/**
* Read a DICOM image input format file encoded in a compressed transfer syntax and extract the
* compressed bitstreams into a file for each frame.
*
* <p>The output file will be named with the specified prefix to which will be appended a 6 digit
* zero padded frame number starting from 1, followed by an appropriate file name extension for
* the transfer syntax.
*
* @param arg two parameters, the inputFile, the outputFile prefix
*/
public static void main(String arg[]) {
try {
if (arg.length == 2) {
DecimalFormat sixDigitZeroPaddedFormat = new DecimalFormat("000000");
AttributeList list = new AttributeList();
list.setDecompressPixelData(false);
list.read(arg[0]);
String fileNameExtension = getFileNameExtensionForCompressedPixelData(list);
OtherByteAttributeMultipleCompressedFrames aPixelData =
(OtherByteAttributeMultipleCompressedFrames) (list.getPixelData());
byte[][] frames = aPixelData.getFrames();
for (int f = 0; f < frames.length; ++f) {
String outputFilename =
arg[1] + sixDigitZeroPaddedFormat.format(f + 1) + "." + fileNameExtension;
System.err.println("Writing " + outputFilename);
FileOutputStream o = new FileOutputStream(outputFilename);
o.write(frames[f]);
o.close();
}
} else {
System.err.println("Error: Incorrect number of arguments");
System.err.println("Usage: UnencapsulateCompressedPixelData inputFile outputFilePrefix");
System.exit(1);
}
} catch (Exception e) {
e.printStackTrace();
}
}
public void TestSafePrivateGEPACSRelated_FromFile() throws Exception {
AttributeList list = new AttributeList();
String testFilePath = System.getProperty("com.pixelmed.test.filepath");
// System.err.println("TestSafePrivateGEPACSRelated.TestSafePrivateGEPACSRelated_FromFile():
// testFilePath = "+testFilePath);
list.read(new java.io.File(testFilePath, "philipsctwithgepacsprivateattributes.dcm"));
// System.err.print("TestSafePrivateGEPACSRelated.TestSafePrivateGEPACSRelated():\n"+list);
list.removeUnsafePrivateAttributes();
assertTrue(
"Checking Creator is not removed", list.get(new AttributeTag(0x0903, 0x0010)) != null);
assertTrue(
"Checking Reject Image Flag is not removed",
list.get(new AttributeTag(0x0903, 0x1010)) != null);
}
public void TestSafePrivatePhilipsPETRelated_ScaleFactors_FromFile() throws Exception {
AttributeList list = new AttributeList();
String testFilePath = System.getProperty("com.pixelmed.test.filepath");
// System.err.println("TestSafePrivatePhilipsPETRelated.TestSafePrivatePhilipsPETRelated_ScaleFactors_FromFile(): testFilePath = "+testFilePath);
list.read(new java.io.File(testFilePath, "philipssuvandactivityscalefactors.dcm"));
// System.err.print("TestSafePrivatePhilipsPETRelated.TestSafePrivatePhilipsPETRelated_ScaleFactors():\n"+list);
list.removeUnsafePrivateAttributes();
assertTrue(
"Checking Creator is not removed", list.get(new AttributeTag(0x7053, 0x0010)) != null);
assertTrue(
"Checking SUV Factor is not removed", list.get(new AttributeTag(0x7053, 0x1000)) != null);
assertTrue(
"Checking Activity Concentration Factor is not removed",
list.get(new AttributeTag(0x7053, 0x1009)) != null);
}
/**
* @param arg the underlying image file name, the superimposed segmentation object file name, and
* optionally the file name basis for a consumer format image rendering
*/
public static void main(String arg[]) {
try {
String underlyingFileName = arg[0];
String superimposedFileName = arg[1];
SuperimposedDicomSegments superimposedSegments =
