/**
* Copy a set of DICOM files, if they match specified criteria.
*
* <p>Does not actually check the Modality value in the file, but matches the SOP Class against
* what is returned from {@link
* com.pixelmed.dicom.SOPClass#getPlausibleStandardSOPClassUIDsForModality(String)
* SOPClass.getPlausibleStandardSOPClassUIDsForModality(String)}.
*
* @param arg array of four strings - the input path, the output path, and the SOP Class UID or
* Modality
*/
public static void main(String arg[]) {
try {
if (arg.length == 3) {
FindAndCopySelectedDicomFiles importer =
new FindAndCopySelectedDicomFiles(new PrintStreamMessageLogger(System.err));
importer.outputPath = arg[1];
importer.sopClasses = new HashSet();
if (arg[2].startsWith("1")) {
// System.err.println("main(): importer.sopClasses.add = \""+arg[2]+"\"");
importer.sopClasses.add(arg[2]);
} else {
String[] sopClasses = SOPClass.getPlausibleStandardSOPClassUIDsForModality(arg[2]);
if (sopClasses == null) {
throw new DicomException(
"Cannot find plausible SOP Standard Classes for modality \"" + arg[2] + "\"");
} else {
for (String sopClass : sopClasses) {
// System.err.println("main(): importer.sopClasses.add = \""+sopClass+"\"");
importer.sopClasses.add(sopClass);
}
}
}
importer.importDicomFiles(arg[0]);
} else {
System.err.println(
"Usage: java -cp ./pixelmed.jar com.pixelmed.apps.FindAndCopySelectedDicomFiles srcdir dstdir sopclass|modality");
}
} catch (Exception e) {
e.printStackTrace(System.err);
System.exit(0);
}
}
/**
* Generate commomn attributes for converted images.
*
* <p>Does NOT add ManufacturerModelName ... that should be added by caller.
*
* <p>Does NOT call
* CodingSchemeIdentification.replaceCodingSchemeIdentificationSequenceWithCodingSchemesUsedInAttributeList
* ... that should be done by caller.
*
* @param list
* @param patientName
* @param patientID
* @param studyID
* @param seriesNumber
* @param instanceNumber
* @param modality may be null
* @param sopClass may be null
* @throws DicomException
* @throws NumberFormatException
*/
public static void generateCommonAttributes(
AttributeList list,
String patientName,
String patientID,
String studyID,
String seriesNumber,
String instanceNumber,
String modality,
String sopClass)
throws DicomException {
UIDGenerator u = new UIDGenerator();
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SOPInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SeriesInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.StudyInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.FrameOfReferenceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.PatientName);
a.addValue(patientName);
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.PatientID);
a.addValue(patientID);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.PatientBirthDate);
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.PatientSex);
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.StudyID);
a.addValue(studyID);
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.ReferringPhysicianName);
a.addValue("^^^^");
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.AccessionNumber);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.SeriesNumber);
a.addValue(seriesNumber);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.InstanceNumber);
a.addValue(instanceNumber);
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.Manufacturer);
a.addValue("PixelMed");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.DeviceSerialNumber);
a.addValue(new java.rmi.dgc.VMID().toString());
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.SoftwareVersions);
a.addValue(VersionAndConstants.getBuildDate());
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.PatientOrientation);
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.BurnedInAnnotation);
a.addValue("NO");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.RecognizableVisualFeatures);
