Examples with BulkData org.dcm4che3.data.BulkData used on opensource projects

Example 1 with BulkData

use of org.dcm4che3.data.BulkData in project karnak by OsiriX-Foundation.

the class Profile method applyCleanPixelData.

public void applyCleanPixelData(Attributes dcmCopy, AttributeEditorContext context, ProfileEntity profileEntity) {
    Object pix = dcmCopy.getValue(Tag.PixelData);
    if ((pix instanceof BulkData || pix instanceof Fragments) && !profileEntity.getMaskEntities().isEmpty() && profiles.stream().anyMatch(p -> p instanceof CleanPixelData)) {
        String sopClassUID = dcmCopy.getString(Tag.SOPClassUID);
        if (!StringUtil.hasText(sopClassUID)) {
            throw new IllegalStateException("DICOM Object does not contain sopClassUID");
        }
        String scuPattern = sopClassUID + ".";
        MaskArea mask = getMask(dcmCopy.getString(Tag.StationName));
        // BurnedInAnnotation
        if (isCleanPixelAllowedDependingImageType(dcmCopy, sopClassUID, scuPattern) && evaluateConditionCleanPixelData(dcmCopy)) {
            context.setMaskArea(mask);
            if (mask == null) {
                throw new IllegalStateException("Clean pixel is not applied: mask not defined in station name");
            }
        } else {
            context.setMaskArea(null);
        }
    }
}

Example 2 with BulkData

use of org.dcm4che3.data.BulkData in project Weasis by nroduit.

the class RawImageIO method readMetaData.

private synchronized DicomMetaData readMetaData() {
    DicomMetaData header = HEADER_CACHE.get(this);
    if (header != null) {
        return header;
    }
    Attributes dcm = new Attributes(tags.size() + attributes.size());
    SpecificCharacterSet cs = attributes.getSpecificCharacterSet();
    dcm.setSpecificCharacterSet(cs.toCodes());
    DicomMediaUtils.fillAttributes(tags, dcm);
    dcm.addAll(attributes);
    File file = imageCV.getFile();
    BulkData bdl = new BulkData(file.toURI().toString(), FileRawImage.HEADER_LENGTH, (int) file.length() - FileRawImage.HEADER_LENGTH, false);
    dcm.setValue(Tag.PixelData, VR.OW, bdl);
    header = new DicomMetaData(dcm, UID.ImplicitVRLittleEndian);
    HEADER_CACHE.put(this, header);
    return header;
}

Example 3 with BulkData

use of org.dcm4che3.data.BulkData in project dcm4che by dcm4che.

the class StowRS method writeFile.

private void writeFile(String contentLocation, OutputStream out, StowChunk stowChunk) throws Exception {
    String bulkdataContentType1 = bulkdataFileContentType.getMediaType();
    StowRSBulkdata stowRSBulkdata = contentLocBulkdata.get(contentLocation);
    XPEGParser parser = stowRSBulkdata.getParser();
    if (bulkdataFileContentType.getBulkdataTypeTag() == Tag.PixelData && tsuid)
        bulkdataContentType1 = bulkdataContentType1 + "; transfer-syntax=" + parser.getTransferSyntaxUID();
    LOG.info("> Bulkdata Content Type: " + bulkdataContentType1);
    writePartHeaders(out, bulkdataContentType1, contentLocation);
    int offset = 0;
    int length = (int) stowRSBulkdata.getFileLength();
    long positionAfterAPPSegments = parser != null ? parser.getPositionAfterAPPSegments() : -1L;
    if (noApp && positionAfterAPPSegments != -1L) {
        offset = (int) positionAfterAPPSegments;
        out.write(-1);
        out.write((byte) JPEG.SOI);
    }
    length -= offset;
    out.write(Files.readAllBytes(stowRSBulkdata.getBulkdataFilePath()), offset, length);
    stowChunk.setAttributes(stowRSBulkdata.bulkdataFile.length());
}

Example 4 with BulkData

use of org.dcm4che3.data.BulkData in project dcm4che by dcm4che.

the class PlanarConfig method processFile.

private char processFile(File file) {
    try {
        Attributes dataset;
        WritePlanarConfiguration writePlanarConfiguration = new WritePlanarConfiguration();
        try (DicomInputStream is = new DicomInputStream(file)) {
            is.setIncludeBulkData(DicomInputStream.IncludeBulkData.URI);
            is.setDicomInputHandler(writePlanarConfiguration);
            dataset = is.readDataset();
        }
        VR.Holder vr = new VR.Holder();
        Object value = dataset.getValue(Tag.PixelData, vr);
        if (value == null) {
            skipped++;
            return 'p';
        }
        ColorPMI colorPMI;
        try {
            colorPMI = ColorPMI.valueOf(dataset.getString(Tag.PhotometricInterpretation));
        } catch (IllegalArgumentException e) {
            skipped++;
            return 'm';
        }
        if (!(value instanceof BulkData)) {
            skipped++;
            return 'c';
        }
        int pc;
        try (RandomAccessFile raf = new RandomAccessFile(file, "rw")) {
            pc = planarConfiguration(file, raf, (BulkData) value, dataset, colorPMI);
            if (pc == dataset.getInt(Tag.PlanarConfiguration, 0)) {
                correct[pc]++;
                return CORRECT_CH[pc];
            }
            if (fix[pc]) {
                writePlanarConfiguration.writeTo(raf, pc);
            }
        }
        wrong[pc]++;
        if (uids && (fix[pc] || !fix[1 - pc]))
            uidslog().println(dataset.getString(Tag.SOPInstanceUID));
        return WRONG_CH[pc];
    } catch (IOException e) {
        System.err.println("Failed to update " + file + ':');
        e.printStackTrace(System.err);
        failed++;
    }
    return 'E';
}

Example 5 with BulkData

use of org.dcm4che3.data.BulkData in project dcm4che by dcm4che.

the class XMLTest method createTestDataset.

private Attributes createTestDataset() {
    Attributes dataset = new Attributes();
    dataset.setString(Tag.SpecificCharacterSet, VR.CS, "ISO 2022 IR 87");
    dataset.setString(Tag.ImageType, VR.CS, "DERIVED", null, "PRIMARY", "", "TEST");
    dataset.setNull(Tag.AccessionNumber, VR.SH);
    Attributes item = new Attributes(2);
    dataset.newSequence(Tag.SourceImageSequence, 1).add(item);
    item.setString(Tag.ReferencedSOPClassUID, VR.UI, UID.CTImageStorage);
    item.setString(Tag.ReferencedSOPInstanceUID, VR.UI, "1.2.3.4");
    dataset.setString(Tag.PatientName, VR.PN, "af^ag=if^ig=pf^pg");
    dataset.setBytes("PRIVATE", 0x00090002, VR.OB, new byte[] { 0, 1 });
    dataset.setDouble(Tag.FrameTime, VR.DS, 33.0);
    dataset.setInt(Tag.SamplesPerPixel, VR.US, 1);
    dataset.setInt(Tag.NumberOfFrames, VR.IS, 1);
    dataset.setInt(Tag.FrameIncrementPointer, VR.AT, Tag.FrameTime);
    dataset.setValue(Tag.OverlayData, VR.OW, new BulkData("someuuid", null, false));
    Fragments frags = dataset.newFragments(Tag.PixelData, VR.OB, 2);
    frags.add(null);
    frags.add(new BulkData(null, "file:/PixelData?offset=1234&length=5678", false));
    return dataset;
}