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Improve how to handle DICOM special modality
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@nroduit
nroduit committed Dec 13, 2023
1 parent 97f733f commit 5c398f7
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Showing 20 changed files with 587 additions and 361 deletions.
2 changes: 2 additions & 0 deletions weasis-core/src/main/java/org/weasis/core/ui/model/layer/LayerType.java
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,8 @@ public enum LayerType {
Boolean.TRUE,
Boolean.TRUE),

DICOM_SEG(95, "DICOM SEG", Boolean.TRUE, Boolean.TRUE, Boolean.FALSE, Boolean.FALSE), // NON-NLS

DICOM_SR(100, "DICOM SR", Boolean.TRUE, Boolean.TRUE, Boolean.FALSE, Boolean.TRUE), // NON-NLS

DICOM_RT(110, "DICOM RT", Boolean.TRUE, Boolean.TRUE, Boolean.FALSE, Boolean.FALSE), // NON-NLS
Expand Down
89 changes: 88 additions & 1 deletion ...com/weasis-dicom-codec/src/main/java/org/weasis/dicom/codec/AbstractKOSpecialElement.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
import java.util.stream.Collectors;
import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.Tag;
Expand All @@ -29,7 +31,7 @@
import org.weasis.dicom.codec.macro.SOPInstanceReferenceAndMAC;
import org.weasis.dicom.codec.macro.SeriesAndInstanceReference;

public class AbstractKOSpecialElement extends DicomSpecialElement {
public class AbstractKOSpecialElement extends HiddenSpecialElement {

public static class Reference {
private final String studyInstanceUID;
Expand Down Expand Up @@ -499,4 +501,89 @@ private static int[] removeFrames(int[] arr1, List<Integer> frameList) {
}
return result.stream().mapToInt(i -> i).toArray();
}

/**
* @param seriesUID the Series Instance UID
* @param specialElements the list of DicomSpecialElement
* @return the KOSpecialElement collection for the given parameters, if the referenced seriesUID
* is null all the KOSpecialElement from specialElements collection are returned. In any case
* all the KOSpecialElement that are writable will be added to the returned collection
* whatever is the seriesUID. These KO are part of the new created one's by users of the
* application
*/
public static Collection<KOSpecialElement> getKoSpecialElements(
Collection<KOSpecialElement> specialElements, String seriesUID) {

if (specialElements == null) {
return Collections.emptySet();
}

SortedSet<KOSpecialElement> koElementSet = null;
for (KOSpecialElement koElement : specialElements) {
Set<String> referencedSeriesInstanceUIDSet = koElement.getReferencedSeriesInstanceUIDSet();
if (seriesUID == null
|| referencedSeriesInstanceUIDSet.contains(seriesUID)
|| koElement.getMediaReader().isEditableDicom()) {

if (koElementSet == null) {
koElementSet = new TreeSet<>(ORDER_BY_DATE);
}
koElementSet.add(koElement);
}
}
return koElementSet == null ? Collections.emptySet() : koElementSet;
}

public static Collection<RejectedKOSpecialElement> getRejectionKoSpecialElements(
Collection<RejectedKOSpecialElement> specialElements, String seriesUID) {

if (specialElements == null) {
return Collections.emptySet();
}

SortedSet<RejectedKOSpecialElement> sortedSet = null;
for (RejectedKOSpecialElement element : specialElements) {
Set<String> referencedSeriesInstanceUIDSet = element.getReferencedSeriesInstanceUIDSet();

if (seriesUID == null
|| referencedSeriesInstanceUIDSet.contains(seriesUID)
|| element.getMediaReader().isEditableDicom()) {

if (sortedSet == null) {
sortedSet = new TreeSet<>(ORDER_BY_DATE);
}
sortedSet.add(element);
}
}
return sortedSet == null ? Collections.emptySet() : sortedSet;
}

public static RejectedKOSpecialElement getRejectionKoSpecialElement(
Collection<RejectedKOSpecialElement> specialElements,
String seriesUID,
String sopUID,
Integer dicomFrameNumber) {

if (specialElements == null) {
return null;
}
List<RejectedKOSpecialElement> koList = null;

for (RejectedKOSpecialElement koElement : specialElements) {
if (isSopuidInReferencedSeriesSequence(
koElement.getReferencedSOPInstanceUIDObject(seriesUID), sopUID, dicomFrameNumber)) {
if (koList == null) {
koList = new ArrayList<>();
}
koList.add(koElement);
}
}

if (koList != null && !koList.isEmpty()) {
// return the most recent Rejection Object
koList.sort(ORDER_BY_DATE);
return koList.getFirst();
}
return null;
}
}
93 changes: 75 additions & 18 deletions weasis-dicom/weasis-dicom-codec/src/main/java/org/weasis/dicom/codec/DicomMediaIO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
import java.util.Map.Entry;
import java.util.Objects;
import java.util.Optional;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.atomic.AtomicInteger;
import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.BulkData;
Expand Down Expand Up @@ -83,6 +84,7 @@ public class DicomMediaIO implements DcmMediaReader {
public static final String SERIES_MIMETYPE = "series/dicom"; // NON-NLS
public static final String SERIES_PR_MIMETYPE = "pr/dicom"; // NON-NLS
public static final String SERIES_KO_MIMETYPE = "ko/dicom"; // NON-NLS
public static final String SERIES_SEG_MIMETYPE = "seg/dicom"; // NON-NLS

public static final String SERIES_ENCAP_DOC_MIMETYPE = "encap/dicom"; // NON-NLS
public static final String UNREADABLE = "unreadable/dicom"; // NON-NLS
Expand Down Expand Up @@ -186,13 +188,12 @@ public class DicomMediaIO implements DcmMediaReader {
}

public static final Map<String, DicomSpecialElementFactory> DCM_ELEMENT_FACTORIES =
new HashMap<>();
new ConcurrentHashMap<>();

static {
/*
* DICOM PR and KO are not displayed with a special viewer but are transversally managed objects. So they are
* not registered from a viewer.
*/
// The hidden type factories are not displayed with a special viewer but are transversally
// managed objects.

