Fix export of multiple files

components/loci-plugins/src/loci/plugins/out/Exporter.java

@@ -387,8 +387,6 @@ else if (store.getImageCount() > 1) {
         store.setPixelsSizeT(new PositiveInteger(1), 0);
       }
 
-      w.setMetadataRetrieve(store);
-
       Object info = imp.getProperty("Info");
       if (info != null) {
         String imageInfo = info.toString();
@@ -459,6 +457,20 @@ else if (cal.frameInterval != 0.0 && cal.getTimeUnit().equals("sec")) {
         }
       }
 
+      if (!w.getFormat().startsWith("OME")) {
+        if (splitZ) {
+          store.setPixelsSizeZ(new PositiveInteger(1), 0);
+        }
+        if (splitC) {
+          store.setPixelsSizeC(new PositiveInteger(1), 0);
+        }
+        if (splitT) {
+          store.setPixelsSizeT(new PositiveInteger(1), 0);
+        }
+      }
+
+      w.setMetadataRetrieve(store);
+
       // prompt for options
 
       String[] codecs = w.getCompressionTypes();
@@ -503,7 +515,7 @@ else if (cal.frameInterval != 0.0 && cal.getTimeUnit().equals("sec")) {
       byte[] plane = null;
       w.setInterleaved(false);
 
-      int no = 0;
+      int[] no = new int[outputFiles.length];
       for (int i=start; i<end; i++) {
         if (doStack) {
           BF.status(false, "Saving plane " + (i + 1) + "/" + size);
@@ -568,7 +580,7 @@ else if (proc instanceof ColorProcessor) {
         }
         else {
           w.changeOutputFile(outputFiles[fileIndex]);
-          w.saveBytes(no++, plane);
+          w.saveBytes(no[fileIndex]++, plane);
         }
       }
       w.close();

components/scifio/src/loci/formats/FormatWriter.java

@@ -338,6 +338,9 @@ public void savePlane(Object plane, int series, boolean lastInSeries,
   public void setId(String id) throws FormatException, IOException {
     if (id.equals(currentId)) return;
     currentId = id;
+    if (out != null) {
+      out.close();
+    }
     out = new RandomAccessOutputStream(currentId);
 
     MetadataRetrieve r = getMetadataRetrieve();

components/scifio/src/loci/formats/out/APNGWriter.java

@@ -103,6 +103,9 @@ public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
 
     writePixels(numFrames == 0 ? "IDAT" : "fdAT", buf, x, y, w, h);
     numFrames++;
+    if (numFrames == getPlaneCount()) {
+      writeFooter();
+    }
   }
 
   /* @see loci.formats.IFormatWriter#canDoStacks() */
@@ -121,6 +124,8 @@ public void setId(String id) throws FormatException, IOException {
     super.setId(id);
 
     if (out.length() == 0) {
+      numFrames = 0;
+
       MetadataRetrieve r = getMetadataRetrieve();
       int width = r.getPixelsSizeX(series).getValue().intValue();
       int height = r.getPixelsSizeY(series).getValue().intValue();
@@ -172,9 +177,6 @@ public void setId(String id) throws FormatException, IOException {
 
   /* @see loci.formats.IFormatHandler#close() */
   public void close() throws IOException {
-    if (out != null) {
-      writeFooter();
-    }
     super.close();
     numFrames = 0;
     numFramesPointer = 0;

components/scifio/src/loci/formats/out/AVIWriter.java

@@ -266,6 +266,9 @@ public void setId(String id) throws FormatException, IOException {
       in.close();
       out.seek(idx1Pos);
     }
+    else {
+      planesWritten = 0;
+    }
 
     out.order(true);
 

components/scifio/src/loci/formats/out/ICSWriter.java

@@ -100,6 +100,10 @@ public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
   {
     checkParams(no, buf, x, y, w, h);
 
+    if (pixels == null) {
+      pixels = new RandomAccessOutputStream(currentId);
+    }
+
     MetadataRetrieve meta = getMetadataRetrieve();
 
     int rgbChannels = getSamplesPerPixel();
@@ -157,6 +161,9 @@ public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
       }
     }
     lastPlane = realIndex;
+
+    pixels.close();
+    pixels = null;
   }
 
   /* @see loci.formats.IFormatWriter#canDoStacks() */
@@ -274,10 +281,6 @@ else if (checkSuffix(currentId, "ics")) {
     if (checkSuffix(currentId, "ids")) {
       pixelOffset = 0;
     }
-
-    if (pixels == null) {
-      pixels = new RandomAccessOutputStream(currentId);
-    }
   }
 
   /* @see loci.formats.IFormatHandler#close() */

components/scifio/src/loci/formats/out/OMETiffWriter.java

@@ -200,7 +200,11 @@ public void saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)
 
     super.saveBytes(no, buf, ifd, x, y, w, h);
 
-    imageLocations[series][no] = currentId;
+    int index = no;
+    while (imageLocations[series][index] != null) {
+      index++;
+    }
+    imageLocations[series][index] = currentId;
   }
 
   // -- IFormatHandler API methods --

components/scifio/src/loci/formats/out/QTWriter.java

@@ -266,6 +266,7 @@ public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
       }
     }
     numWritten++;
+    writeFooter();
   }
 
   /* @see loci.formats.IFormatWriter#canDoStacks() */
@@ -305,13 +306,15 @@ public void setId(String id) throws FormatException, IOException {
 
       writeAtom(8, "wide");
       writeAtom(numBytes + 8, "mdat");
+      numWritten = 0;
     }
     else {
       out.seek(BYTE_COUNT_OFFSET);
 
       RandomAccessInputStream in = new RandomAccessInputStream(currentId);
       in.seek(BYTE_COUNT_OFFSET);
       numBytes = in.readInt() - 8;
+      numWritten = numBytes / (planeSize + pad * height);
       in.close();
     }