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Zeiss CZI: fix dimension calculations when expected planes are missing #1386

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merged 3 commits into from
Nov 4, 2014
Merged

Zeiss CZI: fix dimension calculations when expected planes are missing #1386

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cd26576
Zeiss CZI: fix dimension calculations when expected planes are missing
melissalinkert Oct 23, 2014
269e732
Zeiss CZI: make sure pixel buffer is cleared
melissalinkert Oct 24, 2014
a201513
Zeiss CZI: flag all files as being pixels files
melissalinkert Oct 31, 2014
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21 changes: 7 additions & 14 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 @@ -187,7 +187,7 @@ public String[] getSeriesUsedFiles(boolean noPixels) {
return null;
}
else if (noPixels) {
return new String[] {currentId};
return null;
}
String[] files = new String[pixels.size() + 1];
files[0] = currentId;
Expand Down Expand Up @@ -305,6 +305,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
}
int previousHeight = 0;

Arrays.fill(buf, (byte) 0);
RandomAccessInputStream stream = new RandomAccessInputStream(currentId);
try {
for (SubBlock plane : planes) {
Expand Down Expand Up @@ -646,9 +647,6 @@ protected void initFile(String id) throws FormatException, IOException {
seriesCount /= positions;
positions = 1;
}
else {
ms0.sizeT = 1;
}
}
else if (planes.size() == ms0.sizeT || planes.size() == ms0.imageCount ||
(!isGroupFiles() && positions > 1))
Expand All @@ -659,14 +657,6 @@ else if (planes.size() == ms0.sizeT || planes.size() == ms0.imageCount ||
angles = 1;
seriesCount = 1;
}
ms0.imageCount = getSizeZ() * (isRGB() ? 1 : getSizeC()) * getSizeT();

int newCount = planes.size() / ms0.imageCount;
if (planes.size() - (ms0.imageCount * newCount) <
ms0.imageCount * seriesCount - planes.size() && (planes.size() % seriesCount) != 0)
{
seriesCount = newCount;
}
}

if (seriesCount > 1) {
Expand Down Expand Up @@ -983,6 +973,8 @@ private void calculateDimensions() {
// calculate the dimensions
CoreMetadata ms0 = core.get(0);

ArrayList<Integer> uniqueT = new ArrayList<Integer>();

for (SubBlock plane : planes) {
for (DimensionEntry dimension : plane.directoryEntry.dimensionEntries) {
if (dimension == null) {
Expand Down Expand Up @@ -1025,8 +1017,9 @@ else if (dimension.size > getSizeZ()) {
}
break;
case 'T':
if (dimension.start >= getSizeT()) {
ms0.sizeT = dimension.start + 1;
if (!uniqueT.contains(dimension.start)) {
uniqueT.add(dimension.start);
ms0.sizeT = uniqueT.size();
}
if (dimension.size > getSizeT()) {
ms0.sizeT = dimension.size;
Expand Down