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Make DicomTile objects more accessible #4451

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1 change: 1 addition & 0 deletions components/formats-bsd/src/loci/formats/dicom/DicomTile.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ public class DicomTile {
public Double zOffset;
public int channel;
public boolean last = false;
public int planeIndex = -1;

public boolean isJP2K = false;
public boolean isJPEG = false;
Expand Down
59 changes: 43 additions & 16 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 @@ -172,7 +172,6 @@ public int getTileColumns(int no) {
public byte[] openCompressedBytes(int no, int x, int y) throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);

// TODO: this will result in a lot of redundant lookups, and should be optimized
int tileWidth = getOptimalTileWidth();
int tileHeight = getOptimalTileHeight();
Region boundingBox = new Region(x * tileWidth, y * tileHeight, tileWidth, tileHeight);
Expand Down Expand Up @@ -860,7 +859,7 @@ else if (child.attribute == OPTICAL_PATH_DESCRIPTION) {

for (int p=0; p<imagesPerFile; p++) {
DicomTile tile = new DicomTile();
tile.fileIndex = tilePositions.get(0).size();
tile.fileIndex = getTiles(0).size();
if (m.sizeZ == 1 && fileZOffset != null) {
tile.zOffset = fileZOffset;
}
Expand Down Expand Up @@ -1070,6 +1069,13 @@ else if (info.concatenationIndex == 0) {

watch.start();

int currentCoreIndex = getCoreIndex();
for (Integer key : tilePositions.keySet()) {
setCoreIndex(key);
calculateTilePlaneIndexes();
}
setCoreIndex(currentCoreIndex);

// The metadata store we're working with.
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
Expand Down Expand Up @@ -1707,25 +1713,18 @@ private CodecOptions getTileCodecOptions(DicomTile tile) {
* 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];

public List<DicomTile> getTileList(int no, Region boundingBox, boolean firstTileOnly) {
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)))
{
for (DicomTile tile : getTiles(getCoreIndex())) {
boolean inBoundingBox = boundingBox == null || tile.region.intersects(boundingBox);
boolean validPlane = tile.planeIndex == no;
if (validPlane && inBoundingBox) {
tileList.add(tile);
if (firstTileOnly) {
break;
Expand All @@ -1741,6 +1740,23 @@ private List<DicomTile> getTileList(int no, Region boundingBox, boolean firstTil
return tileList;
}

private void calculateTilePlaneIndexes() {
List<Double> zs = zOffsets.get(getCoreIndex());
List<DicomTile> tiles = getTiles(getCoreIndex());
for (int t=0; t<tiles.size(); t++) {
DicomTile tile = tiles.get(t);
for (int p=0; p<getImageCount(); p++) {
int[] zct = getZCTCoords(p);
boolean validZ = getSizeZ() == 1 || (getSizeZ() <= zs.size() && tile.zOffset.equals(zs.get(zct[0]))) || (getSizeZ() == tiles.size() && t == zct[0]);
boolean validC = tile.channel == zct[1] || getEffectiveSizeC() == 1;
if (validZ && validC) {
tile.planeIndex = p;
break;
}
}
}
}

/**
* Decompress pixel data associated with the given DicomTile.
*/
Expand Down Expand Up @@ -2108,11 +2124,22 @@ public String getImageType() {
}

public List<DicomTile> getTiles() {
return tilePositions.get(0);
return getTiles(0);
}

public List<DicomTile> getTiles(int coreIndex) {
if (tilePositions.containsKey(coreIndex)) {
return tilePositions.get(coreIndex);
}
return new ArrayList<DicomTile>();
}

public List<Double> getZOffsets() {
return zOffsets.get(0);
return getZOffsets(0);
}

public List<Double> getZOffsets(int coreIndex) {
return zOffsets.get(coreIndex);
}

public int getConcatenationIndex() {
Expand Down
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