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

Example 6 with UShortImage

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

the class FRAPData method chopImages.

public void chopImages(int startTimeIndex, int endTimeIndex) {
    UShortImage[] origImages = getImageDataset().getAllImages();
    double[] origTimeSteps = getImageDataset().getImageTimeStamps();
    int numOfZ = getImageDataset().getSizeZ();
    int numOfC = getImageDataset().getSizeC();
    int tolImgLen = (endTimeIndex - startTimeIndex + 1) * numOfZ * numOfC;
    UShortImage[] newImages = new UShortImage[tolImgLen];
    double[] newTimeSteps = new double[endTimeIndex - startTimeIndex + 1];
    System.arraycopy(origImages, startTimeIndex * numOfZ * numOfC, newImages, 0, tolImgLen);
    System.arraycopy(origTimeSteps, startTimeIndex, newTimeSteps, 0, (endTimeIndex - startTimeIndex + 1));
    // shift time to start from 0, it's not necessary
    // double firstTimePoint = newTimeSteps[0];
    // for(int i = 0; i < newTimeSteps.length; i++)
    // {
    // newTimeSteps[i] = newTimeSteps[i] - firstTimePoint;
    // }
    ImageDataset imgDataset = new ImageDataset(newImages, newTimeSteps, numOfZ);
    setImageDataset(imgDataset);
}

Example 7 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage 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 8 with UShortImage

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

the class VFrap_ROIAssistPanel method showComponentOKCancelTableList.

public int[] showComponentOKCancelTableList(final Component requester, String title, String[] columnNames, Object[][] rowData, int listSelectionModel_SelectMode, final RegionInfo[] regionInfoArr, final short[] multiObjectROIPixels) throws UserCancelException {
    DefaultTableModel tableModel = new DefaultTableModel() {

        public boolean isCellEditable(int row, int column) {
            return false;
        }
    };
    tableModel.setDataVector(rowData, columnNames);
    final JTable table = new JTable(tableModel);
    table.setSelectionMode(listSelectionModel_SelectMode);
    JScrollPane scrollPane = new JScrollPane(table);
    table.setPreferredScrollableViewportSize(new Dimension(500, 250));
    table.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

        public void valueChanged(ListSelectionEvent e) {
            if (!e.getValueIsAdjusting()) {
                try {
                    int index = table.getSelectedRow();
                    // System.out.println("list index="+index);
                    RegionInfo keepRegion = regionInfoArr[index];
                    short[] removePixels = multiObjectROIPixels.clone();
                    for (int i = 0; i < removePixels.length; i++) {
                        if (!keepRegion.isIndexInRegion(i)) {
                            removePixels[i] = 0;
                        }
                    }
                    UShortImage ushortImage = new UShortImage(removePixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
                    final ROI newCellROI = new ROI(ushortImage, frapData.getCurrentlyDisplayedROI().getROIName());
                    frapData.addReplaceRoi(newCellROI);
                } catch (Exception e2) {
                    e2.printStackTrace();
                    throw new RuntimeException("Error selecting resolved ROI", e2);
                }
            }
        }
    });
    ScopedExpressionTableCellRenderer.formatTableCellSizes(table);
    int result = DialogUtils.showComponentOKCancelDialog(requester, scrollPane, title);
    if (result != JOptionPane.OK_OPTION) {
        throw UserCancelException.CANCEL_GENERIC;
    }
    return table.getSelectedRows();
}

Example 9 with UShortImage

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

the class VFrap_ROIAssistPanel method createScaledTimeAverageData.

private void createScaledTimeAverageData() throws Exception {
    int numTimes = frapData.getImageDataset().getSizeT();
    long[] timeSum = new long[frapData.getImageDataset().getISize().getXYZ()];
    for (int t = 0; t < numTimes; t++) {
        int pixelIndex = 0;
        for (int z = 0; z < frapData.getImageDataset().getSizeZ(); z++) {
            UShortImage timePointDataImage = frapData.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);
}

Example 10 with UShortImage

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

the class VFrap_ROIAssistPanel method processTimepoint.

private void processTimepoint() {
    new Thread(new Runnable() {

        public void run() {
            try {
                boolean bInvert = !frapData.getCurrentlyDisplayedROI().getROIName().equals(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_CELL.name());
                short[] cellMask = null;
                if (bInvert) {
                    cellMask = frapData.getRoi(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_CELL.name()).getPixelsXYZ();
                }
                short[] shortPixels = new short[lastROISourceDataShort.length];
                for (int i = 0; i < lastROISourceDataShort.length; i++) {
                    shortPixels[i] = (short) (isSet(frapData.getCurrentlyDisplayedROI().getROIName(), lastROISourceDataShort[i], thresholdSlider.getValue(), thresholdSliderIntensityLookup, (cellMask == null ? true : cellMask[i] != 0)) ? 0xFFFF : 0);
                }
                UShortImage ushortImage = new UShortImage(shortPixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
                ROI newCellROI = new ROI(ushortImage, frapData.getCurrentlyDisplayedROI().getROIName());
                final ROI forceValidROI = forceROIValid(newCellROI);
                SwingUtilities.invokeAndWait(new Runnable() {

                    public void run() {
                        // }});
                        frapData.addReplaceRoi(forceValidROI);
                    }
                });
            } catch (final Exception e2) {
                lastROISourceDataShort = null;
                e2.printStackTrace();
                SwingUtilities.invokeLater(new Runnable() {

                    public void run() {
                        // }});
                        DialogUtils.showErrorDialog(VFrap_ROIAssistPanel.this, "Error setting new ROI. " + e2.getMessage());
                    }
                });
            }
        }
    }).start();
}