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Use skipBytes(long) in places where integer overflow is possible #3529

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Apr 2, 2020
Merged

Use skipBytes(long) in places where integer overflow is possible #3529

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8 changes: 4 additions & 4 deletions components/formats-api/src/loci/formats/FormatReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -524,23 +524,23 @@ protected byte[] readPlane(RandomAccessInputStream s, int x, int y,
}
else if (x == 0 && w == getSizeX() && scanlinePad == 0) {
if (isInterleaved()) {
s.skipBytes(y * w * bpp * c);
s.skipBytes((long) y * w * bpp * c);
s.read(buf, 0, h * w * bpp * c);
}
else {
int rowLen = w * bpp;
for (int channel=0; channel<c; channel++) {
s.skipBytes(y * rowLen);
s.skipBytes((long) y * rowLen);
s.read(buf, channel * h * rowLen, h * rowLen);
if (channel < c - 1) {
// no need to skip bytes after reading final channel
s.skipBytes((getSizeY() - y - h) * rowLen);
s.skipBytes((long) (getSizeY() - y - h) * rowLen);
}
}
}
}
else {
int scanlineWidth = getSizeX() + scanlinePad;
long scanlineWidth = getSizeX() + scanlinePad;
if (isInterleaved()) {
s.skipBytes(y * scanlineWidth * bpp * c);
for (int row=0; row<h; row++) {
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3 changes: 2 additions & 1 deletion components/formats-bsd/src/loci/formats/in/AVIReader.java
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Expand Up @@ -237,7 +237,8 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
pad = bytes;
}

in.skipBytes((getSizeX() + pad) * (bmpBitsPerPixel / 8) * (getSizeY() - h - y));
long skipRows = getSizeY() - h - y;
in.skipBytes((getSizeX() + pad) * (bmpBitsPerPixel / 8) * skipRows);

if (getSizeX() == w && pad == 0) {
for (int row=0; row<h; row++) {
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2 changes: 1 addition & 1 deletion components/formats-bsd/src/loci/formats/in/DicomReader.java
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Expand Up @@ -1100,7 +1100,7 @@ private String getHeaderInfo(int tag, String value) throws IOException {
if (skip) {
long skipCount = (long) elementLength;
if (in.getFilePointer() + skipCount <= in.length()) {
in.skipBytes((int) skipCount);
in.skipBytes(skipCount);
}
location += elementLength;
value = "";
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2 changes: 1 addition & 1 deletion components/formats-bsd/src/loci/formats/in/EPSReader.java
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Expand Up @@ -125,7 +125,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
}

byte[] b = new byte[w * h];
int bpp = (int) (byteCounts[0] / (getSizeX() * getSizeY()));
long bpp = byteCounts[0] / (getSizeX() * getSizeY());
in.skipBytes(bpp * y * getSizeX());
for (int row=0; row<h; row++) {
in.skipBytes(x * bpp);
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4 changes: 2 additions & 2 deletions components/formats-bsd/src/loci/formats/tiff/TiffParser.java
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Expand Up @@ -363,8 +363,8 @@ public long[] getIFDOffsets() throws IOException {
while (offset > 0 && offset < in.length()) {
in.seek(offset);
offsets.add(offset);
int nEntries = bigTiff ? (int) in.readLong() : in.readUnsignedShort();
int entryBytes = nEntries * bytesPerEntry;
long nEntries = bigTiff ? in.readLong() : in.readUnsignedShort();
long entryBytes = nEntries * bytesPerEntry;
if (in.getFilePointer() + entryBytes + (bigTiff ? 8 : 4) > in.length()) {
// this can easily happen when writing multiple planes to a file
break;
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/AliconaReader.java
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Expand Up @@ -99,7 +99,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
// so instead of LMLMLM... storage, we have LLLLL...MMMMM...
for (int i=0; i<numBytes; i++) {
in.seek(textureOffset + (no * planeSize * (i + 1)));
in.skipBytes(y * (getSizeX() + pad));
in.skipBytes((long) y * (getSizeX() + pad));
if (getSizeX() == w) {
in.read(buf, i * w * h, w * h);
}
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/BioRadGelReader.java
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Expand Up @@ -116,7 +116,7 @@ else if (in.length() - planeSize > 61000) {
int bpp = FormatTools.getBytesPerPixel(getPixelType());
int pixel = bpp * getSizeC();

in.skipBytes(pixel * getSizeX() * (getSizeY() - h - y));
in.skipBytes((long) pixel * getSizeX() * (getSizeY() - h - y));

