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MCD: calculate channel count based on metadata, not pixel bytes #255

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merged 2 commits into from
Aug 7, 2024
Merged

MCD: calculate channel count based on metadata, not pixel bytes #255

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bc5ec8f
MCD: calculate channel count based on metadata, not pixel bytes
melissalinkert Aug 6, 2024
bd42c7c
MCD: don't allow openBytes to read beyond the end of an acquisition
melissalinkert Aug 6, 2024
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58 changes: 44 additions & 14 deletions src/main/java/com/glencoesoftware/bioformats2raw/MCDReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,8 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
}

LOGGER.debug("Reading raw acquisition #{}", getSeries() - panoramas.size());
in.seek(acquisitions.get(getSeries() - panoramas.size()).start);
Acquisition currentAcq = acquisitions.get(getSeries() - panoramas.size());
in.seek(currentAcq.start);
LOGGER.debug("File offset = {}", in.getFilePointer());

int bpp = FormatTools.getBytesPerPixel(getPixelType());
Expand All @@ -91,10 +92,20 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
for (int row=0; row<h; row++) {
in.skipBytes(x * (skip + bpp));
for (int col=0; col<w; col++) {
in.read(buf, ((row * w) + col) * bpp, bpp);
in.skipBytes(skip);
// don't allow reading past the defined end of the pixel data
// for this acquisition (which may be in the middle of the file)
if (in.getFilePointer() < currentAcq.end) {
in.read(buf, ((row * w) + col) * bpp, bpp);
in.skipBytes(skip);
}
else {
break;
}
}
in.skipBytes((skip + bpp) * (getSizeX() - w - x));
if (in.getFilePointer() >= currentAcq.end) {
break;
}
}

return buf;
Expand Down Expand Up @@ -219,35 +230,48 @@ protected void initFile(String id) throws FormatException, IOException {
m.sizeZ = 1;
m.sizeT = 1;

LOGGER.debug("Acquisition size: {} x {}, {} bytes per pixel",
acq.sizeX, acq.sizeY, acq.bpp);

int plane = acq.sizeX * acq.sizeY * acq.bpp;
long totalBytes = acq.end - acq.start;
LOGGER.debug("Total pixel bytes: {}", totalBytes);
if (totalBytes <= 0) {
LOGGER.debug(
"Skipping acquistiion {} with 0 pixel bytes", acq.description);
"Skipping acquisition {} with 0 pixel bytes", acq.description);
acquisitions.remove(acq);
a--;
continue;
}
long totalPlanes = totalBytes / plane;
LOGGER.debug("Detected {} planes in acquisition", totalPlanes);
if (totalPlanes > Integer.MAX_VALUE) {
throw new FormatException(
"Too many channels (" + totalPlanes + ") for series " + core.size());
}
m.sizeC = (int) totalPlanes;
m.imageCount = m.sizeC * m.sizeZ * m.sizeT;
m.dimensionOrder = "XYCZT";
m.littleEndian = true;
core.add(m);

// the XML defines a big list of all channels across all acquisitions
// map each channel to the correct location in the correct acquisition
acq.channelIndexes = new int[m.sizeC];
acq.channelIndexes = new ArrayList<Integer>();
for (int c=0; c<channels.size(); c++) {
Channel channel = channels.get(c);
if (channel.acqID == acq.id) {
acq.channelIndexes[channel.index] = c;
while (channel.index >= acq.channelIndexes.size()) {
acq.channelIndexes.add(-1);
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Is this meant to signify anything different than null? Are we checking this value anywhere?

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That will get checked in line 291/292. If null is preferable, it would be easy enough to rework that check.

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A ha, gotcha. No, that's fine.

}
acq.channelIndexes.set(channel.index, c);
m.sizeC++;
}
}

m.imageCount = m.sizeC * m.sizeZ * m.sizeT;
if (totalPlanes < m.imageCount) {
LOGGER.warn("Not enough pixel bytes in file; images may be blank");
}

m.dimensionOrder = "XYCZT";
m.littleEndian = true;
core.add(m);
}

MetadataStore store = makeFilterMetadata();
Expand All @@ -263,8 +287,14 @@ protected void initFile(String id) throws FormatException, IOException {
Acquisition acq = acquisitions.get(a);
store.setImageName(acq.description, imageIndex);

for (int c=0; c<acq.channelIndexes.length; c++) {
Channel channel = channels.get(acq.channelIndexes[c]);
for (int c=0; c<acq.channelIndexes.size(); c++) {
int index = acq.channelIndexes.get(c);
if (index < 0) {
LOGGER.warn("Missing channel definition, channel #{}, image #{}",
c, imageIndex);
continue;
}
Channel channel = channels.get(index);

// this is kind of wrong, but the reference viewer
// exposes both the name and label (which are often slightly different)
Expand Down Expand Up @@ -542,7 +572,7 @@ class Acquisition {
public int bpp;

/** Indexes into list of channels; length matches SizeC. */
public int[] channelIndexes;
public List<Integer> channelIndexes;
}

/**
Expand Down