a.addValue("NO");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.ContentQualification);
a.addValue("RESEARCH");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.LossyImageCompression);
a.addValue("00");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.PositionReferenceIndicator);
list.put(a);
}
{
java.util.Date currentDateTime = new java.util.Date();
String currentDate = new java.text.SimpleDateFormat("yyyyMMdd").format(currentDateTime);
String currentTime = new java.text.SimpleDateFormat("HHmmss.SSS").format(currentDateTime);
{
Attribute a = new DateAttribute(TagFromName.StudyDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.StudyTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.SeriesDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.SeriesTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.ContentDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.ContentTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.InstanceCreationDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.InstanceCreationTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.TimezoneOffsetFromUTC);
a.addValue(DateTimeAttribute.getTimeZone(java.util.TimeZone.getDefault(), currentDateTime));
list.put(a);
}
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.InstanceCreatorUID);
a.addValue(VersionAndConstants.instanceCreatorUID);
list.put(a);
}
int numberOfFrames =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.NumberOfFrames, 1);
int samplesPerPixel =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.SamplesPerPixel, 1);
if (sopClass == null) {
// if modality were not null, could actually attempt to guess SOP Class based on modality here
// :(
sopClass = SOPClass.SecondaryCaptureImageStorage;
if (numberOfFrames > 1) {
if (samplesPerPixel == 1) {
int bitsAllocated =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.BitsAllocated, 1);
if (bitsAllocated == 8) {
sopClass = SOPClass.MultiframeGrayscaleByteSecondaryCaptureImageStorage;
} else if (bitsAllocated == 16) {
sopClass = SOPClass.MultiframeGrayscaleWordSecondaryCaptureImageStorage;
} else {
Attribute aPixelData = list.getPixelData();
if (aPixelData instanceof OtherFloatAttribute
|| aPixelData instanceof OtherDoubleAttribute) {
sopClass = SOPClass.ParametricMapStorage;
}
}
} else if (samplesPerPixel == 3) {
sopClass = SOPClass.MultiframeTrueColorSecondaryCaptureImageStorage;
}
}
}
if (sopClass.equals(SOPClass.ParametricMapStorage)) {
addParametricMapFrameTypeSharedFunctionalGroup(list);
{
Attribute a = new CodeStringAttribute(TagFromName.ContentLabel);
a.addValue("LABEL1");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.ContentDescription);
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.ContentCreatorName);
list.put(a);
}
}
if (SOPClass.isEnhancedMultiframeImageStorage(sopClass)) {
if (samplesPerPixel == 1) {
double windowWidth =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.WindowWidth, 0);
if (windowWidth > 0) {
double windowCenter =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.WindowCenter, 0);
String voiLUTFunction =
Attribute.getSingleStringValueOrDefault(list, TagFromName.VOILUTFunction, "LINEAR");
FunctionalGroupUtilities.generateVOILUTFunctionalGroup(
list, numberOfFrames, windowWidth, windowCenter, voiLUTFunction);
list.remove(TagFromName.WindowCenter);
list.remove(TagFromName.WindowWidth);
list.remove(TagFromName.VOILUTFunction);
}
}
double rescaleSlope =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.RescaleSlope, 0);
if (rescaleSlope > 0) {
double rescaleIntercept =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.RescaleIntercept, 0);
String rescaleType =
Attribute.getSingleStringValueOrDefault(list, TagFromName.RescaleType, "US");
FunctionalGroupUtilities.generatePixelValueTransformationFunctionalGroup(
list, numberOfFrames, rescaleSlope, rescaleIntercept, rescaleType);
list.remove(TagFromName.RescaleSlope);
list.remove(TagFromName.RescaleIntercept);