new SuperimposedDicomSegments(superimposedFileName);
Vector<SuperimposedImage> superimposedImages = superimposedSegments.getSuperimposedImages();
if (arg.length > 2) {
String outputFileName = arg[2];
ConsumerFormatImageMaker.convertFileToEightBitImage(
underlyingFileName,
outputFileName,
"jpeg",
0 /*windowCenter*/,
0 /*windowWidth*/,
0 /*imageWidth*/,
0 /*imageHeight*/,
100 /*imageQuality*/,
ConsumerFormatImageMaker.ALL_ANNOTATIONS,
superimposedImages,
null /*arrayOfPerFrameShapes*/,
0 /*debugLevel*/);
} else {
AttributeList underlyingList = new AttributeList();
underlyingList.read(underlyingFileName);
SourceImage underlyingSourceImage = new SourceImage(underlyingList);
GeometryOfVolume underlyingGeometry = new GeometryOfVolumeFromAttributeList(underlyingList);
SingleImagePanel ip = new SingleImagePanel(underlyingSourceImage, null, underlyingGeometry);
ip.setSuperimposedImages(superimposedImages);
javax.swing.JFrame frame = new javax.swing.JFrame();
frame.add(ip);
frame.setSize(underlyingSourceImage.getWidth(), underlyingSourceImage.getHeight());
frame.setVisible(true);
}
} catch (Exception e) {
e.printStackTrace(System.err);
}
}
protected void doSomethingWithDicomFileOnMedia(String mediaFileName) {
// logLn("OurFirstPassMediaImporter.doSomethingWithDicomFile(): "+mediaFileName);
try {
DicomInputStream i = new DicomInputStream(new File(mediaFileName));
AttributeList list = new AttributeList();
list.read(i);
i.close();
String sopInstanceUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.SOPInstanceUID);
if (sopInstanceUID.length() > 0) {
String studyInstanceUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.StudyInstanceUID);
if (studyInstanceUID.length() > 0) {
mapOfSOPInstanceUIDToStudyInstanceUID.put(sopInstanceUID, studyInstanceUID);
} else {
throw new DicomException("Missing StudyInstanceUID");
}
{
CompositeInstanceContext cic = new CompositeInstanceContext(list, false /*forSR*/);
// remove all except patient context ...
cic.removeStudy();
cic.removeSeries();
cic.removeEquipment();
cic.removeFrameOfReference();
cic.removeInstance();
cic.removeSRDocumentGeneral();
Group group = addToGroups(list);
// System.err.println("group = "+group);
mergePatientContext(group, cic);
}
} else {
throw new DicomException("Missing SOPInstanceUID");
}
} catch (Exception e) {
logLn("Error: File " + mediaFileName + " exception " + e);
}
}
/**
* @param filenames
* @exception Exception if internal error
*/
public void loadMultiPanelFromSpecifiedFiles(String filenames[]) throws Exception {
int nFiles = filenames.length;
SingleImagePanel imagePanels[] = new SingleImagePanel[nFiles];
String orientations[][] = new String[nFiles][];
String views[] = new String[nFiles];
String lateralityViewAndModifiers[] = new String[nFiles];
String lateralities[] = new String[nFiles];
int widths[] = new int[nFiles];
int heights[] = new int[nFiles];
PixelSpacing spacing[] = new PixelSpacing[nFiles];
String rowOrientations[] = new String[nFiles];
String columnOrientations[] = new String[nFiles];
HashMap eventContexts = new HashMap();
double maximumHorizontalExtentInMm = 0;
double maximumVerticalExtentInMm = 0;
StructuredReport sr[] = new StructuredReport[nFiles];
int nImages = 0;
int nCAD = 0;
ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
for (int f = 0; f < nFiles; ++f) {
try {
String filename = filenames[f];
DicomInputStream distream = null;
InputStream in = classLoader.getResourceAsStream(filename);
