/**
  * 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);
 }
Esempio n. 4
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  /**
   * @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);
    }
  }
Esempio n. 5
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    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);
      }
    }
Esempio n. 6
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  /**
   * @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();
  }
Esempio n. 7
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 /** @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);
 }
Esempio n. 8
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    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);
      }
    }