list.remove(TagFromName.RescaleType);
}
// four values required
{
Attribute a = new CodeStringAttribute(TagFromName.ImageType);
a.addValue("DERIVED");
a.addValue("PRIMARY");
a.addValue("");
a.addValue("");
list.put(a);
}
} else {
// two values will usually do
{
Attribute a = new CodeStringAttribute(TagFromName.ImageType);
a.addValue("DERIVED");
a.addValue("PRIMARY");
list.put(a);
}
}
if (SOPClass.isMultiframeSecondaryCaptureImageStorage(sopClass)) {
if (list.get(TagFromName.PerFrameFunctionalGroupsSequence) != null) {
{
AttributeTagAttribute a = new AttributeTagAttribute(TagFromName.FrameIncrementPointer);
a.addValue(TagFromName.PerFrameFunctionalGroupsSequence);
list.put(a);
}
} else {
if (numberOfFrames > 1) {
{
AttributeTagAttribute a = new AttributeTagAttribute(TagFromName.FrameIncrementPointer);
a.addValue(TagFromName.PageNumberVector);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.PageNumberVector);
for (int page = 1; page <= numberOfFrames; ++page) {
a.addValue(page);
}
list.put(a);
}
}
}
}
System.err.println(
"CommonConvertedAttributeGeneration.generateCommonAttributes(): SOP Class = " + sopClass);
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SOPClassUID);
a.addValue(sopClass);
list.put(a);
}
if (SOPClass.isSecondaryCaptureImageStorage(sopClass)) {
{
Attribute a = new CodeStringAttribute(TagFromName.ConversionType);
a.addValue("WSD");
list.put(a);
}
}
if (modality == null) {
// could actually attempt to guess modality based on SOP Class here :(
modality = "OT";
}
{
Attribute a = new CodeStringAttribute(TagFromName.Modality);
a.addValue(modality);
list.put(a);
}
{
Attribute a = new SequenceAttribute(TagFromName.AcquisitionContextSequence);
list.put(a);
}
}
/** @param list */
private void doCommonConstructorStuff(AttributeList list) throws DicomException {
String sopClassUID = Attribute.getSingleStringValueOrEmptyString(list, TagFromName.SOPClassUID);
if (SOPClass.isImageStorage(sopClassUID)) {
// System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): is an image");
SourceImage allFramesImage = new SourceImage(list);
Attribute aSegmentSequence = list.get(TagFromName.SegmentSequence);
Attribute aSharedFunctionalGroupsSequence =
list.get(TagFromName.SharedFunctionalGroupsSequence);
Attribute aPerFrameFunctionalGroupsSequence =
list.get(TagFromName.PerFrameFunctionalGroupsSequence);
int numberOfFrames = allFramesImage.getNumberOfBufferedImages();
if (allFramesImage != null
&& numberOfFrames > 0
&& aSegmentSequence != null
&& aSegmentSequence instanceof SequenceAttribute
&& aSharedFunctionalGroupsSequence != null
&& aSharedFunctionalGroupsSequence instanceof SequenceAttribute
&& aPerFrameFunctionalGroupsSequence != null
&& aPerFrameFunctionalGroupsSequence instanceof SequenceAttribute) {
System.err.println(
"SuperimposedDicomSegments.doCommonConstructorStuff(): have a segmentation object with one or more frames");
SequenceAttribute saSegmentSequence = (SequenceAttribute) aSegmentSequence;
int numberOfSegments = saSegmentSequence.getNumberOfItems();
if (numberOfSegments > 0) {
for (int i = 0; i < numberOfSegments; ++i) {
AttributeList itemList = saSegmentSequence.getItem(i).getAttributeList();
String segmentNumber =
Attribute.getSingleStringValueOrEmptyString(
itemList,
TagFromName
.SegmentNumber); // theoretically supposed to start at 1 and increase by 1,
// but don't trust it
if (segmentNumber.length() > 0) {
int[] recommendedDisplayCIELabValues =
Attribute.getIntegerValues(itemList, TagFromName.RecommendedDisplayCIELabValue);
SegmentInformation si = segmentInformationBySegmentNumber.get(segmentNumber);
if (si == null) {
si = new SegmentInformation(segmentNumber, recommendedDisplayCIELabValues);
segmentInformationBySegmentNumber.put(segmentNumber, si);
} else {
throw new DicomException("Duplicate segment number");
}
} else {
throw new DicomException("Missing segment number");
}
}
} else {
System.err.println(
