Merge pull request #1787 from melissalinkert/12843

Zeiss CZI: fix assembly of overlapping tiles
ome · May 18, 2015 · 5943cc3 · 5943cc3
2 parents 8c2ab18 + b681f66
commit 5943cc3
Showing 1 changed file with 6 additions and 26 deletions.
diff --git a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
@@ -299,9 +299,6 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
 
     Region image = new Region(x, y, w, h);
 
-    int currentX = 0;
-    int currentY = 0;
-
     int bpp = FormatTools.getBytesPerPixel(getPixelType());
     int pixel = getRGBChannelCount() * bpp;
     int outputRowLen = w * pixel;
@@ -313,7 +310,6 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
     if (planes.size() == getImageCount()) {
       validScanDim = false;
     }
-    int previousHeight = 0;
 
     Arrays.fill(buf, (byte) 0);
     RandomAccessInputStream stream = new RandomAccessInputStream(currentId);
@@ -322,33 +318,29 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
         if ((plane.seriesIndex == currentSeries && plane.planeIndex == no) ||
           (plane.planeIndex == previousChannel && validScanDim))
         {
-          byte[] rawData = new SubBlock(plane).readPixelData();
-
           if ((prestitched != null && prestitched) || validScanDim) {
             int realX = plane.x;
             int realY = plane.y;
 
-            if (prestitched == null) {
-              currentY = 0;
-            }
-
             Region tile = new Region(plane.col, plane.row, realX, realY);
             if (validScanDim) {
               tile.y += (no / getSizeC());
               image.height = scanDim;
             }
 
             if (tile.intersects(image)) {
+              byte[] rawData = new SubBlock(plane).readPixelData();
               Region intersection = tile.intersection(image);
               int intersectionX = 0;
 
               if (tile.x < image.x) {
                 intersectionX = image.x - tile.x;
               }
 
-              if (tile.x == 0 && outputCol > 0) {
-                outputCol = 0;
-                outputRow += previousHeight;
+              outputCol = (intersection.x - x) * pixel;
+              outputRow = intersection.y - y;
+              if (validScanDim) {
+                outputRow -= tile.y;
               }
 
               int rowLen = pixel * (int) Math.min(intersection.width, realX);
@@ -363,22 +355,10 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
                   rawData, inputOffset, buf, outputOffset, rowLen);
                 outputOffset += outputRowLen;
               }
-
-              outputCol += rowLen;
-              if (outputCol >= w * pixel) {
-                outputCol = 0;
-                outputRow += intersection.height;
-              }
-              previousHeight = intersection.height;
-            }
-
-            currentX += realX;
-            if (currentX >= getSizeX()) {
-              currentX = 0;
-              currentY += realY;
             }
           }
           else {
+            byte[] rawData = new SubBlock(plane).readPixelData();
             RandomAccessInputStream s = new RandomAccessInputStream(rawData);
             try {
               readPlane(s, x, y, w, h, buf);