Examples with ImageException cbit.image.ImageException used on opensource projects

Example 6 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class FRAPData method refreshDependentROIs.

protected void refreshDependentROIs() {
    UShortImage cellROI_2D = null;
    UShortImage bleachedROI_2D = null;
    UShortImage dilatedROI_2D_1 = null;
    UShortImage dilatedROI_2D_2 = null;
    UShortImage dilatedROI_2D_3 = null;
    UShortImage dilatedROI_2D_4 = null;
    UShortImage dilatedROI_2D_5 = null;
    UShortImage erodedROI_2D_0 = null;
    UShortImage erodedROI_2D_1 = null;
    UShortImage erodedROI_2D_2 = null;
    try {
        cellROI_2D = convertToUShortImage(binarize(getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).getRoiImages()[0]), getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).getRoiImages()[0].getOrigin(), getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).getRoiImages()[0].getExtent());
        bleachedROI_2D = convertToUShortImage(AndDescriptor.create(binarize(getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getRoiImages()[0]), binarize(cellROI_2D), null).createInstance(), getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getRoiImages()[0].getOrigin(), getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getRoiImages()[0].getExtent());
        // writeUShortFile(cellROI_2D, new File("D:\\developer\\eclipse\\workspace\\cellROI_2D.bmp"));
        // writeUShortFile(bleachedROI_2D, new File("D:\\developer\\eclipse\\workspace\\bleachedROI_2D.bmp"));
        dilatedROI_2D_1 = fastDilate(bleachedROI_2D, 4, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(8), cellROI_2D,false);
        dilatedROI_2D_2 = fastDilate(bleachedROI_2D, 10, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(16), cellROI_2D,false);
        dilatedROI_2D_3 = fastDilate(bleachedROI_2D, 18, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(24), cellROI_2D,false);
        dilatedROI_2D_4 = fastDilate(bleachedROI_2D, 28, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(32), cellROI_2D,false);
        dilatedROI_2D_5 = fastDilate(bleachedROI_2D, 40, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(40), cellROI_2D,false);
        erodedROI_2D_0 = new UShortImage(bleachedROI_2D);
        // The erode always causes problems if eroding without checking the bleached length and hight.
        // we have to check the min length of the bleahed area to make sure erode within the length.
        Rectangle bleachRect = bleachedROI_2D.getNonzeroBoundingBox();
        int minLen = Math.min(bleachRect.height, bleachRect.width);
        if ((minLen / 2.0) < 5) {
            erodedROI_2D_1 = erodeDilate(bleachedROI_2D, createCircularBinaryKernel(1), bleachedROI_2D, true);
            erodedROI_2D_2 = erodeDilate(bleachedROI_2D, createCircularBinaryKernel(2), bleachedROI_2D, true);
        } else {
            erodedROI_2D_1 = erodeDilate(bleachedROI_2D, createCircularBinaryKernel(2), bleachedROI_2D, true);
            erodedROI_2D_2 = erodeDilate(bleachedROI_2D, createCircularBinaryKernel(5), bleachedROI_2D, true);
        }
        UShortImage reverseErodeROI_2D_1 = new UShortImage(erodedROI_2D_1);
        reverseErodeROI_2D_1.reverse();
        erodedROI_2D_0.and(reverseErodeROI_2D_1);
        UShortImage reverseErodeROI_2D_2 = new UShortImage(erodedROI_2D_2);
        reverseErodeROI_2D_2.reverse();
        erodedROI_2D_1.and(reverseErodeROI_2D_2);
        UShortImage reverseDilateROI_2D_4 = new UShortImage(dilatedROI_2D_4);
        reverseDilateROI_2D_4.reverse();
        dilatedROI_2D_5.and(reverseDilateROI_2D_4);
        UShortImage reverseDilateROI_2D_3 = new UShortImage(dilatedROI_2D_3);
        // writeUShortFile(dilatedROI_2D_3, new File("D:\\developer\\eclipse\\workspace\\dilatedROI_2D_3.bmp"));
        reverseDilateROI_2D_3.reverse();
        // writeUShortFile(reverseDilateROI_2D_3, new File("D:\\developer\\eclipse\\workspace\\dilatedROI_2D_3_reverse.bmp"));
        // writeUShortFile(dilatedROI_2D_4, new File("D:\\developer\\eclipse\\workspace\\dilatedROI_2D_4.bmp"));
        dilatedROI_2D_4.and(reverseDilateROI_2D_3);
        // writeUShortFile(dilatedROI_2D_4, new File("D:\\developer\\eclipse\\workspace\\dilatedROI_2D_4_anded.bmp"));
        UShortImage reverseDilateROI_2D_2 = new UShortImage(dilatedROI_2D_2);
