/**
   * Generates a zero crossing mask for a 2D function. Sets a ModelImage to 255 if a zero crossing
   * is detected.
   *
   * @param slice the slice of the volume which we are working on (0 if from 2D image)
   * @param buffer array in which to find zero crossing
   * @param detectionType the type of zero crossing detection to perform
   */
  public void genZeroXMask(int slice, float[] buffer, int detectionType) {
    float x0, x1, x2, x3;
    int i0, i1, i2, i3;
    int i, j;
    int indexY;
    int length;

    int xDim = srcImage.getExtents()[0];
    int yDim = srcImage.getExtents()[1];

    length = xDim * yDim;

    int xxDim = xDim - 1;
    int yyDim = yDim - 1;
    float level = 0;
    int offset = slice * length;

    for (j = 0; j < yyDim; j++) {
      indexY = j * xDim;

      for (i = 0; i < xxDim; i++) {
        i0 = indexY + i;

        if (detectionType == MARCHING_SQUARES) {
          i1 = i0 + 1;
          i2 = i0 + xDim;
          i3 = i0 + 1 + xDim;

          x0 = buffer[i0];
          x1 = buffer[i1];
          x2 = buffer[i2];
          x3 = buffer[i3];

          if ((x0 >= level)
              && (x1 >= level)
              && (x2 >= level)
              && (x3 >= level)) { // case 0 - no edge
          } else if ((x0 >= level) && (x1 >= level) && (x2 < level) && (x3 >= level)) {

            // case 1 - edge in the lower left
            zXMask.set(offset + i2, 255);
          } else if ((x0 >= level) && (x1 >= level) && (x2 >= level) && (x3 < level)) {

            // case 2 - edge in the lower right
            zXMask.set(offset + i3, 255);
          } else if ((x0 >= level) && (x1 >= level) && (x2 < level) && (x3 < level)) {

            // case 3 - edge horizontally
            zXMask.set(offset + i2, 255);
            zXMask.set(offset + i3, 255);
          } else if ((x0 >= level) && (x1 < level) && (x2 >= level) && (x3 >= level)) {

            // case 4 - edge in the upper right
            zXMask.set(offset + i1, 255);
          } else if ((x0 >= level) && (x1 < level) && (x2 < level) && (x3 >= level)) {

            // case 5 - ambiguous case; either edge in upper right and lower left or
            // edge that goes from the upper right to the lower left
            zXMask.set(offset + i1, 255);
            zXMask.set(offset + i2, 255);
          } else if ((x0 >= level) && (x1 < level) && (x2 >= level) && (x3 < level)) {

            // case 6 - edge going vertically along the right
            zXMask.set(offset + i1, 255);
            zXMask.set(offset + i3, 255);
          } else if ((x0 >= level) && (x1 < level) && (x2 < level) && (x3 < level)) {

            // case 7 - edge in the upper left
            zXMask.set(offset + i0, 255);
          } else if ((x0 < level) && (x1 >= level) && (x2 >= level) && (x3 >= level)) {

            // case 8 - edge in the upper left
            zXMask.set(offset + i0, 255);
          } else if ((x0 < level) && (x1 >= level) && (x2 < level) && (x3 >= level)) {

            // case 9 - edge going vertically along the left
            zXMask.set(offset + i0, 255);
            zXMask.set(offset + i2, 255);
          } else if ((x0 < level) && (x1 >= level) && (x2 >= level) && (x3 < level)) {

            // case 10 - ambiguous case; either edge in upper left and lower right or
            // edge that goes from the upper left to the lower right
            zXMask.set(offset + i0, 255);
            zXMask.set(offset + i3, 255);
          } else if ((x0 < level) && (x1 >= level) && (x2 < level) && (x3 < level)) {

            // case 11 - edge in the upper right
            zXMask.set(offset + i1, 255);
          } else if ((x0 < level) && (x1 < level) && (x2 >= level) && (x3 >= level)) {

            // case 12 - edge going horizontally along the top
            zXMask.set(offset + i0, 255);
            zXMask.set(offset + i1, 255);
          } else if ((x0 < level) && (x1 < level) && (x2 < level) && (x3 >= level)) {

            // case 13 - edge in the lower right
            zXMask.set(offset + i3, 255);
          } else if ((x0 < level) && (x1 < level) && (x2 >= level) && (x3 < level)) {

