Examples with DataBufferByte java.awt.image.DataBufferByte used on opensource projects

Example 46 with DataBufferByte

use of java.awt.image.DataBufferByte in project vcell by virtualcell.

the class ROIMultiPaintManager method updateUndo.

private void updateUndo(UNDO_INIT initType) {
    // Caller of this method is going to do something that CAN be undone so save undo info
    if (initType == UNDO_INIT.ALLZ) {
        undoROIComposite = new BufferedImage[roiComposite.length];
        for (int i = 0; i < roiComposite.length; i++) {
            undoROIComposite[i] = new BufferedImage(roiComposite[0].getWidth(), roiComposite[0].getHeight(), BufferedImage.TYPE_BYTE_INDEXED, getContrastIndexColorModel());
            System.arraycopy((byte[]) ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData(), 0, (byte[]) ((DataBufferByte) undoROIComposite[i].getRaster().getDataBuffer()).getData(), 0, roiComposite[0].getWidth() * roiComposite[0].getHeight());
        }
    }
    if (initType == UNDO_INIT.ONEZ) {
        // Some operations (paint,erase,fill) only need 1 zslice saved for undo
        if (undoROIComposite == null || undoROIComposite[overlayEditorPanelJAI.getZ()] == null) {
            undoROIComposite = new BufferedImage[roiComposite.length];
            undoROIComposite[overlayEditorPanelJAI.getZ()] = new BufferedImage(roiComposite[0].getWidth(), roiComposite[0].getHeight(), BufferedImage.TYPE_BYTE_INDEXED, getContrastIndexColorModel());
        }
        System.arraycopy((byte[]) ((DataBufferByte) roiComposite[overlayEditorPanelJAI.getZ()].getRaster().getDataBuffer()).getData(), 0, (byte[]) ((DataBufferByte) undoROIComposite[overlayEditorPanelJAI.getZ()].getRaster().getDataBuffer()).getData(), 0, roiComposite[0].getWidth() * roiComposite[0].getHeight());
    }
}

Example 47 with DataBufferByte

use of java.awt.image.DataBufferByte in project vcell by virtualcell.

the class ROIMultiPaintManager method getNonZeroBoundingBox.

private ROIMultiPaintManager.Crop3D getNonZeroBoundingBox(boolean bUseROI) {
    Rectangle bounding2D = null;
    int lowZ = Integer.MAX_VALUE;
    int highZ = -1;
    if (bUseROI) {
        int lowX = Integer.MAX_VALUE;
        int lowY = Integer.MAX_VALUE;
        int highX = -1;
        int highY = -1;
        for (int z = 0; z < roiComposite.length; z++) {
            int xyIndex = 0;
            byte[] zSectData = ((DataBufferByte) roiComposite[z].getRaster().getDataBuffer()).getData();
            for (int y = 0; y < roiComposite[0].getHeight(); y++) {
                for (int x = 0; x < roiComposite[0].getWidth(); x++) {
                    if (zSectData[xyIndex] != 0) {
                        lowX = Math.min(lowX, x);
                        lowY = Math.min(lowY, y);
                        highX = Math.max(highX, x);
                        highY = Math.max(highY, y);
                        lowZ = Math.min(lowZ, z);
                        ;
                        highZ = Math.max(highZ, z);
                    }
                    xyIndex++;
                }
            }
        }
        if (lowX != Integer.MAX_VALUE) {
            bounding2D = new Rectangle(lowX, lowY, highX - lowX + 1, highY - lowY + 1);
        }
    } else {
        UShortImage[] images = getImageDataSetChannel().getAllImages();
        for (int z = 0; z < images.length; z++) {
            Rectangle boundingRect = images[z].getNonzeroBoundingBox();
            if (boundingRect != null) {
                lowZ = Math.min(lowZ, z);
                ;
                highZ = Math.max(highZ, z);
                if (bounding2D == null) {
                    bounding2D = boundingRect;
                } else {
                    bounding2D = bounding2D.union(boundingRect);
                }
            }
        }
    }
    if (bounding2D == null) {
        return null;
    }
    ROIMultiPaintManager.Crop3D bounding3D = new ROIMultiPaintManager.Crop3D();
    bounding3D.setBounds(bounding2D.x, bounding2D.y, lowZ, bounding2D.width, bounding2D.height, highZ - lowZ + 1);
    return bounding3D;
}

Example 48 with DataBufferByte

use of java.awt.image.DataBufferByte in project vcell by virtualcell.

the class ROIMultiPaintManager method recoverUndo.

