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Refine series count calculation for .vsi data with no pyramids #4434

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Refine series count calculation for .vsi data with no pyramids #4434

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50 changes: 42 additions & 8 deletions components/formats-gpl/src/loci/formats/in/CellSensReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -529,6 +529,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
Arrays.fill(buf, (byte) 0);

if (getCoreIndex() < core.size() - 1 && getCoreIndex() < rows.size()) {
int tileRows = rows.get(getCoreIndex());
Expand Down Expand Up @@ -598,7 +599,13 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
return buf;
}
else {
return parser.getSamples(ifds.get(getIFDIndex() + no), buf, x, y, w, h);
IFD ifd = ifds.get(getIFDIndex() + no);
if (ifd.getImageWidth() == getSizeX() && ifd.getImageLength() == getSizeY()) {
return parser.getSamples(ifd, buf, x, y, w, h);
}
LOGGER.warn("Using blank plane for unreadable image (found dimensions {}x{})",
ifd.getImageWidth(), ifd.getImageLength());
return buf;
}
}

Expand Down Expand Up @@ -732,6 +739,7 @@ else if (!expectETS && files.size() > 1) {
int seriesCount = files.size();
core.clear();
int ignoredPyramids = 0;
int extraImages = 0;
if (files.size() == 1) {
for (Pyramid pyramid : pyramids) {
if (!pyramid.name.equalsIgnoreCase("Overview")) {
Expand All @@ -743,13 +751,39 @@ else if (!expectETS && files.size() > 1) {

if (ifds.size() > 1) {
if (ifds.get(1).getSamplesPerPixel() == 1) {
seriesCount = 2;
if (channelCount == 0 && zCount == 0) {
channelCount = ifds.size() - 1;
// there may be either 1 or 2 single planes before the channels/Z stack
int uniqueDims = 1;
for (int s=1; s<seriesCount; s++) {
if (ifds.get(s).getImageWidth() != ifds.get(s - 1).getImageWidth() ||
ifds.get(s).getImageLength() != ifds.get(s - 1).getImageLength() ||
ifds.get(s).getSamplesPerPixel() != ifds.get(s - 1).getSamplesPerPixel() ||
ifds.get(s).getBitsPerSample()[0] != ifds.get(s - 1).getBitsPerSample()[0])
{
if (channelCount > 0) {
channelCount--;
break;
}
uniqueDims++;
extraImages++;
}
else {
channelCount++;
}
}
channelCount++;
seriesCount = uniqueDims;
}
else if (zCount > 0) {
zCount /= 2;
channelCount = (ifds.size() - 1) / zCount;
seriesCount = 2;
extraImages = 1;
zCount /= seriesCount;
channelCount = (ifds.size() - extraImages) / zCount;
}
else if (channelCount > 0) {
seriesCount = 2;
extraImages = 1;
zCount = (ifds.size() - extraImages) / channelCount;
}
}
else {
Expand Down Expand Up @@ -832,11 +866,11 @@ else if (zCount > 0) {
ms.sizeT = 1;
ms.sizeC = ms.rgb ? samples : 1;
if (files.size() == 1 && channelCount > 0 &&
channelCount < ifds.size() && s > 0)
channelCount < ifds.size() && s > (extraImages - 1))
{
ms.sizeC *= channelCount;
ms.sizeZ = (ifds.size() - 1) / channelCount;
ms.imageCount = ifds.size() - 1;
ms.sizeZ = (ifds.size() - extraImages) / channelCount;
ms.imageCount = ifds.size() - extraImages;
ms.dimensionOrder = "XYZCT";
}
else {
Expand Down
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