"SuperimposedDicomSegments.doCommonConstructorStuff(): Error: No segments in segmentation object");
}
SequenceAttribute saSharedFunctionalGroupsSequence =
(SequenceAttribute) aSharedFunctionalGroupsSequence;
SequenceAttribute saPerFrameFunctionalGroupsSequence =
(SequenceAttribute) aPerFrameFunctionalGroupsSequence;
SequenceAttribute sharedSegmentIdentificationSequence =
(SequenceAttribute)
(SequenceAttribute.getNamedAttributeFromWithinSequenceWithSingleItem(
saSharedFunctionalGroupsSequence, TagFromName.SegmentIdentificationSequence));
int nPerFrameFunctionalGroupsSequence =
saPerFrameFunctionalGroupsSequence.getNumberOfItems();
if (nPerFrameFunctionalGroupsSequence == numberOfFrames) {
for (int f = 0; f < numberOfFrames; ++f) {
SequenceAttribute useSegmentIdentificationSequence =
sharedSegmentIdentificationSequence;
if (useSegmentIdentificationSequence == null) {
useSegmentIdentificationSequence =
(SequenceAttribute)
(saPerFrameFunctionalGroupsSequence
.getItem(f)
.getAttributeList()
.get(TagFromName.SegmentIdentificationSequence));
}
if (useSegmentIdentificationSequence != null) {
Attribute aReferencedSegmentNumber =
SequenceAttribute.getNamedAttributeFromWithinSequenceWithSingleItem(
useSegmentIdentificationSequence, TagFromName.ReferencedSegmentNumber);
String referencedSegmentNumber =
aReferencedSegmentNumber == null
? ""
: aReferencedSegmentNumber.getSingleStringValueOrEmptyString();
if (referencedSegmentNumber.length() > 0) {
SortedSet<Integer> framesForSegment =
framesForSegmentBySegmentNumber.get(referencedSegmentNumber);
if (framesForSegment == null) {
framesForSegment = new TreeSet<Integer>();
framesForSegmentBySegmentNumber.put(referencedSegmentNumber, framesForSegment);
}
framesForSegment.add(new Integer(f));
} else {
throw new DicomException("Missing ReferencedSegmentNumber for frame " + f);
}
} else {
throw new DicomException("Missing SegmentIdentificationSequence for frame " + f);
}
}
} else {
throw new DicomException(
"Number of frames "
+ numberOfFrames
+ " does not match number of PerFrameFunctionalGroupsSequence items "
+ nPerFrameFunctionalGroupsSequence);
}
// SortedMap<String,SortedSet<Integer>> framesForSegmentBySegmentNumber
for (String segmentNumber : framesForSegmentBySegmentNumber.keySet()) {
// System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): Making
// SourceImageSubset for segmentNumber "+segmentNumber);
SortedSet<Integer> framesForSegment = framesForSegmentBySegmentNumber.get(segmentNumber);
int[] parentFrameNumbers = new int[framesForSegment.size()];
{
int childFrameNumber = 0;
for (Integer parentFrameNumber : framesForSegment) {
// System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff():
// parentFrameNumber["+childFrameNumber+"] = "+parentFrameNumber);
parentFrameNumbers[childFrameNumber++] = parentFrameNumber.intValue();
}
}
SourceImage sourceImageForSegment =
new SourceImageSubset(allFramesImage, parentFrameNumbers);
GeometryOfVolume geometryForSegment =
new GeometryOfVolumeFromAttributeList(list, parentFrameNumbers);
if (!geometryForSegment.isVolumeSampledRegularlyAlongFrameDimension()) {
System.err.println(
"SuperimposedDicomSegments.doCommonConstructorStuff(): Warning: superimposed geometry is not a single regularly sampled volume for segment "
+ segmentNumber);
}
superimposedImagesBySegmentNumber.put(
segmentNumber,
new SuperimposedImage(
sourceImageForSegment,
geometryForSegment,
segmentInformationBySegmentNumber.get(segmentNumber)
.recommendedDisplayCIELabValues));
}
// superimposedGeometry = new GeometryOfVolumeFromAttributeList(list);
// if (!superimposedGeometry.isVolumeSampledRegularlyAlongFrameDimension()) {
// System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): Warning:
// superimposed geometry is not a single regularly sampled volume");
// }
} else {
System.err.println(
"SuperimposedDicomSegments.doCommonConstructorStuff(): Error: Not a valid segmentation object");
}
}
}