        reverseDilateROI_2D_2.reverse();
        dilatedROI_2D_3.and(reverseDilateROI_2D_2);
        UShortImage reverseDilateROI_2D_1 = new UShortImage(dilatedROI_2D_1);
        reverseDilateROI_2D_1.reverse();
        dilatedROI_2D_2.and(reverseDilateROI_2D_1);
        UShortImage reverseBleach_2D = new UShortImage(bleachedROI_2D);
        reverseBleach_2D.reverse();
        dilatedROI_2D_1.and(reverseBleach_2D);
    } catch (ImageException e) {
        e.printStackTrace(System.out);
    }
    ROI roiBleachedRing1_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name());
    if (roiBleachedRing1_2D == null) {
        roiBleachedRing1_2D = new ROI(erodedROI_2D_2, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name());
        addReplaceRoi(roiBleachedRing1_2D);
    } else {
        System.arraycopy(erodedROI_2D_2.getPixels(), 0, roiBleachedRing1_2D.getRoiImages()[0].getPixels(), 0, erodedROI_2D_2.getPixels().length);
    }
    ROI roiBleachedRing2_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name());
    if (roiBleachedRing2_2D == null) {
        roiBleachedRing2_2D = new ROI(erodedROI_2D_1, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name());
        addReplaceRoi(roiBleachedRing2_2D);
    } else {
        System.arraycopy(erodedROI_2D_1.getPixels(), 0, roiBleachedRing2_2D.getRoiImages()[0].getPixels(), 0, erodedROI_2D_1.getPixels().length);
    }
    ROI roiBleachedRing3_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name());
    if (roiBleachedRing3_2D == null) {
        roiBleachedRing3_2D = new ROI(erodedROI_2D_0, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name());
        addReplaceRoi(roiBleachedRing3_2D);
    } else {
        System.arraycopy(erodedROI_2D_0.getPixels(), 0, roiBleachedRing3_2D.getRoiImages()[0].getPixels(), 0, erodedROI_2D_0.getPixels().length);
    }
    ROI roiBleachedRing4_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name());
    if (roiBleachedRing4_2D == null) {
        roiBleachedRing4_2D = new ROI(dilatedROI_2D_1, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name());
        addReplaceRoi(roiBleachedRing4_2D);
    } else {
        System.arraycopy(dilatedROI_2D_1.getPixels(), 0, roiBleachedRing4_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_1.getPixels().length);
    }
    ROI roiBleachedRing5_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name());
    if (roiBleachedRing5_2D == null) {
        roiBleachedRing5_2D = new ROI(dilatedROI_2D_2, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name());
        addReplaceRoi(roiBleachedRing5_2D);
    } else {
        System.arraycopy(dilatedROI_2D_2.getPixels(), 0, roiBleachedRing5_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_2.getPixels().length);
    }
    ROI roiBleachedRing6_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name());
    if (roiBleachedRing6_2D == null) {
        roiBleachedRing6_2D = new ROI(dilatedROI_2D_3, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name());
        addReplaceRoi(roiBleachedRing6_2D);
    } else {
        System.arraycopy(dilatedROI_2D_3.getPixels(), 0, roiBleachedRing6_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_3.getPixels().length);
    }
    ROI roiBleachedRing7_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name());
    if (roiBleachedRing7_2D == null) {
        roiBleachedRing7_2D = new ROI(dilatedROI_2D_4, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name());
        addReplaceRoi(roiBleachedRing7_2D);
    } else {
        System.arraycopy(dilatedROI_2D_4.getPixels(), 0, roiBleachedRing7_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_4.getPixels().length);
    }
    ROI roiBleachedRing8_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name());
    if (roiBleachedRing8_2D == null) {
        roiBleachedRing8_2D = new ROI(dilatedROI_2D_5, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name());
        addReplaceRoi(roiBleachedRing8_2D);
    } else {
        System.arraycopy(dilatedROI_2D_5.getPixels(), 0, roiBleachedRing8_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_5.getPixels().length);
    }
}

Example 7 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class ByteImage method getPixelsCompressed.

/**
 * This method was created in VisualAge.
