DicomCodec.java

/*******************************************************************************
 * Copyright (c) 2016 Weasis Team and others.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 *     Nicolas Roduit - initial API and implementation
 *******************************************************************************/
package org.weasis.dicom.codec;

import java.io.IOException;
import java.net.URI;
import java.util.Dictionary;
import java.util.Hashtable;
import java.util.List;

import org.dcm4che3.data.ItemPointer;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.VR;
import org.dcm4che3.imageio.plugins.rle.RLEImageReaderSpi;
import org.dcm4che3.io.BulkDataDescriptor;
import org.dcm4che3.util.TagUtils;
import org.dcm4che3.util.UIDUtils;
import org.osgi.service.cm.Configuration;
import org.osgi.service.cm.ConfigurationAdmin;
import org.osgi.service.component.ComponentContext;
import org.osgi.service.component.annotations.Activate;
import org.osgi.service.component.annotations.Deactivate;
import org.osgi.service.component.annotations.Reference;
import org.osgi.service.component.annotations.ReferenceCardinality;
import org.osgi.service.component.annotations.ReferencePolicy;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.weasis.core.api.media.data.Codec;
import org.weasis.core.api.media.data.MediaReader;
import org.weasis.core.api.service.AuditLog;
import org.weasis.core.api.service.BundlePreferences;
import org.weasis.core.api.service.BundleTools;

import com.sun.media.imageioimpl.common.ImageioUtil;

@org.osgi.service.component.annotations.Component(service = Codec.class, immediate = false)
public class DicomCodec implements Codec {
    private static final Logger LOGGER = LoggerFactory.getLogger(DicomCodec.class);

    public static final String NAME = "dcm4che"; //$NON-NLS-1$
    public static final String[] FILE_EXTENSIONS = { "dcm", "dicm" }; //$NON-NLS-1$ //$NON-NLS-2$

    private static final String LOGGER_KEY = "always.info.ItemParser"; //$NON-NLS-1$
    private static final String LOGGER_VAL = "org.dcm4che3.imageio.ItemParser"; //$NON-NLS-1$

    public static final BulkDataDescriptor BULKDATA_DESCRIPTOR = new BulkDataDescriptor() {

        @Override
        public boolean isBulkData(List<ItemPointer> itemPointer, String privateCreator, int tag, VR vr, int length) {
            switch (TagUtils.normalizeRepeatingGroup(tag)) {
                case Tag.PixelDataProviderURL:
                case Tag.AudioSampleData:
                case Tag.CurveData:
                case Tag.SpectroscopyData:
                case Tag.OverlayData:
                case Tag.EncapsulatedDocument:
                case Tag.FloatPixelData:
                case Tag.DoubleFloatPixelData:
                case Tag.PixelData:
                    return itemPointer.isEmpty();
                case Tag.WaveformData:
                    return itemPointer.size() == 1 && itemPointer.get(0).sequenceTag == Tag.WaveformSequence;
            }
            if (TagUtils.isPrivateTag(tag)) {
                return length > 5000; // Do no read in memory private value more than 5 KB
            }

            switch (vr) {
                case OB:
                case OD:
                case OF:
                case OL:
                case OW:
                case UN:
                    return length > 64;
            }
            return false;
        }
    };

    private final RLEImageReaderSpi rleImageReaderSpi = new RLEImageReaderSpi();
    // private final DicomImageWriterSpi DicomImageWriterSpi = new DicomImageWriterSpi();
    // private final RawImageReaderSpi RawImageReaderSpi = new RawImageReaderSpi();

    @Override
    public String[] getReaderMIMETypes() {
        return new String[] { DicomMediaIO.MIMETYPE, DicomMediaIO.SERIES_XDSI, DicomMediaIO.IMAGE_MIMETYPE,
            DicomMediaIO.SERIES_VIDEO_MIMETYPE, DicomMediaIO.SERIES_ENCAP_DOC_MIMETYPE };
    }

    @Override
    public String[] getReaderExtensions() {
        return FILE_EXTENSIONS;
    }

    @Override
    public boolean isMimeTypeSupported(String mimeType) {
        if (mimeType != null) {
            for (String mime : getReaderMIMETypes()) {
                if (mimeType.equals(mime)) {
                    return true;
                }
            }
        }
        return false;
    }

    @Override
    public MediaReader getMediaIO(URI media, String mimeType, Hashtable<String, Object> properties) {
        if (isMimeTypeSupported(mimeType)) {
            return new DicomMediaIO(media);
        }
        return null;
    }

    @Override
    public String getCodecName() {
        return NAME;
    }

    @Override
    public String[] getWriterExtensions() {
        return FILE_EXTENSIONS;
    }

