Allow individual label images to be converted

config/checkstyle/checkstyle.xml

@@ -37,7 +37,6 @@
 
     <!-- Checks for Size Violations.                    -->
     <!-- See https://checkstyle.org/config_sizes.html -->
-    <module name="FileLength"/>
     <module name="LineLength">
       <property name="fileExtensions" value="java"/>
     </module>

src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java

@@ -40,8 +40,10 @@
 import loci.common.services.ServiceFactory;
 import loci.formats.FormatException;
 import loci.formats.FormatTools;
+import loci.formats.ImageReader;
 import loci.formats.MetadataTools;
 import loci.formats.codec.CodecOptions;
+import loci.formats.meta.IMetadata;
 import loci.formats.ome.OMEPyramidStore;
 import loci.formats.services.OMEXMLService;
 import loci.formats.tiff.IFD;
@@ -138,6 +140,8 @@ public class PyramidFromDirectoryWriter implements Callable<Void> {
   boolean splitBySeries = false;
   boolean splitByPlane = false;
 
+  String imageFile = null;
+
   private ZarrGroup reader = null;
 
   /** Writer metadata. */
@@ -352,6 +356,25 @@ public void setSplitSinglePlaneTIFFs(boolean split) {
     splitByPlane = split;
   }
 
+  /**
+   * Set an alternate file to use for obtaining OME-XML metadata
+   * If the expected "OME/METADATA.ome.xml" file is not found, then
+   * the provided file will be read using Bio-Formats.
+   * This file is expected to be an original image file, with dimensions
+   * that match the input Zarr.
+   *
+   * @param file path to image file
+   */
+  @Option(
+      names = {"--image-file", "-f"},
+      description =
+        "Image file from which read metadata, if METADATA.ome.xml not found",
+      defaultValue = ""
+  )
+  public void setImageFile(String file) {
+    imageFile = file;
+  }
+
   /**
    * Set the maximum number of workers to use for converting tiles.
    * Defaults to 4 or the number of detected CPUs, whichever is smaller.
@@ -483,6 +506,14 @@ public boolean getSplitSinglePlaneTIFFs() {
     return splitByPlane;
   }
 
+  /**
+   * @return path to image file from which metadata is read,
+   *         if METADATA.ome.xml not present
+   */
+  public String getImageFile() {
+    return imageFile;
+  }
+
   /**
    * @return maximum number of worker threads
    */
@@ -931,6 +962,17 @@ else if (layoutVersion != 3) {
       if (omexml != null && Files.exists(omexml)) {
         xml = DataTools.readFile(omexml.toString());
       }
+      else if (imageFile != null && !imageFile.isEmpty()) {
+        try (ImageReader imageReader = new ImageReader()) {
+          IMetadata srcMetadata = service.createOMEXMLMetadata();
+          imageReader.setMetadataStore(srcMetadata);
+          imageReader.setId(imageFile);
+          xml = service.getOMEXML(srcMetadata);
+        }
+        catch (ServiceException e) {
+          throw new FormatException("Could not get OME-XML from image file", e);
+        }
+      }
       try {
         if (xml != null) {
           metadata = (OMEPyramidStore) service.createOMEXMLMetadata(xml);
@@ -957,8 +999,11 @@ else if (layoutVersion != 3) {
 
     int seriesCount = getSeriesCount();
 
+    boolean flatHierarchy = false;
     if (seriesCount < 1) {
-      throw new FormatException("Found no images to convert.  Corrupt input?");
+      LOG.warn("Series missing from hierarchy, assuming single pyramid");
+      seriesCount = 1;
+      flatHierarchy = true;
     }
 
     if (seriesCount > 1 && legacy) {
@@ -991,6 +1036,18 @@ else if (layoutVersion != 3) {
         PyramidSeries s = new PyramidSeries();
         s.index = seriesIndex;
         s.path = String.valueOf(s.index);
+        if (flatHierarchy) {
+          try {
+            // if we're skipping the series in the hierarchy,
+            // check that there is actually an array at the resolution level
+            ZarrArray.open(inputDirectory.resolve("0"));
+            s.path = "";
+          }
+          catch (IOException e) {
+            throw new FormatException(
+              "Could not handle series index " + s.index + ". Corrupt input?");
+          }
+        }
         series.set(s.index, s);
       }
     }
@@ -1004,9 +1061,26 @@ else if (layoutVersion != 3) {
       }
       findNumberOfResolutions(s);
 
+      int x = metadata.getPixelsSizeX(seriesIndex).getNumberValue().intValue();
+      int y = metadata.getPixelsSizeY(seriesIndex).getNumberValue().intValue();
+
       s.z = metadata.getPixelsSizeZ(seriesIndex).getNumberValue().intValue();
       s.c = metadata.getPixelsSizeC(seriesIndex).getNumberValue().intValue();
       s.t = metadata.getPixelsSizeT(seriesIndex).getNumberValue().intValue();
+
+      // make sure that OME-XML and first resolution array have same dimensions
+      ZarrGroup imgGroup = getZarrGroup(s.path);
+      ZarrArray imgArray = imgGroup.openArray("0");
+      int[] dims = imgArray.getShape();
+      int[] metadataDims = new int[] {s.t, s.c, s.z, y, x};
+      for (int d=0; d<dims.length; d++) {
+        if (dims[d] != metadataDims[d]) {
+          throw new FormatException("Dimension mismatch: " +
+            ("TZCYX".charAt(d)) + ": Zarr (" + dims[d] + "), OME-XML: (" +
+            metadataDims[d] + ")");
+        }
+      }
+
       s.dimensionOrder =
         metadata.getPixelsDimensionOrder(seriesIndex).toString();
       s.planeCount = s.z * s.t;

src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java

@@ -834,6 +834,37 @@ public void testVersionOnly() throws Exception {
       new PyramidFromDirectoryWriter(), new String[] {"--version"});
   }
 
+  /**
+   * Test conversion of a single multiscales, similar to a label image.
+   */
+  @Test
+  public void testLabelImage() throws Exception {
+    input = fake("sizeX", "2000", "sizeY", "1500");
+    assertBioFormats2Raw();
+    output = output.resolve("0");
+    assertTool("-f", input.toString());
+    iteratePixels();
+  }
+
+  /**
+   * Test conversion of a single multiscales (similar to label image),
+   * but intentionally provide incorrect image metadata.
+   */
+  @Test
+  public void testLabelImageWrongSize() throws Exception {
+    input = fake("sizeX", "2000", "sizeY", "1500");
+    assertBioFormats2Raw();
+    output = output.resolve("0");
+    try {
+      assertTool("-f", "test.fake");
+    }
+    catch (ExecutionException e) {
+      // First cause is RuntimeException wrapping the checked FormatException
+      Assert.assertEquals(
+          FormatException.class, e.getCause().getCause().getClass());
+    }
+  }
+
   private void checkRGBIFDs() throws FormatException, IOException {
     try (TiffParser parser = new TiffParser(outputOmeTiff.toString())) {
       IFDList mainIFDs = parser.getMainIFDs();