            // case 14 - edge in the lower left
            zXMask.set(offset + i2, 255);
          } else if ((x0 < level)
              && (x1 < level)
              && (x2 < level)
              && (x3 < level)) { // case 15 - no edge
          }
        } else if (detectionType == NEGATIVE_EDGES) {

          if (buffer[i0] <= 1) {
            zXMask.set(offset + i0, 255);
          }
        } else if (detectionType == OLD_DETECTION) {
          i1 = i0 + 1;
          i2 = i0 + xDim;
          i3 = i0 + 1 + xDim;

          x0 = buffer[i0];
          x1 = buffer[i1];
          x2 = buffer[i2];
          x3 = buffer[i3];

          if ((x0 > level) && (x1 > level) && (x2 > level) && (x3 > level)) {
            zXMask.set(offset + i0, 0);
          } else if ((x0 < level) && (x1 < level) && (x2 < level) && (x3 < level)) {
            zXMask.set(offset + i0, 0);
          } else {
            zXMask.set(offset + i0, 255);
          }
        }
      }
    }

    FileInfoBase[] fileInfo = zXMask.getFileInfo();

    fileInfo[slice].setModality(srcImage.getFileInfo()[slice].getModality());
    fileInfo[slice].setFileDirectory(srcImage.getFileInfo()[slice].getFileDirectory());
    fileInfo[slice].setEndianess(srcImage.getFileInfo()[slice].getEndianess());
    fileInfo[slice].setUnitsOfMeasure(srcImage.getFileInfo()[slice].getUnitsOfMeasure());
    fileInfo[slice].setResolutions(srcImage.getFileInfo()[slice].getResolutions());
    fileInfo[slice].setExtents(zXMask.getExtents());
    fileInfo[slice].setMax(255);
    fileInfo[slice].setMin(0);
    fileInfo[slice].setPixelPadValue(srcImage.getFileInfo()[slice].getPixelPadValue());
    fileInfo[slice].setPhotometric(srcImage.getFileInfo()[slice].getPhotometric());
  }
示例#2
0
  /**
   * This function produces a new image that has been concatenated. Two 2D-images become one 3D
   * image.
   */
  private void cat2D_2D_3D() {

    int length;
    int xDim, yDim;
    int i;
    float[] buffer;
    int cFactor = 1;
    float[] resols = new float[3];
    FileInfoBase[] fileInfo = null;
    FileInfoDicom[] fileInfoDicom = null;

    try {
      resols = new float[3];
      xDim = srcImage1.getExtents()[0];
      yDim = srcImage1.getExtents()[1];

      if (srcImage1.isColorImage()) {
        cFactor = 4;
      }

      length = cFactor * xDim * yDim;
      buffer = new float[length];
      srcImage1.exportData(0, length, buffer);
      destImage.importData(0, buffer, false);
      srcImage2.exportData(0, length, buffer);
      destImage.importData(buffer.length, buffer, true);
    } catch (IOException error) {
      buffer = null;
      destImage.disposeLocal(); // Clean up memory of result image
      destImage = null;
      errorCleanUp("Algorithm Concat. Images: Image(s) locked", true);

      return;
    } catch (OutOfMemoryError e) {
      buffer = null;
      destImage.disposeLocal(); // Clean up memory of result image
      destImage = null;
      errorCleanUp("Algorithm Concat. Images: Out of memory", true);

      return;
    }

    resols[0] = srcImage1.getFileInfo()[0].getResolutions()[0];
    resols[1] = srcImage1.getFileInfo()[0].getResolutions()[1];
    resols[2] = 1;

    if ((srcImage1.getFileInfo()[0] instanceof FileInfoDicom)
        && (srcImage2.getFileInfo()[0] instanceof FileInfoDicom)) {
      fileInfoDicom = new FileInfoDicom[destImage.getExtents()[2]];
      fileInfoDicom[0] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[0]).clone());
      fileInfoDicom[1] = (FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[0]).clone());
      destImage.setFileInfo(fileInfoDicom);
    } else {
      fileInfo = destImage.getFileInfo();

