Examples with UShortImage cbit.vcell.VirtualMicroscopy.UShortImage used on opensource projects

Example 11 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class VFrap_ROIAssistPanel method forceROIValid.

private ROI forceROIValid(ROI validateROI) throws Exception {
    if (validateROI.getROIName().equals(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name())) {
        lastRegionInfos = null;
        SwingUtilities.invokeAndWait(new Runnable() {

            public void run() {
                // }});
                applyROIButton.setEnabled(true);
                resolveROIButton.setEnabled(false);
                fillVoidsButton.setEnabled(false);
            }
        });
        return validateROI;
    }
    if (validateROI.getNonzeroPixelsCount() < 1) {
        return validateROI;
    }
    // 
    // Remove pixels touching only at corners
    // 
    short[] validatePixels = validateROI.getPixelsXYZ();
    // 
    // Remove noise objects
    // 
    lastRegionInfos = calculateRegionInfos(validatePixels);
    Vector<RegionInfo> roiRegionInfoV = new Vector<RegionInfo>();
    for (int i = 0; i < lastRegionInfos.length; i++) {
        if (lastRegionInfos[i].getPixelValue() == 1) {
            roiRegionInfoV.add(lastRegionInfos[i]);
        }
    // System.out.println(lastRegionInfos[i]);
    }
    // if(validateROI.getROIType().equals(RoiType.ROI_CELL) || validateROI.getROIType().equals(RoiType.ROI_BLEACHED)){
    if (roiRegionInfoV.size() > 1) {
        SwingUtilities.invokeAndWait(new Runnable() {

            public void run() {
                applyROIButton.setEnabled(false);
                resolveROIButton.setEnabled(true);
                fillVoidsButton.setEnabled(false);
            }
        });
    } else {
        final boolean hasInternalVoids = fillVoids(validatePixels, true);
        SwingUtilities.invokeAndWait(new Runnable() {

            public void run() {
                // }});
                lastRegionInfos = null;
                applyROIButton.setEnabled(!hasInternalVoids);
                resolveROIButton.setEnabled(false);
                fillVoidsButton.setEnabled(hasInternalVoids);
            }
        });
    }
    UShortImage ushortImage = new UShortImage(validatePixels, validateROI.getRoiImages()[0].getOrigin(), validateROI.getRoiImages()[0].getExtent(), validateROI.getISize().getX(), validateROI.getISize().getY(), validateROI.getISize().getZ());
    ROI newROI = new ROI(ushortImage, validateROI.getROIName());
    if (newROI.compareEqual(validateROI)) {
        return validateROI;
    }
    return newROI;
}

Example 12 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method displaySpecialData.

public void displaySpecialData(short[] specialData, int width, int height) throws Exception {
    if (specialData == null) {
        forceImage();
        return;
    }
    UShortImage specialUShortImage = new UShortImage(specialData, null, null, width, height, 1);
    BufferedImage specialBufferedImage = createUnderlyingImage(specialUShortImage);
    imagePane.setUnderlyingImage(specialBufferedImage, false, null);
}

Example 13 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method getImage.

/**
 * Gets the currently displayed image. * @return BufferedImage
 */
private BufferedImage getImage() {
    if (imageDataset == null) {
        return null;
    }
    int ndx = getImageIndex();
    if (imageDataset == null || ndx >= imageDataset.getAllImages().length) {
        return null;
    }
    UShortImage image = imageDataset.getAllImages()[ndx];
    return createUnderlyingImage(image);
}

Example 14 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class OverlayEditorPanelJAI method getImage.

/**
 * Gets the currently displayed image. * @return BufferedImage
 */
private BufferedImage getImage() {
    if (imageDataset == null) {
        return null;
    }
    int ndx = getImageIndex();
    if (imageDataset == null || ndx >= imageDataset.getAllImages().length) {
        return null;
    }
    UShortImage image = imageDataset.getAllImages()[ndx];
    return createUnderlyingImage(image);
}

Example 15 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class ROIAssistPanel method createScaledTimeAverageData.

private void createScaledTimeAverageData() throws Exception {
    int numTimes = dataToThreshold.getImageDataset().getSizeT();
    long[] timeSum = new long[dataToThreshold.getImageDataset().getISize().getXYZ()];
    for (int t = 0; t < numTimes; t++) {
        int pixelIndex = 0;
        for (int z = 0; z < dataToThreshold.getImageDataset().getSizeZ(); z++) {
            UShortImage timePointDataImage = dataToThreshold.getImageDataset().getImage(z, 0, t);
            for (int y = 0; y < timePointDataImage.getNumY(); y++) {
                for (int x = 0; x < timePointDataImage.getNumX(); x++) {
                    timeSum[pixelIndex] += timePointDataImage.getPixel(x, y, 0) & 0x0000FFFF;
                    pixelIndex++;
                }
            }
        }
    }
    roiTimeAverageDataShort = new short[timeSum.length];
    for (int i = 0; i < timeSum.length; i++) {
        roiTimeAverageDataShort[i] |= ((int) (timeSum[i] / numTimes)) & 0x0000FFFF;
    }
    scaleDataInPlace(roiTimeAverageDataShort);
}