sure an informative exception is thrown when trying to use
+   * OpenCV to downsample int32 data. Uses the API instead of
+   * command line arguments.
+   * See https://github.com/opencv/opencv/issues/7862
+   */
+  @Test
+  public void testUnsupportedOpenCVTypeAPI() throws Exception {
+    input = fake("pixelType", "int32");
+    Converter apiConverter = new Converter();
+    apiConverter.setInputPath(input.toString());
+    apiConverter.setOutputPath(output.toString());
+    apiConverter.setDownsampling(Downsampling.AREA);
+
+    assertThrows(UnsupportedOperationException.class, () -> {
+      apiConverter.call();
+    });
+  }
+
   /**
    * Test that nested storage works equivalently.
    *