 * @return byte[]
 */
public byte[] getPixelsCompressed() throws ImageException {
    try {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        DeflaterOutputStream dos = new DeflaterOutputStream(bos);
        // DeflaterOutputStream dos = new DeflaterOutputStream(bos,new Deflater(5,false));
        dos.write(pixels, 0, pixels.length);
        dos.close();
        return bos.toByteArray();
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new ImageException(e.getMessage());
    }
}

Example 8 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class Image method crop.

static Image crop(Image origImage, Rectangle rect) throws ImageException {
    Object inArray = origImage.getPixelArray();
    Object outArray = Array.newInstance(inArray.getClass().getComponentType(), rect.width * rect.height * origImage.getNumZ());
    for (int k = 0; k < origImage.getNumZ(); k++) {
        for (int j = 0; j < rect.height; j++) {
            for (int i = 0; i < rect.width; i++) {
                int inIndex = rect.x + i + (j + rect.y) * origImage.getNumX() + k * origImage.getNumX() * origImage.getNumY();
                int outIndex = i + j * rect.width + (k * rect.width * rect.height);
                Array.set(outArray, outIndex, Array.get(inArray, inIndex));
            }
        }
    }
    Extent croppedExtent = null;
    if (origImage.getExtent() != null) {
        croppedExtent = new Extent(origImage.getExtent().getX() * rect.width / origImage.getNumX(), origImage.getExtent().getY() * rect.height / origImage.getNumY(), origImage.getExtent().getZ());
    }
    Origin croppedOrigin = null;
    if (origImage.getOrigin() != null) {
        croppedOrigin = new Origin(calcOriginPosition(origImage.getOrigin().getX(), rect.x, origImage.getExtent().getX(), origImage.getNumX()), calcOriginPosition(origImage.getOrigin().getY(), rect.y, origImage.getExtent().getY(), origImage.getNumY()), // origImage.getOrigin().getY()+(rect.y*(origImage.getExtent().getY()/origImage.getNumY())),
        origImage.getExtent().getZ());
    }
    if (origImage instanceof UShortImage) {
        return new UShortImage((short[]) outArray, croppedOrigin, croppedExtent, rect.width, rect.height, origImage.getNumZ());
    } else if (origImage instanceof ByteImage) {
        return new ByteImage((byte[]) outArray, croppedOrigin, croppedExtent, rect.width, rect.height, origImage.getNumZ());
    } else if (origImage instanceof FloatImage) {
        return new FloatImage((float[]) outArray, croppedOrigin, croppedExtent, rect.width, rect.height, origImage.getNumZ());
    }
    throw new ImageException("Crop if Image type " + origImage.getClass().getName() + " not implemented.");
}

Example 9 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class RegionImage method calculateRegions_New.

// 
// Calculate regions using single pass algorithm.  Creates information
// used to generate surfaces as well
// 
private void calculateRegions_New(VCImage vcImage, int dimension, Extent extent, Origin origin, ClientTaskStatusSupport clientTaskStatusSupport) throws ImageException {
    // Find linked pixel values in x,y,z and surface elements locations
    final int EMPTY_REGION = 0;
    final int FIRST_REGION = 1;
    final int ARRAY_SIZE_INCREMENT = 1000;
    byte[] imagePixels = vcImage.getPixels();
    int[] regionPixels = new int[imagePixels.length];
    BitSet xSurfElements = new BitSet(imagePixels.length);
    BitSet ySurfElements = new BitSet(imagePixels.length);
    BitSet zSurfElements = new BitSet(imagePixels.length);
    Vector<Integer>[] regionLinkArr = new Vector[ARRAY_SIZE_INCREMENT];
    int[] regionSizeArr = new int[ARRAY_SIZE_INCREMENT];
    Vector<Byte> regionImagePixelV = new Vector<Byte>();
    // 0 not used
    regionImagePixelV.add((byte) 0);
    byte currentImagePixel;
    int currentRegion;
    int masterIndex = 0;
    int nextAvailableRegion = FIRST_REGION;
    for (int zIndex = 0; zIndex < vcImage.getNumZ(); zIndex++) {
        if (clientTaskStatusSupport != null) {
            if (clientTaskStatusSupport.isInterrupted()) {
                return;
            }
        }
        int zForwardIndex = ((zIndex + 1) < vcImage.getNumZ() ? masterIndex + (vcImage.getNumX() * vcImage.getNumY()) : -1);
        for (int yIndex = 0; yIndex < vcImage.getNumY(); yIndex++) {
            int yForwardIndex = ((yIndex + 1) < vcImage.getNumY() ? masterIndex + vcImage.getNumX() : -1);
