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

Example 61 with UShortImage

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

the class AnnotatedImageDataset method verifyROIdimensions.

/**
 * Method verifyROIdimensions.
 * @param argImageDataset ImageDataset
 * @param argROIs ArrayList<ROI>
 */
private void verifyROIdimensions(ImageDataset argImageDataset, ArrayList<ROI> argROIs) {
    if (rois != null) {
        int imgNumX = argImageDataset.getImage(0, 0, 0).getNumX();
        int imgNumY = argImageDataset.getImage(0, 0, 0).getNumY();
        int imgNumZ = argImageDataset.getSizeZ();
        for (int i = 0; i < argROIs.size(); i++) {
            UShortImage firstROIImage = argROIs.get(i).getRoiImages()[0];
            int roiNumX = firstROIImage.getNumX();
            int roiNumY = firstROIImage.getNumY();
            int roiNumZ = argROIs.get(i).getRoiImages().length;
            if (roiNumX != imgNumX || roiNumY != imgNumY || roiNumZ != imgNumZ) {
                throw new RuntimeException("ROI size (" + roiNumX + "," + roiNumY + "," + roiNumZ + ") doesn't match image size (" + imgNumX + "," + imgNumY + "," + imgNumZ + ")");
            }
        }
    }
}

Example 62 with UShortImage

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

the class MicroscopyXmlReader method getROI.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
private ROI getROI(Element param) throws XmlParseException {
    String roiName = param.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag);
    List<Element> ushortImageElementList = param.getChildren(MicroscopyXMLTags.UShortImageTag);
    Iterator<Element> imageElementIter = ushortImageElementList.iterator();
    UShortImage[] images = new UShortImage[ushortImageElementList.size()];
    int imageIndex = 0;
    while (imageElementIter.hasNext()) {
        images[imageIndex++] = getUShortImage(imageElementIter.next());
    }
    ROI roi = new ROI(images, roiName);
    return roi;
}

Example 63 with UShortImage

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

the class MicroscopyXmlReader method getImageDataset.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
private ImageDataset getImageDataset(Element param, ClientTaskStatusSupport progressListener) throws XmlParseException {
    @SuppressWarnings("unchecked") List<Element> ushortImageElementList = param.getChildren(MicroscopyXMLTags.UShortImageTag);
    Iterator<Element> imageElementIter = ushortImageElementList.iterator();
    UShortImage[] images = new UShortImage[ushortImageElementList.size()];
    // added in Feb 2008, for counting loading progress
    int imageSize = ushortImageElementList.size();
    int imageCount = 0;
    while (imageElementIter.hasNext()) {
        images[imageCount++] = getUShortImage(imageElementIter.next());
        if (progressListener != null) {
            progressListener.setProgress((int) ((imageCount * 100.0) / imageSize));
        }
    }
    Element timeStampListElement = param.getChild(MicroscopyXMLTags.TimeStampListTag);
    double[] timestamps = null;
    if (timeStampListElement != null) {
        String timeStampListText = timeStampListElement.getTextTrim();
        StringTokenizer tokens = new StringTokenizer(timeStampListText, ",\n\r\t ", false);
        ArrayList<Double> times = new ArrayList<Double>();
        while (tokens.hasMoreTokens()) {
            String token = tokens.nextToken();
            times.add(Double.parseDouble(token));
        }
        timestamps = new double[times.size()];
        for (int i = 0; i < timestamps.length; i++) {
            timestamps[i] = times.get(i);
        }
    }
    int numTimeSteps = (timestamps != null) ? (timestamps.length) : (1);
    int numZ = images.length / numTimeSteps;
    ImageDataset imageDataset = new ImageDataset(images, timestamps, numZ);
    return imageDataset;
}

Example 64 with UShortImage

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

the class MicroscopyXmlReader method getUShortImage.

/**
 * This method returns a VCIMage object from a XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @param param org.jdom.Element
 * @return VCImage
 * @throws XmlParseException
 */
private UShortImage getUShortImage(Element param) throws XmlParseException {
    // get the attributes
    Element tempelement = param.getChild(XMLTags.ImageDataTag);
    int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag));
    int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag));
    int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag));
    int compressSize = Integer.parseInt(tempelement.getAttributeValue(XMLTags.CompressedSizeTag));
    final int BYTES_PER_SHORT = 2;
    int UNCOMPRESSED_SIZE_BYTES = aNumX * aNumY * aNumZ * BYTES_PER_SHORT;
    // getpixels
    String hexEncodedBytes = tempelement.getText();
    byte[] rawBytes = org.vcell.util.Hex.toBytes(hexEncodedBytes);
    ByteArrayInputStream rawByteArrayInputStream = new ByteArrayInputStream(rawBytes);
    InputStream rawInputStream = rawByteArrayInputStream;
    if (compressSize != UNCOMPRESSED_SIZE_BYTES) {
        rawInputStream = new InflaterInputStream(rawByteArrayInputStream);
    }
    byte[] shortsAsBytes = new byte[UNCOMPRESSED_SIZE_BYTES];
    int readCount = 0;
    try {
        while ((readCount += rawInputStream.read(shortsAsBytes, readCount, shortsAsBytes.length - readCount)) != shortsAsBytes.length) {
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new XmlParseException("error reading image pixels: ", e);
    } finally {
        if (rawInputStream != null) {
            try {
                rawInputStream.close();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
    }
    ByteBuffer byteBuffer = ByteBuffer.wrap(shortsAsBytes);
    short[] shortPixels = new short[aNumX * aNumY * aNumZ];
    for (int i = 0; i < shortPixels.length; i++) {
        shortPixels[i] = byteBuffer.getShort();
    }
    Element extentElement = param.getChild(XMLTags.ExtentTag);
    Extent extent = null;
    if (extentElement != null) {
        extent = vcellXMLReader.getExtent(extentElement);
    }
    Element originElement = param.getChild(XMLTags.OriginTag);
    Origin origin = null;
    if (originElement != null) {
        origin = vcellXMLReader.getOrigin(originElement);
    }
    // //set attributes
    // String name = this.unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // String annotation = param.getChildText(XMLTags.AnnotationTag);
    UShortImage newimage;
    try {
        newimage = new UShortImage(shortPixels, origin, extent, aNumX, aNumY, aNumZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new XmlParseException("error reading image", e);
    }
    return newimage;
}

Example 65 with UShortImage

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

the class MicroscopyXmlReader method getROI.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
private ROI getROI(Element param) throws XmlParseException {
    String roiName = param.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag);
    @SuppressWarnings("unchecked") List<Element> ushortImageElementList = param.getChildren(MicroscopyXMLTags.UShortImageTag);
    Iterator<Element> imageElementIter = ushortImageElementList.iterator();
    UShortImage[] images = new UShortImage[ushortImageElementList.size()];
    int imageIndex = 0;
    while (imageElementIter.hasNext()) {
        images[imageIndex++] = getUShortImage(imageElementIter.next());
    }
    ROI roi = new ROI(images, roiName);
    return roi;
}