private int[] getActiveOverlayGroupOffsets(ImageReadParam param) {
if (param instanceof DicomImageReadParam) {
DicomImageReadParam dParam = (DicomImageReadParam) param;
Attributes psAttrs = dParam.getPresentationState();
if (psAttrs != null) return Overlays.getActiveOverlayGroupOffsets(psAttrs);
else
return Overlays.getActiveOverlayGroupOffsets(
metadata.getAttributes(), dParam.getOverlayActivationMask());
}
return Overlays.getActiveOverlayGroupOffsets(metadata.getAttributes(), 0xffff);
}
private void applyOverlay(
int gg0000,
WritableRaster raster,
int frameIndex,
ImageReadParam param,
int outBits,
byte[] ovlyData) {
Attributes ovlyAttrs = metadata.getAttributes();
int grayscaleValue = 0xffff;
if (param instanceof DicomImageReadParam) {
DicomImageReadParam dParam = (DicomImageReadParam) param;
Attributes psAttrs = dParam.getPresentationState();
if (psAttrs != null) {
if (psAttrs.containsValue(Tag.OverlayData | gg0000)) ovlyAttrs = psAttrs;
grayscaleValue = Overlays.getRecommendedDisplayGrayscaleValue(psAttrs, gg0000);
} else grayscaleValue = dParam.getOverlayGrayscaleValue();
}
Overlays.applyOverlay(
ovlyData != null ? 0 : frameIndex,
raster,
ovlyAttrs,
gg0000,
grayscaleValue >>> (16 - outBits),
ovlyData);
}
private byte[] extractOverlay(int gg0000, WritableRaster raster) {
Attributes attrs = metadata.getAttributes();
if (attrs.getInt(Tag.OverlayBitsAllocated | gg0000, 1) == 1) return null;
int ovlyRows = attrs.getInt(Tag.OverlayRows | gg0000, 0);
int ovlyColumns = attrs.getInt(Tag.OverlayColumns | gg0000, 0);
int bitPosition = attrs.getInt(Tag.OverlayBitPosition | gg0000, 0);
int mask = 1 << bitPosition;
int length = ovlyRows * ovlyColumns;
byte[] ovlyData = new byte[(((length + 7) >>> 3) + 1) & (~1)];
Overlays.extractFromPixeldata(raster, mask, ovlyData, 0, length);
return ovlyData;
}
private WritableRaster applyLUTs(
WritableRaster raster, int frameIndex, ImageReadParam param, SampleModel sm, int outBits) {
WritableRaster destRaster =
sm.getDataType() == raster.getSampleModel().getDataType()
? raster
: Raster.createWritableRaster(sm, null);
Attributes imgAttrs = metadata.getAttributes();
StoredValue sv = StoredValue.valueOf(imgAttrs);
LookupTableFactory lutParam = new LookupTableFactory(sv);
DicomImageReadParam dParam =
param instanceof DicomImageReadParam
? (DicomImageReadParam) param
: new DicomImageReadParam();
Attributes psAttrs = dParam.getPresentationState();
if (psAttrs != null) {
lutParam.setModalityLUT(psAttrs);
lutParam.setVOI(
selectVOILUT(psAttrs, imgAttrs.getString(Tag.SOPInstanceUID), frameIndex + 1),
0,
0,
false);
lutParam.setPresentationLUT(psAttrs);
} else {
Attributes sharedFctGroups = imgAttrs.getNestedDataset(Tag.SharedFunctionalGroupsSequence);
Attributes frameFctGroups =
imgAttrs.getNestedDataset(Tag.PerFrameFunctionalGroupsSequence, frameIndex);
lutParam.setModalityLUT(
selectFctGroup(
imgAttrs, sharedFctGroups, frameFctGroups, Tag.PixelValueTransformationSequence));
if (dParam.getWindowWidth() != 0) {
lutParam.setWindowCenter(dParam.getWindowCenter());
lutParam.setWindowWidth(dParam.getWindowWidth());
} else
lutParam.setVOI(
selectFctGroup(imgAttrs, sharedFctGroups, frameFctGroups, Tag.FrameVOILUTSequence),
dParam.getWindowIndex(),
dParam.getVOILUTIndex(),
dParam.isPreferWindow());
if (dParam.isAutoWindowing()) lutParam.autoWindowing(imgAttrs, raster);
lutParam.setPresentationLUT(imgAttrs);
}
LookupTable lut = lutParam.createLUT(outBits);
lut.lookup(raster, destRaster);
return destRaster;
}
private ColorModel createColorModel(int bits, int dataType) {
return pmi.createColorModel(bits, dataType, metadata.getAttributes());
}