for (int row=h-1; row>=0; row--) {
in.skipBytes(x * pixel);
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4 changes: 2 additions & 2 deletions components/formats-gpl/src/loci/formats/in/BioRadReader.java
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Expand Up @@ -373,7 +373,7 @@ protected void initFile(String id) throws FormatException, IOException {
// skip image data
int imageLen = getSizeX() * getSizeY();
int bpp = FormatTools.getBytesPerPixel(getPixelType());
in.skipBytes(bpp * getImageCount() * imageLen + 6);
in.skipBytes((long) bpp * getImageCount() * imageLen + 6);

m.sizeZ = getImageCount();
m.sizeC = 1;
Expand Down Expand Up @@ -538,7 +538,7 @@ private void readNotes(RandomAccessInputStream s, boolean add)
throws IOException
{
s.seek(70);
int imageLen = getSizeX() * getSizeY();
long imageLen = getSizeX() * getSizeY();
if (picFiles == null) imageLen *= getImageCount();
else {
imageLen *= (getImageCount() / picFiles.length);
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4 changes: 2 additions & 2 deletions components/formats-gpl/src/loci/formats/in/HISReader.java
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Expand Up @@ -140,8 +140,8 @@ protected void initFile(String id) throws FormatException, IOException {
if (getBitsPerPixel() == 12) {
core.get(i - 1).bitsPerPixel = 16;

int prevSkip = (getSizeX() * getSizeY() * getSizeC() * 12) / 8;
int totalBytes = FormatTools.getPlaneSize(this);
long prevSkip = ((long) getSizeX() * getSizeY() * getSizeC() * 12) / 8;
long totalBytes = FormatTools.getPlaneSize(this);
in.skipBytes(totalBytes - prevSkip);
adjustedBitDepth = true;
}
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/IMODReader.java
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Expand Up @@ -390,7 +390,7 @@ protected void initFile(String id) throws FormatException, IOException {
int surface = in.readShort();

// TODO
in.skipBytes(12 * vsize + 4 * lsize);
in.skipBytes((long) 12 * vsize + (long) 4 * lsize);
}
}

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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/IPLabReader.java
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Expand Up @@ -310,7 +310,7 @@ else if (tag.equals("roi ") &&
store.setROIID(roiID, 0);
store.setImageROIRef(roiID, 0, 0);

in.skipBytes(8 * numRoiPts);
in.skipBytes((long) 8 * numRoiPts);
}
else if (tag.equals("mask")) {
// read in Segmentation Mask
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4 changes: 2 additions & 2 deletions components/formats-gpl/src/loci/formats/in/ImspectorReader.java
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Expand Up @@ -208,7 +208,7 @@ protected void initFile(String id) throws FormatException, IOException {
}
m.pixelType = FormatTools.UINT16;
int bpp = FormatTools.getBytesPerPixel(m.pixelType);
in.skipBytes(m.sizeX * m.sizeY * planesPerBlock.get(0) * bpp + 2);
in.skipBytes((long) m.sizeX * m.sizeY * planesPerBlock.get(0) * bpp + 2);

int tileX = 1;
int tileY = 1;
Expand Down Expand Up @@ -655,7 +655,7 @@ private void findOffset(boolean readStackHeader) throws IOException {
planesPerBlock.get(planesPerBlock.size() - 1) * 2;
if (planeSize > 0 && in.getFilePointer() + planeSize < in.length()) {
pixelsOffsets.add(in.getFilePointer());
in.skipBytes((int) planeSize + 2);
in.skipBytes(planeSize + 2);
}
else {
planesPerBlock.remove(planesPerBlock.size() - 1);
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8 changes: 4 additions & 4 deletions components/formats-gpl/src/loci/formats/in/IvisionReader.java
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Expand Up @@ -109,7 +109,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);

int planeSize = getSizeX() * getSizeY() * getSizeC();
long planeSize = (long) getSizeX() * getSizeY() * getSizeC();
if (color16) planeSize = 2 * (planeSize / 3);
else if (squareRoot) planeSize *= 2;
else if (hasPaddingByte) {
Expand All @@ -129,15 +129,15 @@ else if (squareRoot) {
}
else if (hasPaddingByte) {
int next = 0;
in.skipBytes(y * getSizeX() * getSizeC());
in.skipBytes((long) y * getSizeX() * getSizeC());
for (int row=0; row<h; row++) {
in.skipBytes(x * getSizeC());
in.skipBytes((long) x * getSizeC());
for (int col=0; col<w; col++) {
in.skipBytes(1);
in.read(buf, next, getSizeC());
next += getSizeC();
}
in.skipBytes(getSizeC() * (getSizeX() - w - x));
in.skipBytes((long) getSizeC() * (getSizeX() - w - x));
}
}
else readPlane(in, x, y, w, h, buf);
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/LIFReader.java
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Expand Up @@ -328,7 +328,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
long planeSize = (long) getSizeX() * getSizeY() * bpp;
long nextOffset = index + 1 < offsets.size() ?
offsets.get(index + 1).longValue() : endPointer;
int bytesToSkip = (int) (nextOffset - offset - planeSize * getImageCount());
long bytesToSkip = nextOffset - offset - planeSize * getImageCount();
bytesToSkip /= getSizeY();
if ((getSizeX() % 4) == 0) bytesToSkip = 0;