      for (i = 0; (i < destImage.getExtents()[2]) && !threadStopped; i++) {
        fileInfo[i].setModality(srcImage1.getFileInfo()[0].getModality());
        fileInfo[i].setFileDirectory(srcImage1.getFileInfo()[0].getFileDirectory());
        fileInfo[i].setEndianess(srcImage1.getFileInfo()[0].getEndianess());
        fileInfo[i].setUnitsOfMeasure(srcImage1.getFileInfo()[0].getUnitsOfMeasure());
        fileInfo[i].setResolutions(resols);
        fileInfo[i].setExtents(destImage.getExtents());
        fileInfo[i].setMax(destImage.getMax());
        fileInfo[i].setMin(destImage.getMin());
        fileInfo[i].setImageOrientation(srcImage1.getImageOrientation());
        fileInfo[i].setPixelPadValue(srcImage1.getFileInfo()[0].getPixelPadValue());
        fileInfo[i].setPhotometric(srcImage1.getFileInfo()[0].getPhotometric());
        fileInfo[i].setAxisOrientation(srcImage1.getAxisOrientation());
      }

      if (srcImage1.getFileInfo()[0] instanceof FileInfoImageXML) {

        if (((FileInfoImageXML) srcImage1.getFileInfo()[0]).getPSetHashtable() != null) {
          ((FileInfoImageXML) fileInfo[0])
              .setPSetHashtable(((FileInfoImageXML) srcImage1.getFileInfo()[0]).getPSetHashtable());
        }
      }

      if (srcImage2.getFileInfo()[0] instanceof FileInfoImageXML) {

        if (((FileInfoImageXML) srcImage2.getFileInfo()[0]).getPSetHashtable() != null) {
          ((FileInfoImageXML) fileInfo[1])
              .setPSetHashtable(((FileInfoImageXML) srcImage2.getFileInfo()[0]).getPSetHashtable());
        }
      }
    }

    if (threadStopped) {
      buffer = null;
      finalize();

      return;
    }

    setCompleted(true);

    fileInfo = null;
    fileInfoDicom = null;
  }
示例#3
0
  /** cat. */
  private void cat3D_4D_4D() {

    int length;
    int xDim, yDim;
    float[] buffer;
    int cFactor = 1;
    int i, j;
    float[] resols = new float[3];
    float[] origins = new float[3];
    FileInfoBase[] fileInfo = null;
    FileInfoDicom[] fileInfoDicom = null;
    int srcALength, srcBLength;

    try {
      fireProgressStateChanged(srcImage1.getImageName(), "Concatenating images ...");
      resols = new float[4];
      origins = new float[4];
      xDim = srcImage1.getExtents()[0];
      yDim = srcImage1.getExtents()[1];

      if (srcImage1.isColorImage()) {
        cFactor = 4;
      }

      length = cFactor * xDim * yDim;
      buffer = new float[length];

      int nImages;

      if (srcImage1.getNDims() > srcImage2.getNDims()) {
        nImages =
            (srcImage1.getExtents()[2] * srcImage1.getExtents()[3]) + srcImage2.getExtents()[2];

        for (i = 0;
            (i < (srcImage1.getExtents()[2] * srcImage1.getExtents()[3])) && !threadStopped;
            i++) {
          fireProgressStateChanged(Math.round((float) (i) / (nImages - 1) * 100));

          srcImage1.exportData(i * length, length, buffer);
          destImage.importData(i * length, buffer, false);
        }

        if (threadStopped) {
          buffer = null;
          finalize();

          return;
        }

        for (j = 0; (j < srcImage2.getExtents()[2]) && !threadStopped; j++) {
          fireProgressStateChanged(Math.round((float) (i + j) / (nImages - 1) * 100));

          srcImage2.exportData(j * length, length, buffer);
          destImage.importData((i + j) * length, buffer, false);
        }

        if (threadStopped) {
          buffer = null;
          finalize();

          return;
        }

        destImage.calcMinMax();
      } else {
        nImages =
            (srcImage2.getExtents()[2] * srcImage2.getExtents()[3]) + srcImage1.getExtents()[2];

        for (j = 0; (j < srcImage1.getExtents()[2]) && !threadStopped; j++) {
          fireProgressStateChanged(Math.round((float) (j) / (nImages - 1) * 100));

          srcImage1.exportData(j * length, length, buffer);
          destImage.importData(j * length, buffer, false);
        }

        if (threadStopped) {
          buffer = null;
          finalize();

          return;
        }

        for (i = 0;
            (i < (srcImage2.getExtents()[2] * srcImage2.getExtents()[3])) && !threadStopped;
            i++) {
          fireProgressStateChanged(Math.round((float) (i + j) / (nImages - 1) * 100));

