/* ***** BEGIN LICENSE BLOCK *****
* Version: MPL 1.1/GPL 2.0/LGPL 2.1
*
* The contents of this file are subject to the Mozilla Public License Version
* 1.1 (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
* http://www.mozilla.org/MPL/
*
* Software distributed under the License is distributed on an "AS IS" basis,
* WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
* for the specific language governing rights and limitations under the
* License.
*
* The Original Code is part of dcm4che, an implementation of DICOM(TM) in
* Java(TM), hosted at https://github.com/gunterze/dcm4che.
*
* The Initial Developer of the Original Code is
* Agfa Healthcare.
* Portions created by the Initial Developer are Copyright (C) 2013
* the Initial Developer. All Rights Reserved.
*
* Contributor(s):
* See @authors listed below
*
* Alternatively, the contents of this file may be used under the terms of
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* the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
* in which case the provisions of the GPL or the LGPL are applicable instead
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* ***** END LICENSE BLOCK ***** */
package org.dcm4che3.emf;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.UID;
import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.BulkData;
import org.dcm4che3.data.Fragments;
import org.dcm4che3.data.Sequence;
import org.dcm4che3.data.VR;
/**
* @author Gunter Zeilinger <gunterze@gmail.com>
*
*/
public class MultiframeExtractor {
private enum Impl {
EnhancedCTImageExtractor(UID.CTImageStorage),
EnhancedMRImageExtractor(UID.MRImageStorage) {
Attributes extract(MultiframeExtractor mfe, Attributes emf, int frame) {
Attributes sf = super.extract(mfe, emf, frame);
setEchoTime(sf);
setScanningSequence(sf);
setSequenceVariant(sf);
setScanOptions(sf);
return sf;
}
void setEchoTime(Attributes sf) {
double echoTime = sf.getDouble(Tag.EffectiveEchoTime, 0);
if (echoTime == 0)
sf.setNull(Tag.EchoTime, VR.DS);
else
sf.setDouble(Tag.EchoTime, VR.DS, echoTime);
}
void setScanningSequence(Attributes sf) {
ArrayList<String> list = new ArrayList<String>(3);
String eps = sf.getString(Tag.EchoPulseSequence);
if (!"GRADIENT".equals(eps))
list.add("SE");
if (!"SPIN".equals(eps))
list.add("GR");
if ("YES".equals(sf.getString(Tag.InversionRecovery)))
list.add("IR");
if ("YES".equals(sf.getString(Tag.EchoPlanarPulseSequence)))
list.add("EP");
sf.setString(Tag.ScanningSequence, VR.CS,
list.toArray(new String[list.size()]));
}
void setSequenceVariant(Attributes sf) {
ArrayList<String> list = new ArrayList<String>(5);
if (!"SINGLE".equals(sf.getString(Tag.SegmentedKSpaceTraversal)))
list.add("SK");
String mf = sf.getString(Tag.MagnetizationTransfer);
if (mf != null && !"NONE".equals(mf))
list.add("MTC");
String ssps = sf.getString(Tag.SteadyStatePulseSequence);
if (ssps != null && !"NONE".equals(ssps))
list.add("TIME_REVERSED".equals(ssps) ? "TRSS" :"SS");
String sp = sf.getString(Tag.Spoiling);
if (sp != null && !"NONE".equals(sp))
list.add("SP");
String op = sf.getString(Tag.OversamplingPhase);
if (op != null && !"NONE".equals(op))
list.add("OSP");
if (list.isEmpty())
list.add("NONE");
sf.setString(Tag.SequenceVariant, VR.CS,
list.toArray(new String[list.size()]));
}
void setScanOptions(Attributes sf) {
