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

Example 66 with UShortImage

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

the class MicroscopyXmlproducer method getXML.

/**
 * This method returns a XML representation for a Biomodel object.
 * Creation date: (2/14/2001 3:41:13 PM)
 * @param param cbit.vcell.biomodel.BioModel
 * @return Element
 * @throws XmlParseException
 * @throws cbit.vcell.parser.ExpressionException
 */
public static Element getXML(ImageDataset param, Xmlproducer vcellXMLProducer, ClientTaskStatusSupport progressListener, boolean bSaveCompressed) throws XmlParseException, cbit.vcell.parser.ExpressionException {
    Element imageDatasetNode = new Element(MicroscopyXMLTags.ImageDatasetTag);
    // Get ImageDataset
    UShortImage[] images = param.getAllImages();
    // added in Feb 2008, for counting saving progress
    int imageSize = images.length;
    int imageCount = 0;
    for (int i = 0; i < images.length; i++) {
        imageDatasetNode.addContent(getXML(images[i], vcellXMLProducer, bSaveCompressed));
        imageCount++;
        // suppose image data set takes 95% and roi takes 5% of total progress.
        if (progressListener != null) {
            progressListener.setProgress(((int) ((imageCount * 95) / (double) imageSize)));
        }
    }
    if (param.getImageTimeStamps() != null) {
        Element timeStampListNode = new Element(MicroscopyXMLTags.TimeStampListTag);
        double[] timeStamps = param.getImageTimeStamps();
        StringBuilder stringBuilder = new StringBuilder();
        stringBuilder.append(timeStamps[0]);
        for (int i = 1; i < timeStamps.length; i++) {
            stringBuilder.append(",");
            stringBuilder.append(timeStamps[i]);
        }
        timeStampListNode.addContent(stringBuilder.toString());
        imageDatasetNode.addContent(timeStampListNode);
    }
    return imageDatasetNode;
}

Example 67 with UShortImage

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

the class MicroscopyXmlproducer method getXML.

/**
 * This method returns a XML representation for a Biomodel object.
 * Creation date: (2/14/2001 3:41:13 PM)
 * @param param cbit.vcell.biomodel.BioModel
 * @return Element
 * @throws XmlParseException
 * @throws cbit.vcell.parser.ExpressionException
 */
private static Element getXML(ROI param, Xmlproducer vcellXMLProducer, boolean bSaveCompressed) throws XmlParseException, cbit.vcell.parser.ExpressionException {
    Element roiNode = new Element(MicroscopyXMLTags.ROITag);
    UShortImage[] images = param.getRoiImages();
    for (int i = 0; i < images.length; i++) {
        roiNode.addContent(getXML(param.getRoiImages()[i], vcellXMLProducer, bSaveCompressed));
    }
    roiNode.setAttribute(MicroscopyXMLTags.ROITypeAttrTag, param.getROIName());
    return roiNode;
}

Example 68 with UShortImage

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

the class NonGUIFRAPTest method runXMLFile.

