Merge pull request #4173 from melissalinkert/bfconvert-remove-channels

bfconvert: remove extra channels if `-channel` was used

Author: dgault

components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java

@@ -41,6 +41,7 @@
 import java.io.IOException;
 import java.util.Iterator;
 import java.util.HashMap;
+import java.util.List;
 import java.util.TreeMap;
 import java.util.SortedMap;
 
@@ -86,6 +87,7 @@
 import loci.formats.services.OMEXMLServiceImpl;
 
 import ome.xml.meta.OMEXMLMetadataRoot;
+import ome.xml.model.Channel;
 import ome.xml.model.Image;
 import ome.xml.model.Pixels;
 import ome.xml.model.enums.PixelType;
@@ -599,11 +601,22 @@ public boolean testConvert(IFormatWriter writer, String[] args)
         String xml = service.getOMEXML(service.asRetrieve(store));
         OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) store.getRoot();
         IMetadata meta = service.createOMEXMLMetadata(xml);
+        OMEXMLMetadataRoot newRoot = (OMEXMLMetadataRoot) meta.getRoot();
         if (series >= 0) {
-          Image exportImage = new Image(root.getImage(series));
-          Pixels exportPixels = new Pixels(root.getImage(series).getPixels());
+          Image exportImage = newRoot.getImage(series);
+          Pixels exportPixels = newRoot.getImage(series).getPixels();
+
+          if (channel >= 0) {
+            List<Channel> channels = exportPixels.copyChannelList();
+
+            for (int c=0; c<channels.size(); c++) {
+              if (c != channel) {
+                exportPixels.removeChannel(channels.get(c));
+              }
+            }
+          }
+
           exportImage.setPixels(exportPixels);
-          OMEXMLMetadataRoot newRoot = (OMEXMLMetadataRoot) meta.getRoot();
           while (newRoot.sizeOfImageList() > 0) {
             newRoot.removeImage(newRoot.getImage(0));
           }
@@ -647,6 +660,17 @@ public boolean testConvert(IFormatWriter writer, String[] args)
               store.setPixelsType(PixelType.UINT8, i);
             }
 
+            if (channel >= 0) {
+              Pixels exportPixels = newRoot.getImage(i).getPixels();
+              List<Channel> channels = exportPixels.copyChannelList();
+
+              for (int c=0; c<channels.size(); c++) {
+                if (c != channel) {
+                  exportPixels.removeChannel(channels.get(c));
+                }
+              }
+            }
+
             if (channel >= 0) {
               meta.setPixelsSizeC(new PositiveInteger(1), i);
             }

components/bio-formats-tools/test/loci/formats/tools/ImageConverterTest.java

@@ -42,17 +42,21 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 
+import loci.common.services.ServiceFactory;
 import loci.formats.ClassList;
 import loci.formats.IFormatReader;
 import loci.formats.ImageReader;
 import loci.formats.ImageWriter;
 import loci.formats.FormatException;
+import loci.formats.meta.IMetadata;
 import loci.formats.tools.ImageConverter;
 import loci.formats.in.ICSReader;
 import loci.formats.in.OMETiffReader;
 import loci.formats.in.TiffDelegateReader;
 import loci.formats.in.TiffReader;
 import loci.formats.out.OMETiffWriter;
+import loci.formats.services.OMEXMLService;
+import loci.formats.tiff.TiffParser;
 
 import org.apache.commons.lang.ArrayUtils;
 import org.testng.annotations.AfterClass;
@@ -369,6 +373,27 @@ public void testConvertResolutions() throws FormatException, IOException {
     assertConversion(args);
   }
 
+  @Test
+  public void testConvertSingleChannel() throws FormatException, IOException {
+    outFile = getOutFile("single-channel.ome.tiff");
+    String[] args = {
+      "single-channel&sizeC=3.fake", "-channel", "1", outFile.getAbsolutePath()
+    };
+    assertConversion(args);
+
+    try (TiffParser parser = new TiffParser(outFile.getAbsolutePath())) {
+      String comment = parser.getComment();
+
+      final OMEXMLService service =
+        new ServiceFactory().getInstance(OMEXMLService.class);
+      IMetadata meta = service.createOMEXMLMetadata(comment);
+      assertEquals(meta.getChannelCount(0), 1);
+    }
+    catch (Exception e) {
+      throw new FormatException(e);
+    }
+  }
+
   private Path getTempSubdir() throws IOException {
     Path subdir = Files.createTempDirectory(tempDir, "ImageConverterTest");
     subdir.toFile().deleteOnExit();