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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/LeicaReader.java
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Expand Up @@ -1079,7 +1079,7 @@ private void parseDimensionTag(int seriesIndex)
addSeriesMeta("Maximum voxel intensity", getString(true));
addSeriesMeta("Minimum voxel intensity", getString(true));
int len = in.readInt();
in.skipBytes(len * 2 + 4);
in.skipBytes((long) len * 2 + 4);

len = in.readInt();
for (int j=0; j<len; j++) {
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/LiFlimReader.java
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Expand Up @@ -231,7 +231,7 @@ else if (TypeUINT12) {
int thisSeries = getSeries();
for (int i=0; i<thisSeries; i++) {
setSeries(i);
in.skipBytes(getImageCount() * FormatTools.getPlaneSize(this));
in.skipBytes((long) getImageCount() * FormatTools.getPlaneSize(this));
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@sbesson sbesson Mar 17, 2020 •
edited
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This seems to have impacted the non-regression tests for one li-flim sample file - see https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-test-folder/52532/console. We might need to look at the data with or without this PR to establish whether the configuration needs to be regenerated or there is an issue with this change.

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@melissalinkert melissalinkert Mar 17, 2020 •
edited
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Reasonably certain that the configuration needs to be updated, as proposed here: https://github.com/openmicroscopy/data_repo_config/pull/445

Note that without that change, the MD5s for series 0 and series 1 were the same, which points to this PR fixing a problem.

}
setSeries(thisSeries);
readPlane(in, x, y, w, h, buf);
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/MetamorphReader.java
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Expand Up @@ -1680,7 +1680,7 @@ private void parseUIC4Tags(long uic4offset) throws IOException {
hasAbsoluteZValid = true;
break;
case 46:
in.skipBytes(mmPlanes * 8); // TODO
in.skipBytes((long) mmPlanes * 8); // TODO
break;
default:
in.skipBytes(4);
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/NAFReader.java
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Expand Up @@ -145,7 +145,7 @@ protected void initFile(String id) throws FormatException, IOException {
String name = in.readCString();

if (i == 0) {
in.skipBytes((int) (92 - in.getFilePointer() + pointer));
in.skipBytes(92 - in.getFilePointer() + pointer);
while (true) {
int check = in.readInt();
if (check > in.getFilePointer()) {
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/OpenlabReader.java
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Expand Up @@ -395,7 +395,7 @@ protected void initFile(String id) throws FormatException, IOException {
in.skipBytes(16);
long pointer = in.getFilePointer();
planes[imagesFound].planeName = readCString().trim();
in.skipBytes((int) (256 - in.getFilePointer() + pointer));
in.skipBytes(256 - in.getFilePointer() + pointer);

planes[imagesFound].planeOffset = in.getFilePointer();

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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/PSDReader.java
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Expand Up @@ -274,7 +274,7 @@ protected void initFile(String id) throws FormatException, IOException {
int[] lens = new int[h[i]];
for (int cc=0; cc<c[i]; cc++) {
boolean compressed = in.readShort() == 1;
if (!compressed) in.skipBytes(w[i] * h[i]);
if (!compressed) in.skipBytes((long) w[i] * h[i]);
else {
for (int y=0; y<h[i]; y++) {
lens[y] = in.readShort();
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4 changes: 2 additions & 2 deletions components/formats-gpl/src/loci/formats/in/PhotoshopTiffReader.java
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Expand Up @@ -248,7 +248,7 @@ else if (sourceData instanceof TiffIFDEntry) {
addGlobalMetaList("Layer name", layerNames[layer]);
core.add(layerCore);
}
tag.skipBytes((int) (fp + len - tag.getFilePointer()));
tag.skipBytes(fp + len - tag.getFilePointer());
}

nLayers = core.size() - 1;
Expand Down Expand Up @@ -282,7 +282,7 @@ else if (compression[layer] == PACKBITS) {
}
}
}
else tag.skipBytes(length + skip);
else tag.skipBytes((long) length + skip);
}

