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DICOM: initial precompressed tile reading
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@melissalinkert
melissalinkert committed Apr 16, 2024
1 parent 38cc402 commit 894444b
Showing 1 changed file with 164 additions and 36 deletions.
200 changes: 164 additions & 36 deletions components/formats-bsd/src/loci/formats/in/DicomReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@
import loci.formats.codec.JPEG2000Codec;
import loci.formats.codec.JPEGCodec;
import loci.formats.codec.PackbitsCodec;
import loci.formats.codec.PassthroughCodec;
import loci.formats.meta.MetadataStore;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
Expand Down Expand Up @@ -145,6 +146,91 @@ public DicomReader() {
hasCompanionFiles = true;
}

// -- ICompressedTileReader API methods --

@Override
public int getTileRows(int no) {
FormatTools.assertId(currentId, true, 1);

return (int) Math.ceil((double) getSizeY() / originalY);
}

@Override
public int getTileColumns(int no) {
FormatTools.assertId(currentId, true, 1);

return (int) Math.ceil((double) getSizeX() / originalY);
}

@Override
public byte[] openCompressedBytes(int no, int x, int y) throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);

Region boundingBox = new Region(x * originalX, y * originalY, originalX, originalY);

List<DicomTile> tiles = getTileList(no, boundingBox, true);
if (tiles == null || tiles.size() == 0) {
throw new FormatException("Could not find valid tile; no=" + no + ", x=" + x + ", y=" + y);
}
DicomTile tile = tiles.get(0);
byte[] buf = new byte[(int) (tile.endOffset - tile.fileOffset)];
try (RandomAccessInputStream stream = new RandomAccessInputStream(tile.file)) {
if (tile.fileOffset >= stream.length()) {
LOGGER.error("attempted to read beyond end of file ({}, {})", tile.fileOffset, tile.file);
return buf;
}
LOGGER.debug("reading from offset = {}, file = {}", tile.fileOffset, tile.file);
stream.seek(tile.fileOffset);
stream.read(buf, 0, (int) (tile.endOffset - tile.fileOffset));
}
return buf;
}

@Override
public byte[] openCompressedBytes(int no, byte[] buf, int x, int y) throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);

Region boundingBox = new Region(x * originalX, y * originalY, originalX, originalY);

List<DicomTile> tiles = getTileList(no, boundingBox, true);
if (tiles == null || tiles.size() == 0) {
throw new FormatException("Could not find valid tile; no=" + no + ", x=" + x + ", y=" + y);
}
DicomTile tile = tiles.get(0);
try (RandomAccessInputStream stream = new RandomAccessInputStream(tile.file)) {
if (tile.fileOffset >= stream.length()) {
LOGGER.error("attempted to read beyond end of file ({}, {})", tile.fileOffset, tile.file);
return buf;
}
LOGGER.debug("reading from offset = {}, file = {}", tile.fileOffset, tile.file);
stream.seek(tile.fileOffset);
stream.read(buf, 0, (int) (tile.endOffset - tile.fileOffset));
}
return buf;
}

@Override
public Codec getTileCodec(int no) throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);

List<DicomTile> tiles = getTileList(no, null, true);
if (tiles == null || tiles.size() == 0) {
throw new FormatException("Could not find valid tile; no=" + no);
}
return getTileCodec(tiles.get(0));
}

@Override
public CodecOptions getTileCodecOptions(int no, int x, int y) throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);

List<DicomTile> tiles = getTileList(no, null, true);
if (tiles == null || tiles.size() == 0) {
throw new FormatException("Could not find valid tile; no=" + no + ", x=" + x + ", y=" + y);
}
return getTileCodecOptions(tiles.get(0));
}

// -- IFormatReader API methods --

/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
Expand Down Expand Up @@ -282,33 +368,18 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
int bpp = FormatTools.getBytesPerPixel(getPixelType());
int pixel = bpp * getRGBChannelCount();
Region currentRegion = new Region(x, y, w, h);
int z = getZCTCoords(no)[0];
int c = getZCTCoords(no)[1];

if (!tilePositions.containsKey(getCoreIndex())) {
LOGGER.warn("No tiles for core index = {}", getCoreIndex());
return buf;
}