            currentImagePixel = imagePixels[masterIndex];
            if (regionPixels[masterIndex] != EMPTY_REGION) {
                currentRegion = regionPixels[masterIndex];
            } else {
                currentRegion = nextAvailableRegion;
                if (currentRegion >= regionLinkArr.length) {
                    // make more room for arrays
                    Vector<Integer>[] temp = new Vector[regionLinkArr.length + ARRAY_SIZE_INCREMENT];
                    System.arraycopy(regionLinkArr, 0, temp, 0, regionLinkArr.length);
                    regionLinkArr = temp;
                    int[] temp2 = new int[regionSizeArr.length + ARRAY_SIZE_INCREMENT];
                    System.arraycopy(regionSizeArr, 0, temp2, 0, regionSizeArr.length);
                    regionSizeArr = temp2;
                }
                regionPixels[masterIndex] = currentRegion;
                if (regionImagePixelV.size() != currentRegion) {
                    throw new ImageException("Mismatch between region and pixel buffer");
                }
                regionImagePixelV.add(currentImagePixel);
                nextAvailableRegion += 1;
            }
            for (int xIndex = 0; xIndex < vcImage.getNumX(); xIndex++) {
                if (imagePixels[masterIndex] == currentImagePixel) {
                    if (regionPixels[masterIndex] != EMPTY_REGION) {
                        if (currentRegion != regionPixels[masterIndex]) {
                            createLink(regionLinkArr, currentRegion, regionPixels, masterIndex);
                        }
                    } else {
                        regionPixels[masterIndex] = currentRegion;
                    }
                } else {
                    xSurfElements.set(masterIndex - 1);
                    currentImagePixel = imagePixels[masterIndex];
                    if (regionPixels[masterIndex] != EMPTY_REGION) {
                        currentRegion = regionPixels[masterIndex];
                    } else {
                        currentRegion = nextAvailableRegion;
                        if (currentRegion >= regionLinkArr.length) {
                            // make more room for arrays
                            Vector<Integer>[] temp = new Vector[regionLinkArr.length + ARRAY_SIZE_INCREMENT];
                            System.arraycopy(regionLinkArr, 0, temp, 0, regionLinkArr.length);
                            regionLinkArr = temp;
                            int[] temp2 = new int[regionSizeArr.length + ARRAY_SIZE_INCREMENT];
                            System.arraycopy(regionSizeArr, 0, temp2, 0, regionSizeArr.length);
                            regionSizeArr = temp2;
                        }
                        regionPixels[masterIndex] = currentRegion;
                        if (regionImagePixelV.size() != currentRegion) {
                            throw new ImageException("Mismatch between region and pixel buffer");
                        }
                        regionImagePixelV.add(currentImagePixel);
                        nextAvailableRegion += 1;
                    }
                }
                regionSizeArr[currentRegion] += 1;
                // }
                if (yForwardIndex != -1) {
                    if (imagePixels[yForwardIndex] == currentImagePixel) {
                        if (regionPixels[yForwardIndex] == EMPTY_REGION) {
                            regionPixels[yForwardIndex] = currentRegion;
                        } else if (currentRegion != regionPixels[yForwardIndex]) {
                            createLink(regionLinkArr, currentRegion, regionPixels, yForwardIndex);
                        }
                    } else {
                        ySurfElements.set(masterIndex);
                    }
                    yForwardIndex += 1;
                }
                if (zForwardIndex != -1) {
                    if (imagePixels[zForwardIndex] == currentImagePixel) {
                        if (regionPixels[zForwardIndex] == EMPTY_REGION) {
                            regionPixels[zForwardIndex] = currentRegion;
                        } else if (currentRegion != regionPixels[zForwardIndex]) {
                            createLink(regionLinkArr, currentRegion, regionPixels, zForwardIndex);
                        }
