Merge branch 'master' into gcs

glencoesoftware · Aug 19, 2024 · 45f5725 · 45f5725
2 parents 893ddd8 + ece12b6
commit 45f5725
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Showing 2 changed files with 45 additions and 15 deletions.
diff --git a/build.gradle b/build.gradle
@@ -37,7 +37,7 @@ configurations.all {
 
 dependencies {
     implementation 'net.java.dev.jna:jna:5.10.0'
-    implementation 'ome:formats-gpl:7.3.0'
+    implementation 'ome:formats-gpl:7.3.1'
     implementation 'info.picocli:picocli:4.7.5'
     implementation 'com.univocity:univocity-parsers:2.8.4'
     implementation 'dev.zarr:jzarr:0.4.2'

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/MCDReader.java b/src/main/java/com/glencoesoftware/bioformats2raw/MCDReader.java
@@ -76,7 +76,8 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
     }
 
     LOGGER.debug("Reading raw acquisition #{}", getSeries() - panoramas.size());
-    in.seek(acquisitions.get(getSeries() - panoramas.size()).start);
+    Acquisition currentAcq = acquisitions.get(getSeries() - panoramas.size());
+    in.seek(currentAcq.start);
     LOGGER.debug("File offset = {}", in.getFilePointer());
 
     int bpp = FormatTools.getBytesPerPixel(getPixelType());
@@ -91,10 +92,20 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
     for (int row=0; row<h; row++) {
       in.skipBytes(x * (skip + bpp));
       for (int col=0; col<w; col++) {
-        in.read(buf, ((row * w) + col) * bpp, bpp);
-        in.skipBytes(skip);
+        // don't allow reading past the defined end of the pixel data
+        // for this acquisition (which may be in the middle of the file)
+        if (in.getFilePointer() < currentAcq.end) {
+          in.read(buf, ((row * w) + col) * bpp, bpp);
+          in.skipBytes(skip);
+        }
+        else {
+          break;
+        }
       }
       in.skipBytes((skip + bpp) * (getSizeX() - w - x));
+      if (in.getFilePointer() >= currentAcq.end) {
+        break;
+      }
     }
 
     return buf;
@@ -219,35 +230,48 @@ protected void initFile(String id) throws FormatException, IOException {
       m.sizeZ = 1;
       m.sizeT = 1;
 
+      LOGGER.debug("Acquisition size: {} x {}, {} bytes per pixel",
+        acq.sizeX, acq.sizeY, acq.bpp);
+
       int plane = acq.sizeX * acq.sizeY * acq.bpp;
       long totalBytes = acq.end - acq.start;
+      LOGGER.debug("Total pixel bytes: {}", totalBytes);
       if (totalBytes <= 0) {
         LOGGER.debug(
-          "Skipping acquistiion {} with 0 pixel bytes", acq.description);
+          "Skipping acquisition {} with 0 pixel bytes", acq.description);
         acquisitions.remove(acq);
         a--;
         continue;
       }
       long totalPlanes = totalBytes / plane;
+      LOGGER.debug("Detected {} planes in acquisition", totalPlanes);
       if (totalPlanes > Integer.MAX_VALUE) {
         throw new FormatException(
           "Too many channels (" + totalPlanes + ") for series " + core.size());
       }
-      m.sizeC = (int) totalPlanes;
-      m.imageCount = m.sizeC * m.sizeZ * m.sizeT;
-      m.dimensionOrder = "XYCZT";
-      m.littleEndian = true;
-      core.add(m);
 
       // the XML defines a big list of all channels across all acquisitions
       // map each channel to the correct location in the correct acquisition
-      acq.channelIndexes = new int[m.sizeC];
+      acq.channelIndexes = new ArrayList<Integer>();
       for (int c=0; c<channels.size(); c++) {
         Channel channel = channels.get(c);
         if (channel.acqID == acq.id) {
-          acq.channelIndexes[channel.index] = c;
+          while (channel.index >= acq.channelIndexes.size()) {
+            acq.channelIndexes.add(-1);
+          }
+          acq.channelIndexes.set(channel.index, c);
+          m.sizeC++;
         }
       }
+
+      m.imageCount = m.sizeC * m.sizeZ * m.sizeT;
+      if (totalPlanes < m.imageCount) {
+        LOGGER.warn("Not enough pixel bytes in file; images may be blank");
+      }
+
+      m.dimensionOrder = "XYCZT";
+      m.littleEndian = true;
+      core.add(m);
     }
 
     MetadataStore store = makeFilterMetadata();
@@ -263,8 +287,14 @@ protected void initFile(String id) throws FormatException, IOException {
       Acquisition acq = acquisitions.get(a);
       store.setImageName(acq.description, imageIndex);
 
-      for (int c=0; c<acq.channelIndexes.length; c++) {
-        Channel channel = channels.get(acq.channelIndexes[c]);
+      for (int c=0; c<acq.channelIndexes.size(); c++) {
+        int index = acq.channelIndexes.get(c);
+        if (index < 0) {
+          LOGGER.warn("Missing channel definition, channel #{}, image #{}",
+            c, imageIndex);
+          continue;
+        }
+        Channel channel = channels.get(index);
 
         // this is kind of wrong, but the reference viewer
         // exposes both the name and label (which are often slightly different)
@@ -542,7 +572,7 @@ class Acquisition {
     public int bpp;
 
     /** Indexes into list of channels; length matches SizeC. */
-    public int[] channelIndexes;
+    public List<Integer> channelIndexes;
   }
 
   /**