          srcImage2.exportData(i * buffer.length, length, buffer);
          destImage.importData((i + j) * buffer.length, buffer, false);
        }

        if (threadStopped) {
          buffer = null;
          finalize();

          return;
        }

        destImage.calcMinMax();
      }
    } catch (IOException error) {
      buffer = null;
      destImage.disposeLocal(); // Clean up memory of result image
      destImage = null;
      errorCleanUp("Algorithm Concat. Images: Image(s) locked", true);

      return;
    } catch (OutOfMemoryError e) {
      buffer = null;
      destImage.disposeLocal(); // Clean up memory of result image
      destImage = null;
      errorCleanUp("Algorithm Concat. Images: Out of memory", true);

      return;
    }

    resols[0] = srcImage1.getFileInfo()[0].getResolutions()[0];
    resols[1] = srcImage1.getFileInfo()[0].getResolutions()[1];
    resols[2] = srcImage1.getFileInfo()[0].getResolutions()[2];
    resols[3] = srcImage1.getFileInfo()[0].getResolutions()[3];
    origins[0] = srcImage1.getFileInfo()[0].getOrigin()[0];
    origins[1] = srcImage1.getFileInfo()[0].getOrigin()[1];
    origins[2] = srcImage1.getFileInfo()[0].getOrigin()[2];
    origins[3] = srcImage1.getFileInfo()[0].getOrigin()[3];

    if ((srcImage1.getFileInfo()[0] instanceof FileInfoDicom)
        && (srcImage2.getFileInfo()[0] instanceof FileInfoDicom)) {
      fileInfoDicom = new FileInfoDicom[destImage.getExtents()[2] * destImage.getExtents()[3]];

      if (srcImage1.getNDims() > srcImage2.getNDims()) {
        srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];

        for (i = 0; (i < srcALength) && !threadStopped; i++) {
          fileInfoDicom[i] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[i]).clone());
          fileInfoDicom[i].setOrigin(origins);
        }

        for (i = 0; (i < srcImage2.getExtents()[2]) && !threadStopped; i++) {
          fileInfoDicom[srcALength + i] =
              (FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[i]).clone());
          fileInfoDicom[srcALength + i].setOrigin(origins);
        }
      } else {
        srcBLength = srcImage2.getExtents()[2] * srcImage2.getExtents()[3];

        for (i = 0; (i < srcImage1.getExtents()[2]) && !threadStopped; i++) {
          fileInfoDicom[i] = (FileInfoDicom) (((FileInfoDicom) srcImage1.getFileInfo()[i]).clone());
          fileInfoDicom[i].setOrigin(origins);
        }

        for (i = 0; (i < srcBLength) && !threadStopped; i++) {
          fileInfoDicom[srcImage1.getExtents()[2] + i] =
              (FileInfoDicom) (((FileInfoDicom) srcImage2.getFileInfo()[i]).clone());
          fileInfoDicom[srcImage1.getExtents()[2] + i].setOrigin(origins);
        }
      }

      destImage.setFileInfo(fileInfoDicom);
    } else {
      fileInfo = destImage.getFileInfo();

      for (i = 0;
          (i < (destImage.getExtents()[2] * destImage.getExtents()[3])) && !threadStopped;
          i++) {
        fileInfo[i].setModality(srcImage1.getFileInfo()[0].getModality());
        fileInfo[i].setFileDirectory(srcImage1.getFileInfo()[0].getFileDirectory());
        fileInfo[i].setEndianess(srcImage1.getFileInfo()[0].getEndianess());
        fileInfo[i].setUnitsOfMeasure(srcImage1.getFileInfo()[0].getUnitsOfMeasure());
        fileInfo[i].setResolutions(resols);
        fileInfo[i].setExtents(destImage.getExtents());
        fileInfo[i].setMax(destImage.getMax());
        fileInfo[i].setMin(destImage.getMin());
        fileInfo[i].setImageOrientation(srcImage1.getImageOrientation());
        fileInfo[i].setPixelPadValue(srcImage1.getFileInfo()[0].getPixelPadValue());
        fileInfo[i].setPhotometric(srcImage1.getFileInfo()[0].getPhotometric());
        fileInfo[i].setAxisOrientation(srcImage1.getAxisOrientation());
      }

      if (srcImage1.getFileInfo()[0] instanceof FileInfoImageXML) {

        if (srcImage1.getNDims() > srcImage2.getNDims()) {
          srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];