public static void runXMLFile(String xmlFileName, String testDirectoryPath) throws Exception {
    String xmlString = XmlUtil.getXMLString(xmlFileName);
    // System.out.println(xmlString);
    MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
    FRAPStudy frapStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
    if (frapStudy == null || frapStudy.getFrapData() == null) {
        throw new Exception("no FrapData in file " + xmlFileName);
    }
    if (frapStudy.getFrapData().getImageDataset().getSizeC() != 1 || frapStudy.getFrapData().getImageDataset().getSizeZ() != 1) {
        throw new Exception("Only single channel, single z test implemented");
    }
    File imageDataSetZipFile = getCanonicalFilename(testDirectoryPath, null);
    File cellROIFile = getCanonicalFilename(testDirectoryPath, FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    File bleachROIFile = getCanonicalFilename(testDirectoryPath, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    File backgroundROIFile = getCanonicalFilename(testDirectoryPath, FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
    FileOutputStream fos = new FileOutputStream(imageDataSetZipFile);
    BufferedOutputStream bos = new BufferedOutputStream(fos);
    ZipOutputStream zos = new ZipOutputStream(bos);
    ImageDataset imageDataset = frapStudy.getFrapData().getImageDataset();
    System.out.println(imageDataset.getISize());
    StringBuffer timeStampsSB = new StringBuffer();
    for (int i = 0; i < imageDataset.getSizeT(); i++) {
        // ZipEntry zipEntry = new ZipEntry((i<10?"00":(i<100?"0":""))+i+".bmp");
        ZipEntry zipEntry = new ZipEntry((i < 10 ? "00" : (i < 100 ? "0" : "")) + i + ".tif");
        zos.putNextEntry(zipEntry);
        UShortImage timePointImage = imageDataset.getImage(0, 0, i);
        File tempF = writeTempTiff(timePointImage.getPixels(), timePointImage.getNumX(), timePointImage.getNumY());
        FileInputStream fis = new FileInputStream(tempF);
        byte[] tempbytes = new byte[(int) tempF.length()];
        int offset = 0;
        while ((offset += fis.read(tempbytes, offset, tempbytes.length - offset)) != tempbytes.length) {
        }
        zos.write(tempbytes);
        // writeUShortFile(timePointImage, zos);
        timeStampsSB.append((i != 0 ? "," : "") + imageDataset.getImageTimeStamps()[i]);
        zos.closeEntry();
        fis.close();
        tempF.delete();
    }
    zos.close();
    fos.close();
    // fos = new FileOutputStream(cellROIFile);
    ROI cellROI = frapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    File cellTempF = writeTempTiff(cellROI.getRoiImages()[0].getPixels(), cellROI.getRoiImages()[0].getNumX(), cellROI.getRoiImages()[0].getNumY());
    FileUtils.copyFile(cellTempF, cellROIFile);
    cellTempF.delete();
    // writeUShortFile(cellROI.getRoiImages()[0], fos);
    // fos.close();
    // fos = new FileOutputStream(bleachROIFile);
    ROI bleachROI = frapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    File bleachTempf = writeTempTiff(bleachROI.getRoiImages()[0].getPixels(), bleachROI.getRoiImages()[0].getNumX(), bleachROI.getRoiImages()[0].getNumY());
    FileUtils.copyFile(bleachTempf, bleachROIFile);
    bleachTempf.delete();
    // writeUShortFile(bleachROI.getRoiImages()[0],fos);
    // fos.close();
    // fos = new FileOutputStream(backgroundROIFile);
    ROI backgroundROI = frapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
    File backgroundTempf = writeTempTiff(backgroundROI.getRoiImages()[0].getPixels(), backgroundROI.getRoiImages()[0].getNumX(), backgroundROI.getRoiImages()[0].getNumY());
    FileUtils.copyFile(backgroundTempf, backgroundROIFile);
    backgroundTempf.delete();
    // writeUShortFile(backgroundROI.getRoiImages()[0],fos);
    // fos.close();
    checkExternalDataSameAsOriginal(frapStudy, testDirectoryPath);
    // if(true){System.exit(0);}
    String[] args = new String[] { // frapStudy.getFrapModelParameters().getPureDiffModelParameters().secondaryMobileFraction,
    testDirectoryPath, imageDataSetZipFile.getAbsolutePath(), cellROIFile.getAbsolutePath(), bleachROIFile.getAbsolutePath(), backgroundROIFile.getAbsolutePath(), new File(testDirectoryPath, "testCreated.xml").getAbsolutePath(), timeStampsSB.toString(), imageDataset.getExtent().getX() + "," + imageDataset.getExtent().getY() + "," + imageDataset.getExtent().getZ() };
    NonGUIFRAPTest.runSolver(args);
}

Example 69 with UShortImage

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

the class FrapDataUtils method createFrapData.

public static FRAPData createFrapData(ArrayList<SourceDataInfo> sourceDataInfoArr, double[] times, int slice, Double maxIntensity, ClientTaskStatusSupport progressListener) throws ImageException {
    if (sourceDataInfoArr.size() != times.length) {
        throw new ImageException("Error FRAPData.createFrapData: times array length must equal SourceDataInfo vector size");
    }
    // construct
    int XY_SIZE = sourceDataInfoArr.get(0).getXSize() * sourceDataInfoArr.get(0).getYSize();
    int SLICE_OFFSET = slice * XY_SIZE;
    // slice always 2D data
    int Z_SIZE = 1;
    // find scale factor to scale up the data to avoid losing precision when casting double to short
    double linearScaleFactor = 1;
    if (maxIntensity != null) {
        double maxDataValue = 0;
        for (int i = 0; i < times.length; i++) {
            if (sourceDataInfoArr.get(i).getMinMax() != null) {
                maxDataValue = Math.max(maxDataValue, sourceDataInfoArr.get(i).getMinMax().getMax());
            } else {
                double[] doubleData = (double[]) sourceDataInfoArr.get(i).getData();
                for (int j = 0; j < doubleData.length; j++) {
                    maxDataValue = Math.max(maxDataValue, doubleData[j]);
                }
            }
        }
        linearScaleFactor = maxIntensity.doubleValue() / maxDataValue;
    }
    // saving each time step 2D double array to a UShortImage
    UShortImage[] dataImages = new UShortImage[times.length];
    for (int i = 0; i < times.length; i++) {
        double[] doubleData = (double[]) sourceDataInfoArr.get(i).getData();
        short[] shortData = new short[XY_SIZE];
        for (int j = 0; j < shortData.length; j++) {
            shortData[j] = (short) (doubleData[j + (SLICE_OFFSET)] * linearScaleFactor);
        }
        dataImages[i] = new UShortImage(shortData, sourceDataInfoArr.get(i).getOrigin(), sourceDataInfoArr.get(i).getExtent(), sourceDataInfoArr.get(i).getXSize(), sourceDataInfoArr.get(i).getYSize(), Z_SIZE);
        if (progressListener != null) {
            int progress = (int) (((i + 1) * 1.0 / times.length) * 100);
            progressListener.setProgress(progress);
        }
    }
    ImageDataset imageDataSet = new ImageDataset(dataImages, times, Z_SIZE);
    FRAPData frapData = new FRAPData(imageDataSet, new String[] { FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name(), FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name(), FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name() });
    return frapData;
}

Example 70 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 + ")");
            }
        }
    }
}