ArrayList<String> list = new ArrayList<String>(3);
String per = sf.getString(Tag.RectilinearPhaseEncodeReordering);
if (per != null && !"LINEAR".equals(per))
list.add("PER");
String frameType3 = sf.getString(Tag.ImageType, 2);
if ("ANGIO".equals(frameType3))
sf.setString(Tag.AngioFlag, VR.CS, "Y");
if (frameType3.startsWith("CARD"))
list.add("CG");
if (frameType3.endsWith("RESP_GATED"))
list.add("RG");
String pfd = sf.getString(Tag.PartialFourierDirection);
if ("PHASE".equals(pfd))
list.add("PFP");
if ("FREQUENCY".equals(pfd))
list.add("PFF");
String sp = sf.getString(Tag.SpatialPresaturation);
if (sp != null && !"NONE".equals(sp))
list.add("SP");
String sss = sf.getString(Tag.SpectrallySelectedSuppression);
if (sss != null && sss.startsWith("FAT"))
list.add("FS");
String fc = sf.getString(Tag.FlowCompensation);
if (fc != null && !"NONE".equals(fc))
list.add("FC");
sf.setString(Tag.ScanOptions, VR.CS,
list.toArray(new String[list.size()]));
}
},
EnhancedPETImageExtractor(UID.PositronEmissionTomographyImageStorage);
private final String sfcuid;
Impl(String sfcuid) {
this.sfcuid = sfcuid;
}
Attributes extract(MultiframeExtractor mfe, Attributes emf, int frame) {
return mfe.extract(emf, frame, sfcuid);
}
}
private static final HashMap<String,Impl> impls = new HashMap<String,Impl>(8);
static {
impls.put(UID.EnhancedCTImageStorage, Impl.EnhancedCTImageExtractor);
impls.put(UID.EnhancedMRImageStorage, Impl.EnhancedMRImageExtractor);
impls.put(UID.EnhancedPETImageStorage, Impl.EnhancedPETImageExtractor);
}
private static final int[] EXCLUDE_TAGS = {
Tag.ReferencedImageEvidenceSequence,
Tag.SourceImageEvidenceSequence,
Tag.DimensionIndexSequence,
Tag.NumberOfFrames,
Tag.SharedFunctionalGroupsSequence,
Tag.PerFrameFunctionalGroupsSequence,
Tag.PixelData };
private boolean preserveSeriesInstanceUID;
private String instanceNumberFormat = "%s%04d";
private UIDMapper uidMapper = new HashUIDMapper();
private NumberOfFramesAccessor nofAccessor = new NumberOfFramesAccessor();
public static boolean isSupportedSOPClass(String cuid) {
return impls.containsKey(cuid);
}
public static String legacySOPClassUID(String mfcuid) {
Impl impl = impls.get(mfcuid);
return impl != null ? impl.sfcuid : null;
}
public final boolean isPreserveSeriesInstanceUID() {
return preserveSeriesInstanceUID;
}
public final void setPreserveSeriesInstanceUID(
boolean preserveSeriesInstanceUID) {
this.preserveSeriesInstanceUID = preserveSeriesInstanceUID;
}
public final String getInstanceNumberFormat() {
return instanceNumberFormat;
}
public final void setInstanceNumberFormat(String instanceNumberFormat) {
String.format(instanceNumberFormat, "1", 1);
this.instanceNumberFormat = instanceNumberFormat;
}
public final UIDMapper getUIDMapper() {
return uidMapper;
}
public final void setUIDMapper(UIDMapper uidMapper) {
if (uidMapper == null)
throw new NullPointerException();
this.uidMapper = uidMapper;
}
public final NumberOfFramesAccessor getNumberOfFramesAccessorr() {
return nofAccessor;
}
public final void setNumberOfFramesAccessor(NumberOfFramesAccessor accessor) {
if (accessor == null)
throw new NullPointerException();
this.nofAccessor = accessor;
}
/** Extract specified frame from Enhanced Multi-frame image and return it
* as correponding legacy Single-frame image.
