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Zeiss CZI: fix assembly of overlapping tiles #1787

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merged 2 commits into from
May 18, 2015
Merged

Zeiss CZI: fix assembly of overlapping tiles #1787

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6d0b9dd
Zeiss CZI: fix assembly of overlapping tiles
melissalinkert May 7, 2015
b681f66
Fix output row calculation for linescan images
melissalinkert May 11, 2015
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32 changes: 6 additions & 26 deletions components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -298,9 +298,6 @@ 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;
Expand All @@ -312,7 +309,6 @@ 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);
Expand All @@ -321,33 +317,29 @@ 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);
Expand All @@ -362,22 +354,10 @@ 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);
Expand Down