if (in != null) {
distream = new DicomInputStream(in);
} else {
distream = new DicomInputStream(new File(filename));
}
AttributeList list = new AttributeList();
list.read(distream);
if (list.isImage()) {
int i = nImages++;
System.err.println("IMAGE [" + i + "] is file " + f + " (" + filenames[f] + ")");
orientations[i] = getPatientOrientation(list);
// System.err.println("IMAGE ["+i+"] orientation="+(orientations[i] == null &&
// orientations[i].length == 2 ? "" : (orientations[i][0] + " " + orientations[i][1])));
views[i] = getView(list);
// System.err.println("IMAGE ["+i+"] view="+views[i]);
lateralityViewAndModifiers[i] = getImageLateralityViewModifierAndViewModifier(list);
// System.err.println("IMAGE ["+i+"]
// lateralityViewAndModifiers="+lateralityViewAndModifiers[i]);
// System.err.println("File "+filenames[f]+": "+lateralityViewAndModifiers[i]);
lateralities[i] = getLaterality(list);
// System.err.println("IMAGE ["+i+"] laterality="+lateralities[i]);
spacing[i] = new PixelSpacing(list);
// System.err.println("IMAGE ["+i+"] spacing="+spacing[i]);
SourceImage sImg = new SourceImage(list);
BufferedImage img = sImg.getBufferedImage();
widths[i] = sImg.getWidth();
heights[i] = sImg.getHeight();
boolean shareVOIEventsInStudy =
false; // does not seem to work anyway, since adding VOITransform to panel constructor
// :(
EventContext eventContext = new EventContext(Integer.toString(i));
SingleImagePanel imagePanel = makeNewImagePanel(sImg, eventContext);
imagePanel.setDemographicAndTechniqueAnnotations(
new DemographicAndTechniqueAnnotations(list),
"SansSerif",
Font.PLAIN,
10,
Color.pink);
imagePanel.setOrientationAnnotations(
new OrientationAnnotations(rowOrientations[i], columnOrientations[i]),
"SansSerif",
Font.PLAIN,
20,
Color.pink);
imagePanel.setPixelSpacingInSourceImage(
spacing[i].getSpacing(), spacing[i].getDescription());
if (Attribute.getSingleStringValueOrEmptyString(list, TagFromName.VOILUTFunction)
.equals("SIGMOID")) {
imagePanel.setVOIFunctionToLogistic();
}
imagePanels[i] = imagePanel;
} else {
throw new DicomException("Unsupported SOP Class in file " + filenames[f]);
}
} catch (Exception e) { // FileNotFoundException,IOException,DicomException
e.printStackTrace(System.err);
}
}
// int imagesPerRow = nImages; // i.e., 1 -> 1, 2 -> 1, 4 -> 4, 5 -> 4, 8 -> 4
// int imagesPerCol = 1;
int imagesPerRow = nImages >= 8 ? 8 : nImages; // i.e., 1 -> 1, 2 -> 1, 4 -> 4, 5 -> 4, 8 -> 4
int imagesPerCol =
(nImages - 1) / imagesPerRow + 1; // i.e., 1 -> 1, 2 -> 2, 4 -> 1, 5 -> 2, 8 -> 2
int singleWidth = frameWidth / imagesPerRow;
int singleHeight = frameHeight / imagesPerCol;
if (nImages == 1 && singleWidth > singleHeight) {
singleWidth =
singleWidth / 2; // use only half the screen for a single view and a landscape monitor
}
for (int i = 0; i < nImages; ++i) {
DisplayedAreaSelection displayedAreaSelection = null;
displayedAreaSelection =
new DisplayedAreaSelection(
widths[i],
heights[i],
0,
0,
widths[i],
heights[i],
true, // in case spacing was not supplied
0,
0,
0,
0,
0,
false /*crop*/);
imagePanels[i].setDisplayedAreaSelection(displayedAreaSelection);
imagePanels[i].setPreTransformImageRelativeCoordinates(null);
}
SingleImagePanel.deconstructAllSingleImagePanelsInContainer(multiPanel);
multiPanel.removeAll();
multiPanel.setLayout(new GridLayout(imagesPerCol, imagesPerRow));
multiPanel.setBackground(Color.black);