// look for any tiles that match the requested tile and plane
List<Double> zs = zOffsets.get(getCoreIndex());
List<DicomTile> tiles = tilePositions.get(getCoreIndex());
for (int t=0; t<tiles.size(); t++) {
DicomTile tile = tiles.get(t);
if ((getSizeZ() == 1 || (getSizeZ() <= zs.size() && tile.zOffset.equals(zs.get(z))) || (getSizeZ() == tiles.size() && t == z)) &&
(tile.channel == c || getEffectiveSizeC() == 1) &&
tile.region.intersects(currentRegion))
{
byte[] tileBuf = new byte[tile.region.width * tile.region.height * pixel];
Region intersection = tile.region.intersection(currentRegion);
getTile(tile, tileBuf, intersection.x - tile.region.x, intersection.y - tile.region.y,
intersection.width, intersection.height);

for (int row=0; row<intersection.height; row++) {
int srcIndex = row * intersection.width * pixel;
int destIndex = pixel * ((intersection.y - y + row) * w + (intersection.x - x));
System.arraycopy(tileBuf, srcIndex, buf, destIndex, intersection.width * pixel);
}
List<DicomTile> tiles = getTileList(no, currentRegion, false);
for (DicomTile tile : tiles) {
byte[] tileBuf = new byte[tile.region.width * tile.region.height * pixel];
Region intersection = tile.region.intersection(currentRegion);
getTile(tile, tileBuf, intersection.x - tile.region.x, intersection.y - tile.region.y,
intersection.width, intersection.height);

for (int row=0; row<intersection.height; row++) {
int srcIndex = row * intersection.width * pixel;
int destIndex = pixel * ((intersection.y - y + row) * w + (intersection.x - x));
System.arraycopy(tileBuf, srcIndex, buf, destIndex, intersection.width * pixel);
}
}

Expand Down Expand Up @@ -1496,6 +1567,70 @@ private void attachCompanionFiles() throws IOException {
}
}

/**
* Get a Codec that can be used to decompress the given tile.
*/
private Codec getTileCodec(DicomTile tile) {
Codec codec = new PassthroughCodec();
if (tile.isRLE) {
codec = new PackbitsCodec();
}
else if (tile.isJPEG) {
codec = new JPEGCodec();
}
else if (tile.isJP2K) {
codec = new JPEG2000Codec();
}
return codec;
}

/**
* Get a CodecOptions that can be used to decompress the given tile.
*/
private CodecOptions getTileCodecOptions(DicomTile tile) {
CodecOptions options = new CodecOptions();
options.maxBytes = tile.region.width * tile.region.height;
options.littleEndian = isLittleEndian();
options.interleaved = isInterleaved();

return options;
}

/**
* Get a list of tiles corresponding to the given plane.
* If the bounding box is not null, then only tiles intersecting with
* the bounding box will be returned.
* If the "firstTileOnly" flag is set, then this will return as soon
* as one matching tile is found.
*/
private List<DicomTile> getTileList(int no, Region boundingBox, boolean firstTileOnly) {
int z = getZCTCoords(no)[0];
int c = getZCTCoords(no)[1];

List<DicomTile> tileList = new ArrayList<DicomTile>();
if (!tilePositions.containsKey(getCoreIndex())) {
LOGGER.warn("No tiles for core index = {}", getCoreIndex());
return tileList;
}

// look for any tiles that match the requested tile and plane
List<Double> zs = zOffsets.get(getCoreIndex());
List<DicomTile> tiles = tilePositions.get(getCoreIndex());
for (int t=0; t<tiles.size(); t++) {
DicomTile tile = tiles.get(t);
if ((getSizeZ() == 1 || (getSizeZ() <= zs.size() && tile.zOffset.equals(zs.get(z))) || (getSizeZ() == tiles.size() && t == z)) &&
(tile.channel == c || getEffectiveSizeC() == 1) &&
(boundingBox == null || tile.region.intersects(boundingBox)))
{
tileList.add(tile);
if (firstTileOnly) {
break;
}
}
}
return tileList;
}

/**
* Decompress pixel data associated with the given DicomTile.
*/
Expand All @@ -1513,12 +1648,12 @@ private void getTile(DicomTile tile, byte[] buf, int x, int y, int w, int h)
LOGGER.debug("reading from offset = {}, file = {}", tile.fileOffset, tile.file);
stream.seek(tile.fileOffset);

Codec codec = getTileCodec(tile);
CodecOptions options = getTileCodecOptions(tile);

if (tile.isRLE) {
// plane is compressed using run-length encoding
CodecOptions options = new CodecOptions();
options.maxBytes = tile.region.width * tile.region.height;
for (int c=0; c<ec; c++) {
PackbitsCodec codec = new PackbitsCodec();
byte[] t = null;

if (bpp > 1) {
Expand Down Expand Up @@ -1611,13 +1746,6 @@ else if (pt < b.length - 2) {
System.arraycopy(tmp, 0, b, 0, b.length);
}

Codec codec = null;
CodecOptions options = new CodecOptions();
options.littleEndian = isLittleEndian();
options.interleaved = isInterleaved();
if (tile.isJPEG) codec = new JPEGCodec();
else codec = new JPEG2000Codec();

try {
b = codec.decompress(b, options);
}
Expand Down

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