          for (i = 0; (i < srcALength) && !threadStopped; i++) {

            if (((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable() != null) {
              ((FileInfoImageXML) fileInfo[i])
                  .setPSetHashtable(
                      ((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable());
            }
          }
        } else {

          for (i = 0; (i < srcImage1.getExtents()[2]) && !threadStopped; i++) {

            if (((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable() != null) {
              ((FileInfoImageXML) fileInfo[i])
                  .setPSetHashtable(
                      ((FileInfoImageXML) srcImage1.getFileInfo()[i]).getPSetHashtable());
            }
          }
        }
      }

      if (srcImage2.getFileInfo()[0] instanceof FileInfoImageXML) {

        if (srcImage1.getNDims() > srcImage2.getNDims()) {
          srcALength = srcImage1.getExtents()[2] * srcImage1.getExtents()[3];

          for (i = 0; (i < srcImage2.getExtents()[2]) && !threadStopped; i++) {

            if (((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable() != null) {
              ((FileInfoImageXML) fileInfo[srcALength + i])
                  .setPSetHashtable(
                      ((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable());
            }
          }

        } else {
          srcBLength = srcImage2.getExtents()[2] * srcImage2.getExtents()[3];

          for (i = 0; (i < srcBLength) && !threadStopped; i++) {

            if (((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable() != null) {
              ((FileInfoImageXML) fileInfo[srcImage1.getExtents()[2] + i])
                  .setPSetHashtable(
                      ((FileInfoImageXML) srcImage2.getFileInfo()[i]).getPSetHashtable());
            }
          }
        }
      }
    }

    if (threadStopped) {
      buffer = null;
      finalize();

      return;
    }

    setCompleted(true);
    fileInfo = null;
    fileInfoDicom = null;
  }
  /**
   * Use the GUI results to set up the variables needed to run the algorithm.
   *
   * @return <code>true</code> if parameters set successfully, <code>false</code> otherwise.
   */
  private boolean setVariables() {
    String tmpStr;

    tmpStr = textXDim.getText();
    try {
      subXDim = Integer.parseInt(tmpStr);
    } catch (NumberFormatException e) {
      MipavUtil.displayError("New XDIM string is not a valid integer");
      textXDim.requestFocus();
      textXDim.selectAll();

      return false;
    }
    if (subXDim < 3) {
      MipavUtil.displayError("New XDIM must be at least 3");
      textXDim.requestFocus();
      textXDim.selectAll();

      return false;
    } else if (subXDim > image.getExtents()[0]) {
      MipavUtil.displayError("New XDIM cannot exceed " + image.getExtents()[0]);
      textXDim.requestFocus();
      textXDim.selectAll();

      return false;
    }

    tmpStr = textYDim.getText();
    try {
      subYDim = Integer.parseInt(tmpStr);
    } catch (NumberFormatException e) {
      MipavUtil.displayError("New YDIM string is not a valid integer");
      textYDim.requestFocus();
      textYDim.selectAll();

      return false;
    }
    if (subYDim < 3) {
      MipavUtil.displayError("New YDIM must be at least 3");
      textYDim.requestFocus();
      textYDim.selectAll();

      return false;
    } else if (subYDim > image.getExtents()[1]) {
      MipavUtil.displayError("New YDIM cannot exceed " + image.getExtents()[1]);
      textYDim.requestFocus();
      textYDim.selectAll();

      return false;
    }

    tmpStr = textNumberImages.getText();
    try {
      numberOfImagesInMosaic = Integer.parseInt(tmpStr);
    } catch (NumberFormatException e) {
      MipavUtil.displayError("New numberOfImagesInMosaic string is not a valid integer");
      textNumberImages.requestFocus();
      textNumberImages.selectAll();

      return false;
    }
    if (numberOfImagesInMosaic < 1) {
      MipavUtil.displayError("New numberOfImagesInMosaic must be at least 1");
      textNumberImages.requestFocus();
      textNumberImages.selectAll();

      return false;
    } else if (numberOfImagesInMosaic > (subXDim * subYDim)) {
      MipavUtil.displayError("New numberOfImagesInMosaic cannot exceed (newXDim) * (newYDim)");
      textNumberImages.requestFocus();
      textNumberImages.selectAll();

      return false;
    }

    displayLoc = NEW;

    return true;
  }