for (int x = 0; x < imagesPerCol; ++x) {
for (int y = 0; y < imagesPerRow; ++y) {
int i = x * imagesPerRow + y;
if (i < nImages) {
imagePanels[i].setPreferredSize(new Dimension(singleWidth, singleHeight));
multiPanel.add(imagePanels[i]);
}
}
}
frame.getContentPane().validate();
frame.getContentPane().repaint();
}
/** @param filename */
public SuperimposedDicomSegments(String filename) throws DicomException, IOException {
// no need to call super(), does nothing
AttributeList list = new AttributeList();
list.read(filename);
doCommonConstructorStuff(list);
}
protected void doSomethingWithDicomFileOnMedia(String mediaFileName) {
// logLn("OurFirstPassMediaImporter.doSomethingWithDicomFile(): "+mediaFileName);
try {
DicomInputStream i = new DicomInputStream(new File(mediaFileName));
AttributeList list = new AttributeList();
list.read(i);
i.close();
String sopInstanceUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.SOPInstanceUID);
if (sopInstanceUID.length() > 0) {
Group group = mapOfSOPInstanceUIDToGroup.get(sopInstanceUID);
// System.err.println("group = "+group);
// System.err.println("Groups size = "+groups.size());
if (group == null) {
if (groups.size() == 1) {
group = groups.toArray(singleGroupArray)[0];
} else {
throw new DicomException(
"Cannot merge context for second set if more than one group");
}
}
if (group != null) {
logLn("In group " + group.identity);
if (group.context != null) {
CompositeInstanceContext.removePatient(
list); // remove anything hanging around, such as empty attributes
list.putAll(
group.context
.getAttributeList()); // overwrite all patient context in list that was read
// in
} else {
throw new DicomException(
"Missing group context for SOPInstanceUID on second pass"); // should not be
// possible
}
ClinicalTrialsAttributes.addContributingEquipmentSequence(
list,
true,
new CodedSequenceItem("109103", "DCM", "Modifying Equipment"),
"PixelMed", // Manufacturer
"PixelMed", // Institution Name
"Software Development", // Institutional Department Name
"Bangor, PA", // Institution Address
null, // Station Name
"com.pixelmed.apps.MergeCompositeContext", // Manufacturer's Model Name
null, // Device Serial Number
"Vers. " + VersionAndConstants.getBuildDate(), // Software Version(s)
"Merged patient context");
list.removeGroupLengthAttributes();
list.removeMetaInformationHeaderAttributes();
list.remove(TagFromName.DataSetTrailingPadding);
FileMetaInformation.addFileMetaInformation(
list, TransferSyntax.ExplicitVRLittleEndian, ourAETitle);
File dstFile =
new File(
dstFolderName,
MoveDicomFilesIntoHierarchy.makeHierarchicalPathFromAttributes(list));
if (dstFile.exists()) {
throw new DicomException(
"\""
+ mediaFileName
+ "\": new file \""
+ dstFile
+ "\" already exists - not overwriting");
} else {
File dstParentDirectory = dstFile.getParentFile();
if (!dstParentDirectory.exists()) {
if (!dstParentDirectory.mkdirs()) {
throw new DicomException(
"\""
+ mediaFileName
+ "\": parent directory creation failed for \""
+ dstFile
+ "\"");
}
}
logLn("Writing with new context file " + dstFile);
list.write(dstFile, TransferSyntax.ExplicitVRLittleEndian, true, true);
}
} else {
throw new DicomException(
"Missing group for SOPInstanceUID on second pass"); // should not be possible for
// single set case
}
} else {
throw new DicomException("Missing SOPInstanceUID");
}
} catch (Exception e) {
logLn("Error: File " + mediaFileName + " exception " + e);
}
}