*
* @param emf Enhanced Multi-frame image
* @param frame 0 based frame index
* @return legacy Single-frame image
*/
public Attributes extract(Attributes emf, int frame) {
return implFor(emf.getString(Tag.SOPClassUID))
.extract(this, emf, frame);
}
private static Impl implFor(String mfcuid) {
Impl impl = impls.get(mfcuid);
if (impl == null)
throw new IllegalArgumentException(
"Unsupported SOP Class: " + mfcuid);
return impl;
}
private Attributes extract(Attributes emf, int frame, String cuid) {
Attributes sfgs = emf.getNestedDataset(Tag.SharedFunctionalGroupsSequence);
if (sfgs == null)
throw new IllegalArgumentException(
"Missing (5200,9229) Shared Functional Groups Sequence");
Attributes fgs = emf.getNestedDataset(Tag.PerFrameFunctionalGroupsSequence, frame);
if (fgs == null)
throw new IllegalArgumentException(
"Missing (5200,9230) Per-frame Functional Groups Sequence Item for frame #" + (frame + 1));
Attributes dest = new Attributes(emf.size() * 2);
dest.addNotSelected(emf, EXCLUDE_TAGS);
addFunctionGroups(dest, sfgs);
addFunctionGroups(dest, fgs);
addPixelData(dest, emf, frame);
dest.setString(Tag.SOPClassUID, VR.UI, cuid);
dest.setString(Tag.SOPInstanceUID, VR.UI, uidMapper.get(
dest.getString(Tag.SOPInstanceUID)) + '.' + (frame + 1));
dest.setString(Tag.InstanceNumber, VR.IS,
createInstanceNumber(dest.getString(Tag.InstanceNumber, ""), frame));
dest.setString(Tag.ImageType, VR.CS, dest.getStrings(Tag.FrameType));
dest.remove(Tag.FrameType);
if (!preserveSeriesInstanceUID)
dest.setString(Tag.SeriesInstanceUID, VR.UI, uidMapper.get(
dest.getString(Tag.SeriesInstanceUID)));
adjustReferencedImages(dest, Tag.ReferencedImageSequence);
adjustReferencedImages(dest, Tag.SourceImageSequence);
return dest;
}
private void adjustReferencedImages(Attributes attrs, int sqtag) {
Sequence sq = attrs.getSequence(sqtag);
if (sq == null)
return;
ArrayList<Attributes> newRefs = new ArrayList<Attributes>();
for (Iterator<Attributes> itr = sq.iterator(); itr.hasNext();) {
Attributes ref = (Attributes) itr.next();
String cuid = legacySOPClassUID(ref.getString(Tag.ReferencedSOPClassUID));
if (cuid == null)
continue;
itr.remove();
String iuid = uidMapper.get(ref.getString(Tag.ReferencedSOPInstanceUID));
int[] frames = ref.getInts(Tag.ReferencedFrameNumber);
int n = frames == null ? nofAccessor.getNumberOfFrames(iuid)
: frames.length;
ref.remove(Tag.ReferencedFrameNumber);
ref.setString(Tag.ReferencedSOPClassUID, VR.UI, cuid);
for (int i = 0; i < n; i++) {
Attributes newRef = new Attributes(ref);
newRef.setString(Tag.ReferencedSOPInstanceUID, VR.UI,
iuid + '.' + (frames != null ? frames[i] : (i+1)));
newRefs.add(newRef);
}
}
for (Attributes ref : newRefs)
sq.add(ref);
}
private void addFunctionGroups(Attributes dest, Attributes fgs) {
dest.addSelected(fgs, Tag.ReferencedImageSequence);
Attributes fg;
for (int sqTag : fgs.tags())
if (sqTag != Tag.ReferencedImageSequence
&& (fg = fgs.getNestedDataset(sqTag)) != null)
dest.addAll(fg);
}
private void addPixelData(Attributes dest, Attributes src, int frame) {
VR.Holder vr = new VR.Holder();
Object pixelData = src.getValue(Tag.PixelData, vr);
if (pixelData instanceof byte[]) {
dest.setBytes(Tag.PixelData, vr.vr, extractPixelData(
(byte[]) pixelData, frame, calcFrameLength(src)));
} else if (pixelData instanceof BulkData) {
dest.setValue(Tag.PixelData, vr.vr, extractPixelData(
(BulkData) pixelData, frame, calcFrameLength(src)));
} else {
Fragments destFrags = dest.newFragments(Tag.PixelData, vr.vr, 2);
destFrags.add(null);
destFrags.add(((Fragments) pixelData).get(frame + 1));
}
}
private BulkData extractPixelData(BulkData src, int frame,
int length) {
return new BulkData(src.uriWithoutQuery(),
src.offset() + frame * length, length,
src.bigEndian);
}
private byte[] extractPixelData(byte[] src, int frame, int length) {
byte[] dest = new byte[length];
System.arraycopy(src, frame * length, dest, 0, length);
return dest;
}
private int calcFrameLength(Attributes src) {
return src.getInt(Tag.Rows, 0)
* src.getInt(Tag.Columns, 0)
* (src.getInt(Tag.BitsAllocated, 8) >> 3)
* src.getInt(Tag.NumberOfSamples, 1);
}
private String createInstanceNumber(String mfinstno, int frame) {
String s = String.format(instanceNumberFormat, mfinstno, frame + 1);
return s.length() > 16 ? s.substring(s.length() - 16) : s;
}
}