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

Example 56 with UShortImage

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

the class VFrap_OverlayEditorPanelJAI method updateLabel.

/**
 * Updates cursor probe label. * @param x int
 * @param y int
 */
protected void updateLabel(int inx, int iny) {
    if (imageDataset == null) {
        return;
    }
    float zoom = imagePane.getZoom();
    if ((inx / zoom) >= imageDataset.getISize().getX() || (iny / zoom) >= imageDataset.getISize().getY()) {
        inx = -1;
        iny = -1;
    }
    int x = (int) (inx / zoom);
    int y = (int) (iny / zoom);
    UShortImage[] images = imageDataset.getAllImages();
    sb.setLength(0);
    boolean bMultipleZ = imageDataset.getSizeZ() > 1;
    if (bMultipleZ) {
        sb.append("; Z=");
        sb.append(getZ() + 1);
        sb.append("/");
        sb.append(imageDataset.getSizeZ());
    }
    if (imageDataset.getSizeT() > 1) {
        sb.append((bMultipleZ ? "; " : "") + "T=");
        sb.append(imageDataset.getImageTimeStamps()[getT()]);
        // add the indicator to show it is the no. x image among total images.
        sb.append("  (" + (getT() + 1) + "" + "/" + imageDataset.getImageTimeStamps().length + ")");
    }
    // BufferedImage image = ImageTools.makeImage(images[ndx].getPixels(), images[ndx].getNumX(), images[ndx].getNumY());
    // int w = image == null ? -1 : image.getWidth();
    // int h = image == null ? -1 : image.getHeight();
    int w = imageDataset == null ? -1 : imageDataset.getISize().getX();
    int h = imageDataset == null ? -1 : imageDataset.getISize().getY();
    if (x >= w)
        x = w - 1;
    if (y >= h)
        y = h - 1;
    if (x >= 0 && y >= 0 && inx >= 0 && iny >= 0 && x < imageDataset.getISize().getX() && y < imageDataset.getISize().getY()) {
        if (images.length > 1)
            sb.append("; ");
        sb.append("X=");
        sb.append(x);
        if (w > 0) {
            sb.append("/");
            sb.append(w);
        }
        sb.append("; Y=");
        sb.append(y);
        if (h > 0) {
            sb.append("/");
            sb.append(h);
        }
        sb.append("; zoom(" + NumberUtils.formatNumber(imagePane.getZoom(), 3) + ")");
        sb.append("; contr(" + imagePane.getContrastDescription() + ")");
        if (imageDataset != null) {
            // Raster r = image.getRaster();
            // double[] pix = r.getPixel(x, y, (double[]) null);
            short[] pix = null;
            try {
                pix = new short[imageDataset.getSizeC()];
                for (int i = 0; i < pix.length; i++) {
                    pix[i] = imageDataset.getImage(getZ(), i, getT()).getPixel(x, y, 0);
                }
            } catch (Exception e) {
                pix = null;
                e.printStackTrace();
            // do nothing
            }
            sb.append("; value" + (isOriginalValueScaled() ? "(scld)" : ""));
            if (pix != null) {
                sb.append(pix.length > 1 ? "s=(" : "=");
                for (int i = 0; i < pix.length; i++) {
                    if (i > 0)
                        sb.append(", ");
                    sb.append((pix[i] & 0x0000FFFF));
                }
                if (pix.length > 1)
                    sb.append(")");
            } else {
                sb.append(" error");
            }
            if (isOriginalValueScaled()) {
                sb.append("; value(orig)");
                if (pix != null) {
                    sb.append(pix.length > 1 ? "s=(" : "=");
                    for (int i = 0; i < pix.length; i++) {
                        if (i > 0)
                            sb.append(", ");
                        sb.append(NumberUtils.formatNumber((((pix[i] & 0x0000FFFF)) - originalOffsetFactor) / originalScaleFactor, 6));
                    }
                    if (pix.length > 1)
                        sb.append(")");
                } else {
                    sb.append(" error");
                }
            }
        // sb.append(" udnerly="+Integer.toHexString(imagePane.getUnderlyingImage().getRGB(x, y)));
        }
    } else {
        sb.append("; zoom(" + NumberUtils.formatNumber(imagePane.getZoom(), 3) + ")");
        sb.append("; contr(" + imagePane.getContrastDescription() + ")");
    }
    sb.append(" ");
    textLabel.setText(sb.toString());
}

Example 57 with UShortImage

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

the class VFrap_ROIAssistPanel method resolveCurrentROI.