private void recoverUndo() {
    try {
        if (roiComposite == null || undoROIComposite == null || roiComposite.length != undoROIComposite.length) {
            throw new Exception("Undo operation has wrong undo information");
        } else {
            // Reset to last undo
            for (int i = 0; i < roiComposite.length; i++) {
                if (undoROIComposite[i] != null) {
                    if (roiComposite[i].getWidth() != undoROIComposite[i].getWidth() || roiComposite[i].getHeight() != undoROIComposite[i].getHeight()) {
                        throw new Exception("Undo operation z-slice size not match");
                    }
                    System.arraycopy((byte[]) ((DataBufferByte) undoROIComposite[i].getRaster().getDataBuffer()).getData(), 0, (byte[]) ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData(), 0, roiComposite[0].getWidth() * roiComposite[0].getHeight());
                }
            }
            undoROIComposite = null;
            overlayEditorPanelJAI.setAllROICompositeImage(roiComposite, OverlayEditorPanelJAI.FRAP_DATA_FILL_PROPERTY);
            overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_FILL_PROPERTY);
        }
    } catch (Exception e) {
        e.printStackTrace();
        // Something is wrong, throw out undo
        undoROIComposite = null;
        System.out.println("Error: undoROIComposite inconsistent state.\n" + e.getMessage());
    }
    updateUndoAfter(false);
}

Example 49 with DataBufferByte

use of java.awt.image.DataBufferByte in project vcell by virtualcell.

the class ROIMultiPaintManager method applyPixelClasses.

private void applyPixelClasses(VCPixelClass[] vcPixelClasses, Component parentComponent) {
    if (vcPixelClasses != null) {
        int backgroundIndex = -1;
        int[] pixelValMapPixelClassIndex = new int[256];
        Arrays.fill(pixelValMapPixelClassIndex, -1);
        String[][] rowData = new String[vcPixelClasses.length][1];
        for (int i = 0; i < vcPixelClasses.length; i++) {
            pixelValMapPixelClassIndex[vcPixelClasses[i].getPixel()] = i;
            rowData[i][0] = vcPixelClasses[i].getPixelClassName();
            if (vcPixelClasses[i].getPixel() == 0 && vcPixelClasses[i].getPixelClassName().equals(RESERVED_NAME_BACKGROUND)) {
                // choose background automatically
                backgroundIndex = i;
            }
        }
        // Create ROIs from VCPixelclasses
        // start 1 after background index color
        int roiCount = 1;
        int[] pixelClassIndexMaproiIndex = new int[vcPixelClasses.length];
        for (int i = 0; i < vcPixelClasses.length; i++) {
            if (i == backgroundIndex) {
                // background
                pixelClassIndexMaproiIndex[i] = 0;
                continue;
            }
            overlayEditorPanelJAI.addROIName(vcPixelClasses[i].getPixelClassName(), true, vcPixelClasses[0].getPixelClassName(), true, /*true,true,*/
            roiCount);
            pixelClassIndexMaproiIndex[i] = roiCount;
            roiCount++;
        }
        // fill in rois using pixel value and VCPixelClass mappings
        for (int zindex = 0; zindex < roiComposite.length; zindex++) {
            byte[] zdata = ((DataBufferByte) roiComposite[zindex].getRaster().getDataBuffer()).getData();
            UShortImage uShortImage = initImageDataSetChannels[0].getImage(zindex, 0, 0);
            for (int xyindex = 0; xyindex < zdata.length; xyindex++) {
                // unsigned short
                int pixelval = uShortImage.getPixels()[xyindex] & 0x000000FF;
                zdata[xyindex] = (byte) pixelClassIndexMaproiIndex[pixelValMapPixelClassIndex[pixelval]];
            }
        }
    }
}

Example 50 with DataBufferByte

use of java.awt.image.DataBufferByte in project vcell by virtualcell.

the class ROIMultiPaintManager method askApplyHighlightToROI.

private boolean askApplyHighlightToROI() {
    UShortImage[] roiZ = overlayEditorPanelJAI.getHighliteInfo().getRoiImages();
    boolean bOverWrite = true;
    // Check for existing ROI
    final String OVERWRITE_ALL = "Overwrite any existing Domain Regionss";
    final String KEEP_EXISTING = "Keep existing Domain Regions when overlapping";
    final String CANCEL_ROI_UPDATE = "Cancel";
    // boolean bHadAny = false;
    for (int i = 0; i < roiZ.length; i++) {
        boolean bDone = false;
        short[] pixels = roiZ[i].getPixels();
        byte[] compositePixels = ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData();
        for (int j = 0; j < compositePixels.length; j++) {
            // bHadAny|= pixels[j] != 0;
            if (compositePixels[j] != 0 && pixels[j] != 0) /* && compositePixels[j] != (byte)roiColorIndex*/
            {
                bDone = true;
                String result = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Some areas of the new Domain Regions overlap with existing Domain Regions.", new String[] { OVERWRITE_ALL, KEEP_EXISTING, CANCEL_ROI_UPDATE }, OVERWRITE_ALL);
                if (result.equals(KEEP_EXISTING)) {
                    bOverWrite = false;
                } else if (result.equals(CANCEL_ROI_UPDATE)) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
                break;
            }
        }
        if (bDone) {
            break;
        }
    }
    return bOverWrite;
}