                    } else {
                        zSurfElements.set(masterIndex);
                    }
                    zForwardIndex += 1;
                }
                masterIndex += 1;
            }
        }
    }
    // System.out.println(xSurfElements.cardinality()+" "+ySurfElements.cardinality()+" "+zSurfElements.cardinality());
    // System.out.println("----------link time "+((System.currentTimeMillis()-startTime)/1000.0));
    // startTime = System.currentTimeMillis();
    // Distribute links
    Vector<Integer>[] collector = new Vector[nextAvailableRegion];
    for (int i = 1; i < nextAvailableRegion; /*regionSizeArr.length*/
    i++) {
        // 0 not used
        if (regionSizeArr[i] != 0) {
            collector[i] = (Vector) (regionLinkArr[i] != null ? regionLinkArr[i].clone() : null);
        }
    }
    for (int i = 1; i < nextAvailableRegion; /*regionSizeArr.length*/
    i++) {
        // 0 not used
        if (clientTaskStatusSupport != null && clientTaskStatusSupport.isInterrupted()) {
            return;
        }
        // System.out.print("region="+i+" size="+regionSizeArr[i]);
        Vector<Integer> intV = regionLinkArr[i];
        for (int j = 0; intV != null && j < intV.size(); j++) {
            // System.out.print((j==0?" - ":" ")+intV.elementAt(j));
            // Collect
            Vector<Integer> collectIntV = collector[intV.elementAt(j)];
            if (collectIntV == null) {
                collectIntV = new Vector<Integer>();
                collector[intV.elementAt(j)] = collectIntV;
                if (regionLinkArr[intV.elementAt(j)] != null) {
                    collectIntV.addAll(regionLinkArr[intV.elementAt(j)]);
                }
            }
            if (!collectIntV.contains(i)) {
                collectIntV.add(i);
            }
        }
    // System.out.println();
    }
    // System.out.println("----------distribute link time "+((System.currentTimeMillis()-startTime)/1000.0));
    // startTime = System.currentTimeMillis();
    // for (int i = 1; i < collector.length; i++) {// 0 not used
    // if(regionSizeArr[i] != 0){
    // System.out.print("Collect region="+i+" size="+regionSizeArr[i]);
    // Vector<Integer> intV = collector[i];
    // for (int j = 0; intV!= null && j < intV.size();j++) {
    // System.out.print((j==0?" - ":" ")+intV.elementAt(j));
    // }
    // System.out.println();
    // }
    // }
    // Gather links into distinct regions
    // Map link-regions(implicit) to distinct-regions
    int[] linkRegionMap = new int[collector.length];
    int totalSize = 0;
    Vector<Vector<Integer>> regionsV = new Vector<Vector<Integer>>();
    Vector<Integer> regionsSizeV = new Vector<Integer>();
    BitSet checkFlagBS = new BitSet(collector.length);
    for (int i = 1; i < collector.length; i++) {
        // 0 not used
        if (clientTaskStatusSupport != null && clientTaskStatusSupport.isInterrupted()) {
            return;
        }
        if (checkFlagBS.get(i)) {
            continue;
        }
        checkFlagBS.set(i);
        Vector<Integer> holderV = new Vector<Integer>();
        holderV.add(i);
        if (collector[i] != null) {
            holderV.addAll(collector[i]);
        }
        int checkIndex = 0;
        // 
        boolean[] holderVContainsFlag = new boolean[collector.length];
        for (int j = 0; j < holderV.size(); j++) {
            holderVContainsFlag[holderV.elementAt(j)] = true;
        }
        // 
        while (true) {
            if (collector[holderV.elementAt(checkIndex)] != null) {
                Vector<Integer> newLinksV = collector[holderV.elementAt(checkIndex)];
                for (int j = 0; j < newLinksV.size(); j++) {
                    if (!checkFlagBS.get(newLinksV.elementAt(j)) && !holderVContainsFlag[newLinksV.elementAt(j)]) // !holderV.contains(newLinksV.elementAt(j))
                    {
                        holderV.add(newLinksV.elementAt(j));
                        holderVContainsFlag[newLinksV.elementAt(j)] = true;
                    }
                }
            }
            checkFlagBS.set(holderV.elementAt(checkIndex));
            checkIndex += 1;
            if (checkIndex == holderV.size()) {
                break;
            }
        }
        regionsV.add(holderV);
        if (regionsV.size() > 0x0000FFFF) {
            // unsigned short max, must match getShortEncodedRegionIndexImage()