private void resolveCurrentROI(RegionInfo keepRegion) throws Exception {
    short[] removePixels = frapData.getCurrentlyDisplayedROI().getPixelsXYZ();
    for (int i = 0; i < removePixels.length; i++) {
        if (!keepRegion.isIndexInRegion(i)) {
            removePixels[i] = 0;
        }
    }
    final boolean hasInternalVoids = fillVoids(removePixels, true);
    UShortImage ushortImage = new UShortImage(removePixels, frapData.getCurrentlyDisplayedROI().getRoiImages()[0].getOrigin(), frapData.getCurrentlyDisplayedROI().getRoiImages()[0].getExtent(), frapData.getCurrentlyDisplayedROI().getISize().getX(), frapData.getCurrentlyDisplayedROI().getISize().getY(), frapData.getCurrentlyDisplayedROI().getISize().getZ());
    final ROI newCellROI = new ROI(ushortImage, frapData.getCurrentlyDisplayedROI().getROIName());
    SwingUtilities.invokeAndWait(new Runnable() {

        public void run() {
            // }});
            frapData.addReplaceRoi(newCellROI);
            applyROIButton.setEnabled(!hasInternalVoids);
            resolveROIButton.setEnabled(false);
            fillVoidsButton.setEnabled(hasInternalVoids);
        }
    });
}

Example 58 with UShortImage

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

the class ClientRequestManager method createFDOSWithChannels.

public static FieldDataFileOperationSpec createFDOSWithChannels(ImageDataset[] imagedataSets, Integer saveOnlyThisTimePointIndex) {
    final FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    // [time][var][data]
    int numXY = imagedataSets[0].getISize().getX() * imagedataSets[0].getISize().getY();
    int numXYZ = imagedataSets[0].getSizeZ() * numXY;
    fdos.variableTypes = new VariableType[imagedataSets.length];
    fdos.varNames = new String[imagedataSets.length];
    short[][][] shortData = new short[(saveOnlyThisTimePointIndex != null ? 1 : imagedataSets[0].getSizeT())][imagedataSets.length][numXYZ];
    for (int c = 0; c < imagedataSets.length; c += 1) {
        fdos.variableTypes[c] = VariableType.VOLUME;
        fdos.varNames[c] = "Channel" + c;
        for (int t = 0; t < imagedataSets[c].getSizeT(); t += 1) {
            if (saveOnlyThisTimePointIndex != null && saveOnlyThisTimePointIndex.intValue() != t) {
                continue;
            }
            int zOffset = 0;
            for (int z = 0; z < imagedataSets[c].getSizeZ(); z += 1) {
                UShortImage ushortImage = imagedataSets[c].getImage(z, 0, t);
                System.arraycopy(ushortImage.getPixels(), 0, shortData[(saveOnlyThisTimePointIndex != null ? 0 : t)][c], zOffset, numXY);
                // shortData[t][c] = ushortImage.getPixels();
                zOffset += numXY;
            }
        }
    }
    fdos.shortSpecData = shortData;
    fdos.times = imagedataSets[0].getImageTimeStamps();
    if (fdos.times == null) {
        fdos.times = new double[imagedataSets[0].getSizeT()];
        for (int i = 0; i < fdos.times.length; i += 1) {
            fdos.times[i] = i;
        }
    }
    fdos.origin = (imagedataSets[0].getAllImages()[0].getOrigin() != null ? imagedataSets[0].getAllImages()[0].getOrigin() : new Origin(0, 0, 0));
    fdos.extent = (imagedataSets[0].getExtent() != null) ? (imagedataSets[0].getExtent()) : (new Extent(1, 1, 1));
    fdos.isize = imagedataSets[0].getISize();
    return fdos;
}

Example 59 with UShortImage

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

the class OverlayEditorPanelJAI method createHighlightImageFromROI.

/**
 * Method createHighlightImageFromROI.
 * @return BufferedImage
 */
private BufferedImage createHighlightImageFromROI(ROI highlightImageROI) {
    UShortImage roiImage = highlightImageROI.getRoiImages()[getRoiImageIndex()];
    int width = roiImage.getNumX();
    int height = roiImage.getNumY();
    BufferedImage hiLiteImage = new BufferedImage(width, height, BufferedImage.TYPE_BYTE_INDEXED, getHiliteColorModel());
    byte[] hiLiteArr = ((DataBufferByte) hiLiteImage.getRaster().getDataBuffer()).getData();
    for (int i = 0; i < roiImage.getPixels().length; i++) {
        hiLiteArr[i] = (roiImage.getPixels()[i] != 0 ? (byte) highlightColor.getRed() : 0);
    }
    return hiLiteImage;
}

Example 60 with UShortImage

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

the class OverlayEditorPanelJAI method updateLabel.