    @Override
    public String[] getWriterMIMETypes() {
        return new String[] { DicomMediaIO.MIMETYPE };
    }

    // ================================================================================
    // OSGI service implementation
    // ================================================================================

    @Activate
    protected void activate(ComponentContext context) {
        LOGGER.info("Activate DicomCodec"); //$NON-NLS-1$

        /**
         * Set value for dicom root UID which should be registered at the
         * http://www.iana.org/assignments/enterprise-numbers <br>
         * Default value is 2.25, this enables users to generate OIDs without any registration procedure
         *
         * @see http://www.dclunie.com/medical-image-faq/html/part2.html#UUID <br>
         *      http://www.oid-info.com/get/2.25 <br>
         *      http://www.itu.int/ITU-T/asn1/uuid.html<br>
         *      http://healthcaresecprivacy.blogspot.ch/2011/02/creating-and-using-unique-id-uuid-oid.html
         */
        String weasisRootUID = BundleTools.SYSTEM_PREFERENCES.getProperty("weasis.dicom.root.uid", UIDUtils.getRoot()); //$NON-NLS-1$
        UIDUtils.setRoot(weasisRootUID);

        // Register SPI in imageio registry with the classloader of this bundle (provides also the classpath for
        // discovering the SPI files). Here are the codecs:
        // org.dcm4che3.imageioimpl.plugins.rle.RLEImageReaderSpi
        // org.dcm4che3.imageioimpl.plugins.dcm.DicomImageReaderSpi
        // org.dcm4che3.imageioimpl.plugins.dcm.DicomImageWriterSpi
        ImageioUtil.registerServiceProvider(rleImageReaderSpi);
        ImageioUtil.registerServiceProvider(DicomMediaIO.dicomImageReaderSpi);

        ConfigurationAdmin confAdmin =
            BundlePreferences.getService(context.getBundleContext(), ConfigurationAdmin.class);
        if (confAdmin != null) {
            try {
                Configuration logConfiguration = AuditLog.getLogConfiguration(confAdmin, LOGGER_KEY, LOGGER_VAL);
                if (logConfiguration == null) {
                    logConfiguration = confAdmin
                        .createFactoryConfiguration("org.apache.sling.commons.log.LogManager.factory.config", null); //$NON-NLS-1$
                    Dictionary<String, Object> loggingProperties = new Hashtable<>();
                    loggingProperties.put("org.apache.sling.commons.log.level", "INFO"); //$NON-NLS-1$ //$NON-NLS-2$
                    loggingProperties.put("org.apache.sling.commons.log.names", LOGGER_VAL); //$NON-NLS-1$
                    // add this property to give us something unique to re-find this configuration
                    loggingProperties.put(LOGGER_KEY, LOGGER_VAL);
                    logConfiguration.update(loggingProperties);
                }
            } catch (IOException e) {
                LOGGER.error("", e); //$NON-NLS-1$
            }
        }
    }

    @Deactivate
    protected void deactivate(ComponentContext context) {
        LOGGER.info("Deactivate DicomCodec"); //$NON-NLS-1$
        ImageioUtil.deregisterServiceProvider(rleImageReaderSpi);
        ImageioUtil.deregisterServiceProvider(DicomMediaIO.dicomImageReaderSpi);
    }

    @Reference(service = DicomSpecialElementFactory.class, cardinality = ReferenceCardinality.MULTIPLE, policy = ReferencePolicy.DYNAMIC, unbind = "removeDicomSpecialElementFactory")
    void addDicomSpecialElementFactory(DicomSpecialElementFactory factory) {
        String name = factory.getClass().getName();
        for (String modality : factory.getModalities()) {
            DicomSpecialElementFactory prev = DicomMediaIO.DCM_ELEMENT_FACTORIES.put(modality, factory);
            if (prev != null) {
                LOGGER.warn("{} factory has been replaced by {}", prev.getClass().getName(), name); //$NON-NLS-1$
            }
            LOGGER.info("Register DicomSpecialElementFactory: {} => {}", modality, name); //$NON-NLS-1$
        }
    }

    void removeDicomSpecialElementFactory(DicomSpecialElementFactory factory) {
        String name = factory.getClass().getName();
        for (String modality : factory.getModalities()) {
            DicomSpecialElementFactory f = DicomMediaIO.DCM_ELEMENT_FACTORIES.get(modality);
            if (factory.equals(f)) {
                DicomMediaIO.DCM_ELEMENT_FACTORIES.remove(modality);
                LOGGER.info("Unregister DicomSpecialElementFactory: {} => {}", modality, name); //$NON-NLS-1$
            } else {
                LOGGER.warn("{}: Unregistering {} has no effect, {} is registered instead", modality, name, //$NON-NLS-1$
                    f.getClass().getName());
            }
        }
    }

}