            throw new ImageException("Error: image segmentation contains more than " + (0x0000FFFF) + " distinct regions.");
        }
        int regionSize = 0;
        byte pixelCheck = regionImagePixelV.elementAt(holderV.elementAt(0));
        for (int j = 0; j < holderV.size(); j++) {
            if (pixelCheck != regionImagePixelV.elementAt(holderV.elementAt(j))) {
                throw new ImageException("Linked regions have different image pixel values");
            }
            linkRegionMap[holderV.elementAt(j)] = regionsV.size() - 1;
            // System.out.print((j!=0?" ":"")+holderV.elementAt(j));
            regionSize += regionSizeArr[holderV.elementAt(j)];
            totalSize += regionSizeArr[holderV.elementAt(j)];
        }
        regionsSizeV.add(regionSize);
    // System.out.println();
    }
    if (totalSize != vcImage.getNumXYZ()) {
        throw new ImageException("Accumulated regions size does not equal image size");
    }
    // System.out.println("----------gather link distinct regions time "+((System.currentTimeMillis()-startTime)/1000.0));
    // startTime = System.currentTimeMillis();
    // //Create bitmasks of distinct regions
    // BitSet[] regionBitMaskBS = new BitSet[regionsV.size()];
    // for (int i = 0; i < regionBitMaskBS.length; i++) {
    // regionBitMaskBS[i] = new BitSet(regionPixels.length);
    // }
    // for (int i = 0; i < regionPixels.length; i++) {
    // regionBitMaskBS[linkRegionMap[regionPixels[i]]].set(i);
    // }
    // System.out.println("----------bitmask time "+((System.currentTimeMillis()-startTime)/1000.0));
    // startTime = System.currentTimeMillis();
    // Create RegionInfos
    regionInfos = new RegionInfo[regionsV.size()];
    for (int i = 0; i < regionsV.size(); i++) {
        regionInfos[i] = new RegionInfo(regionImagePixelV.elementAt(regionsV.elementAt(i).elementAt(0)) & 0x000000FF, regionsSizeV.elementAt(i), i, // regionBitMaskBS[i]
        null);
    }
    // System.out.println("----------regioninfo time "+((System.currentTimeMillis()-startTime)/1000.0));
    // startTime = System.currentTimeMillis();
    mapImageIndexToLinkRegion = regionPixels;
    mapLinkRegionToDistinctRegion = linkRegionMap;
    if (dimension != 0) {
        generateSurfaceCollection(regionsV.size(), // regionPixels,linkRegionMap,
        vcImage, xSurfElements, ySurfElements, zSurfElements, dimension, extent, origin);
    }
    if (surfaceCollection != null && debug_bCheckPolygonQuality) {
        verifyQuadVertexOrdering(debug_maxQuadAngle);
    }
    // Taubin smoothing
    if (surfaceCollection != null && filterCutoffFrequency < RegionImage.NO_SMOOTHING) {
        TaubinSmoothing taubinSmoothing = new TaubinSmoothingWrong();
        TaubinSmoothingSpecification taubinSpec = TaubinSmoothingSpecification.getInstance(filterCutoffFrequency);
        taubinSmoothing.smooth(surfaceCollection, taubinSpec);
    }
    // startTime = System.currentTimeMillis();
    if (surfaceCollection != null && debug_bCheckPolygonQuality) {
        verifyQuadVertexOrdering(debug_maxQuadAngle);
    }
// System.out.println("Total Num Regions = "+regionsV.size());
// System.out.println("Total Size = "+totalSize);
}

Example 10 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class GeometryViewer method refreshSourceDataInfo.

/**
 * connEtoM2:  (Geometry.this --> ImagePlaneManagerPanel1.sourceDataInfo)
 * @param value cbit.vcell.geometry.Geometry
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void refreshSourceDataInfo() {
    if (getGeometry() == null) {
        return;
    }
    GeometrySpec geometrySpec = getGeometry().getGeometrySpec();
    if (geometrySpec.getSampledImage().isDirty()) {
        return;
    }
    VCImage sampledImage = geometrySpec.getSampledImage().getCurrentValue();
    try {
        SourceDataInfo sdi = new SourceDataInfo(SourceDataInfo.INDEX_TYPE, sampledImage.getPixels(), geometrySpec.getExtent(), geometrySpec.getOrigin(), null, 0, sampledImage.getNumX(), 1, sampledImage.getNumY(), sampledImage.getNumX(), sampledImage.getNumZ(), sampledImage.getNumX() * sampledImage.getNumY());
        getImagePlaneManagerPanel1().setSourceDataInfo(sdi);
    } catch (ImageException e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, e.getMessage());
    } catch (Exception e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}