/**
 * Updates cursor probe label. * @param x int
 * @param y int
 */
private void updateLabel(int inx, int iny) {
    if (imageDataset == null) {
        return;
    }
    float zoom = imagePane.getZoom();
    if ((inx / zoom) >= imageDataset.getISize().getX() || (iny / zoom) >= imageDataset.getISize().getY()) {
        inx = -1;
        iny = -1;
    }
    int x = (int) (inx / zoom);
    int y = (int) (iny / zoom);
    UShortImage[] images = imageDataset.getAllImages();
    sb.setLength(0);
    boolean bMultipleZ = imageDataset.getSizeZ() > 1;
    if (bMultipleZ) {
        sb.append("; Z=");
        sb.append(getZ() + 1);
        sb.append("/");
        sb.append(imageDataset.getSizeZ());
        if (calcCoords != null) {
            sb.append(" " + NumberUtils.formatNumber(calcCoords.calcZ(getZ()), 6) + "/" + NumberUtils.formatNumber(calcCoords.extentZ(), 6));
        }
    }
    if (imageDataset.getSizeT() > 1) {
        sb.append((bMultipleZ ? "; " : "") + "T=");
        sb.append(imageDataset.getImageTimeStamps()[getT()]);
    }
    int w = imageDataset == null ? -1 : imageDataset.getISize().getX();
    int h = imageDataset == null ? -1 : imageDataset.getISize().getY();
    if (x >= w)
        x = w - 1;
    if (y >= h)
        y = h - 1;
    if (x >= 0 && y >= 0 && inx >= 0 && iny >= 0 && x < imageDataset.getISize().getX() && y < imageDataset.getISize().getY()) {
        if (images.length > 1)
            sb.append("; ");
        sb.append("X=");
        sb.append(x);
        if (w > 0) {
            sb.append("/");
            sb.append(w);
            if (calcCoords != null) {
                sb.append(" " + NumberUtils.formatNumber(calcCoords.calcX(inx), 6) + "/" + NumberUtils.formatNumber(calcCoords.extentX(), 6));
            }
        }
        sb.append("; Y=");
        sb.append(y);
        if (h > 0) {
            sb.append("/");
            sb.append(h);
            if (calcCoords != null) {
                sb.append(" " + NumberUtils.formatNumber(calcCoords.calcY(iny), 6) + "/" + NumberUtils.formatNumber(calcCoords.extentY(), 6));
            }
        }
        sb.append("; zoom(" + NumberUtils.formatNumber(imagePane.getZoom(), 3) + ")");
        sb.append("; contr(" + imagePane.getContrastDescription() + ")");
        if (imageDataset != null) {
            short[] pix = null;
            try {
                pix = new short[imageDataset.getSizeC()];
                for (int i = 0; i < pix.length; i++) {
                    pix[i] = imageDataset.getImage(getZ(), i, getT()).getPixel(x, y, 0);
                }
            } catch (Exception e) {
                pix = null;
                e.printStackTrace();
            // do nothing
            }
            sb.append("; value(img)" + (isOriginalValueScaled() ? "(scld)" : ""));
            if (pix != null) {
                if (histogramPanel.isVisible()) {
                    histogramPanel.setSpecialValue((int) (pix[0] & 0x0000FFFF));
                }
                sb.append(pix.length > 1 ? "s=(" : "=");
                for (int i = 0; i < pix.length; i++) {
                    if (i > 0)
                        sb.append(", ");
                    sb.append((int) (pix[i] & 0x0000FFFF));
                }
                if (pix.length > 1)
                    sb.append(")");
            } else {
                sb.append(" error");
            }
            if (isOriginalValueScaled()) {
                sb.append("; value(img)(orig)");
                if (pix != null) {
                    sb.append(pix.length > 1 ? "s=(" : "=");
                    for (int i = 0; i < pix.length; i++) {
                        if (i > 0)
                            sb.append(", ");
                        sb.append(NumberUtils.formatNumber((((int) (pix[i] & 0x0000FFFF)) - originalOffsetFactor) / originalScaleFactor, 6));
                    }
                    if (pix.length > 1)
                        sb.append(")");
                } else {
                    sb.append(" error");
                }
            }
        }
        if (allROICompositeImageArr != null) {
            // System.out.println(getZ()+" "+x+" "+y);
            DataBufferByte dataBufferByte = (DataBufferByte) (allROICompositeImageArr[getZ()].getRaster().getDataBuffer());
            sb.append(" val(roi)=" + dataBufferByte.getData()[y * allROICompositeImageArr[0].getWidth() + x]);
        }
    } else {
        sb.append((sb.length() != 0 ? "; " : "") + "zoom(" + NumberUtils.formatNumber(imagePane.getZoom(), 3) + ")");
        sb.append("; contr(" + imagePane.getContrastDescription() + ")");
        if (histogramPanel.isVisible()) {
            histogramPanel.setSpecialValue(null);
        }
    }
    sb.append(" ");
    textLabel.setText(sb.toString());
}