MetadataStore store = makeFilterMetadata();
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11 changes: 6 additions & 5 deletions components/formats-gpl/src/loci/formats/in/SDTReader.java
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Expand Up @@ -178,7 +178,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
if (info.mcstaPoints == getSizeT()) {
times = getSizeT();
}
int planeSize = paddedWidth * sizeY * times * bpp;
long planeSize = (long) paddedWidth * sizeY * times * bpp;

// remove width padding if we can be reasonably certain
// that the unpadded width is correct
Expand Down Expand Up @@ -316,11 +316,12 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
codec.skip(channel * planeSize + y * paddedWidth * bpp * times);
}
else {
in.skipBytes(channel * planeSize + y * paddedWidth * bpp * times);
in.skipBytes(
channel * planeSize + (long) y * paddedWidth * bpp * times);
}

for (int row = 0; row < h; row++) {
readPixels(rowBuf, in, codec, x * bpp * times);
readPixels(rowBuf, in, codec, (long) x * bpp * times);
if (intensity) {
System.arraycopy(rowBuf, 0, b, row * bpp * times * w, b.length);
}
Expand All @@ -334,7 +335,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
}
}
if (codec == null) {
in.skipBytes(bpp * times * (paddedWidth - x - w));
in.skipBytes((long) bpp * times * (paddedWidth - x - w));
}
else {
codec.skip(bpp * times * (paddedWidth - x - w));
Expand Down Expand Up @@ -469,7 +470,7 @@ protected void initFile(String id) throws FormatException, IOException {
MetadataTools.populatePixels(store, this);
}

private void readPixels(byte[] rowBuf, RandomAccessInputStream in, ZipInputStream codec, int skip)
private void readPixels(byte[] rowBuf, RandomAccessInputStream in, ZipInputStream codec, long skip)
throws IOException
{
if (codec == null) {
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/SlidebookReader.java
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Expand Up @@ -668,7 +668,7 @@ else if (n == 'd') {
in.seek(in.getFilePointer() - 1);
long nSkipped = in.getFilePointer() - fp;
if (nSkipped < 8) {
in.skipBytes((int) (8 - nSkipped));
in.skipBytes(8 - nSkipped);
}
String objective = readCString().trim();
in.seek(fp + 144);
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4 changes: 2 additions & 2 deletions components/formats-gpl/src/loci/formats/in/TargaReader.java
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Expand Up @@ -95,8 +95,8 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
while (bpp % 8 != 0) bpp++;
bpp /= 8;

int rowSkip = orientation < 2 ? (getSizeY() - h - y) : y;
int colSkip = (orientation % 2) == 1 ? (getSizeX() - w - x) : x;
long rowSkip = orientation < 2 ? (getSizeY() - h - y) : y;
long colSkip = (orientation % 2) == 1 ? (getSizeX() - w - x) : x;

try {
s.skipBytes(rowSkip * getSizeX() * bpp);
Expand Down
4 changes: 2 additions & 2 deletions components/formats-gpl/src/loci/formats/in/VisitechReader.java
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Expand Up @@ -129,8 +129,8 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
s.order(isLittleEndian());
s.seek(pixelOffsets[fileIndex]);

int paddingBytes =
(int) (s.length() - s.getFilePointer() - div * plane) / (div - 1);
long paddingBytes =
(s.length() - s.getFilePointer() - div * plane) / (div - 1);
if (planeIndex > 0) {
s.skipBytes((plane + paddingBytes) * planeIndex);
}
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4 changes: 2 additions & 2 deletions components/formats-gpl/src/loci/formats/in/ZeissLMSReader.java
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Expand Up @@ -89,7 +89,7 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);

in.seek(offsets.get(getSeriesCount() - getSeries() - 1));
in.skipBytes(no * FormatTools.getPlaneSize(this));
in.skipBytes((long) no * FormatTools.getPlaneSize(this));
readPlane(in, x, y, w, h, buf);

return buf;
Expand Down Expand Up @@ -144,7 +144,7 @@ public void initFile(String id) throws FormatException, IOException {
seekToNextMarker();
in.skipBytes(50);
offsets.add(in.getFilePointer());
in.skipBytes(thumb.sizeX * thumb.sizeY * thumb.sizeC);
in.skipBytes((long) thumb.sizeX * thumb.sizeY * thumb.sizeC);

seekToNextMarker();
in.skipBytes(50);
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2 changes: 1 addition & 1 deletion components/formats-gpl/src/loci/formats/in/ZeissZVIReader.java
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Expand Up @@ -598,7 +598,7 @@ private void parseROIs(RandomAccessInputStream s, int imageNum, String name, Met
int length = s.readInt();

Shape nshape = new Shape();
s.skipBytes(length + 6);
s.skipBytes((long) length + 6);

long shapeAttrOffset = s.getFilePointer();
int shapeAttrLength = s.readInt();
Expand Down