DCM_ELEMENT_FACTORIES.put(
"PR",
new DicomSpecialElementFactory() {
Expand All @@ -207,11 +208,17 @@ public String[] getModalities() {
return new String[] {"PR"};
}

@Override
public boolean isHidden() {
return true;
}

@Override
public DicomSpecialElement buildDicomSpecialElement(DicomMediaIO mediaIO) {
return new PRSpecialElement(mediaIO);
}
});

DCM_ELEMENT_FACTORIES.put(
"KO",
new DicomSpecialElementFactory() {
Expand All @@ -226,6 +233,11 @@ public String[] getModalities() {
return new String[] {"KO"};
}

@Override
public boolean isHidden() {
return true;
}

@Override
public DicomSpecialElement buildDicomSpecialElement(DicomMediaIO mediaIO) {
if (RejectedKOSpecialElement.isRejectionKOS(mediaIO)) {
Expand All @@ -234,6 +246,31 @@ public DicomSpecialElement buildDicomSpecialElement(DicomMediaIO mediaIO) {
return new KOSpecialElement(mediaIO);
}
});

DCM_ELEMENT_FACTORIES.put(
"SEG",
new DicomSpecialElementFactory() {

@Override
public String getSeriesMimeType() {
return SERIES_SEG_MIMETYPE;
}

@Override
public String[] getModalities() {
return new String[] {"SEG"};
}

@Override
public boolean isHidden() {
return true;
}

@Override
public DicomSpecialElement buildDicomSpecialElement(DicomMediaIO mediaIO) {
return new SegSpecialElement(mediaIO);
}
});
}

private static final SoftHashMap<DicomMediaIO, DicomMetaData> HEADER_CACHE =
Expand Down Expand Up @@ -325,7 +362,7 @@ public synchronized boolean isReadableDicom() {
return false;
}

if (tags.size() == 0) {
if (tags.isEmpty()) {
try {
DicomMetaData md = readMetaData();
Attributes fmi = md.getFileMetaInformation();
Expand All @@ -347,7 +384,11 @@ public synchronized boolean isReadableDicom() {
// MPEG4 AVC/H.264 BD 1.2.840.10008.1.2.4.103
mimeType = SERIES_VIDEO_MIMETYPE;
} else {
mimeType = IMAGE_MIMETYPE;
if ("1.2.840.10008.5.1.4.1.1.66.4".equals(mediaStorageSOPClassUID)) {
mimeType = SERIES_SEG_MIMETYPE; // Do not display SEG images
} else {
mimeType = IMAGE_MIMETYPE;
}
}
} else {
boolean special = setDicomSpecialType(header);
Expand Down Expand Up @@ -423,7 +464,7 @@ public Iterator<Entry<TagW, Object>> getTagEntrySetIterator() {
}

private void writeInstanceTags(DicomMetaData md) {
if (tags.size() > 0 || md == null || md.getDicomObject() == null) {
if (!tags.isEmpty() || md == null || md.getDicomObject() == null) {
return;
}
Attributes fmi = md.getFileMetaInformation();
Expand Down Expand Up @@ -698,8 +739,9 @@ public synchronized MediaElement[] getMediaElement() {
} else if (SERIES_ENCAP_DOC_MIMETYPE.equals(mimeType)) {
image = new MediaElement[] {new DicomEncapDocElement(this, null)};
} else {
DicomSpecialElementFactory factory = getDicomSpecialElementFactory();
if (numberOfFrame > 0) {
image = new MediaElement[numberOfFrame];
image = new MediaElement[factory == null ? numberOfFrame : numberOfFrame + 1];
for (int i = 0; i < image.length; i++) {
image[i] = new DicomImageElement(this, i);
}
Expand All @@ -712,25 +754,30 @@ public synchronized MediaElement[] getMediaElement() {
image[i].setTag(TagD.get(Tag.InstanceNumber), nb);
}
}
} else {
String modality = TagD.getTagValue(this, Tag.Modality, String.class);
if (modality != null) {
DicomSpecialElementFactory factory = DCM_ELEMENT_FACTORIES.get(modality);
if (factory != null) {
image = new MediaElement[1];
image[0] = factory.buildDicomSpecialElement(this);
}
if (factory != null) {
image[numberOfFrame] = factory.buildDicomSpecialElement(this);
}
if (image == null) {
} else {
if (factory == null) {
// Corrupted image => should have one frame
image = new MediaElement[0];
} else {
image = new MediaElement[] {factory.buildDicomSpecialElement(this)};
}
}
}
}
return image;
}

private DicomSpecialElementFactory getDicomSpecialElementFactory() {
String modality = TagD.getTagValue(this, Tag.Modality, String.class);
if (modality != null) {
return DCM_ELEMENT_FACTORIES.get(modality);
}
return null;
}

@Override
public MediaSeries<MediaElement> getMediaSeries() {
Series<MediaElement> series = null;
Expand Down Expand Up @@ -880,4 +927,14 @@ private synchronized DicomMetaData readMetaData() throws IOException {
reader.dispose();
}
}

public static boolean isHiddenModality(String modality) {
if (modality != null) {
DicomSpecialElementFactory factory = DCM_ELEMENT_FACTORIES.get(modality);
if (factory != null) {
return factory.isHidden();
}
}
return false;
}
}
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