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

Example 26 with ImageDataset

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

the class FRAPOptimizationUtils method refreshNormalizedMeasurementError.

/*
	 * Calculate Measurement error for data that is normalized 
	 * and averaged at each ROI ring.
	 * The first dimension is ROI rings(according to the Enum in FRAPData)
	 * The second dimension is time points (from starting index to the end) 
	 */
public static double[][] refreshNormalizedMeasurementError(FRAPStudy frapStudy) throws Exception {
    FRAPData fData = frapStudy.getFrapData();
    ImageDataset imgDataset = fData.getImageDataset();
    double[] timeStamp = imgDataset.getImageTimeStamps();
    int startIndexRecovery = frapStudy.getStartingIndexForRecovery();
    int roiLen = FRAPData.VFRAP_ROI_ENUM.values().length;
    double[][] sigma = new double[roiLen][timeStamp.length - startIndexRecovery];
    double[] prebleachAvg = FrapDataUtils.calculatePreBleachAverageXYZ(fData, startIndexRecovery);
    for (int roiIdx = 0; roiIdx < roiLen; roiIdx++) {
        ROI roi = fData.getRoi((FRAPData.VFRAP_ROI_ENUM.values()[roiIdx]).name());
        if (roi != null) {
            short[] roiData = roi.getPixelsXYZ();
            for (int timeIdx = startIndexRecovery; timeIdx < timeStamp.length; timeIdx++) {
                short[] rawTimeData = AnnotatedImageDataset.collectAllZAtOneTimepointIntoOneArray(imgDataset, timeIdx);
                if (roiData.length != rawTimeData.length || roiData.length != prebleachAvg.length || rawTimeData.length != prebleachAvg.length) {
                    throw new Exception("ROI data and image data are not in the same length.");
                } else {
                    // loop through ROI
                    int roiPixelCounter = 0;
                    double sigmaVal = 0;
                    for (int i = 0; i < roiData.length; i++) {
                        if (roiData[i] != 0) {
                            sigmaVal = sigmaVal + ((rawTimeData[i] & 0x0000FFFF)) / (prebleachAvg[i] * prebleachAvg[i]);
                            roiPixelCounter++;
                        }
                    }
                    if (roiPixelCounter == 0) {
                        sigmaVal = 0;
                    } else {
                        sigmaVal = Math.sqrt(sigmaVal) / roiPixelCounter;
                    }
                    sigma[roiIdx][timeIdx - startIndexRecovery] = sigmaVal;
                }
            }
        }
    }
    // }
    return sigma;
}

Example 27 with ImageDataset

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

the class FRAPStudy method getCartesianMesh.

public CartesianMesh getCartesianMesh() throws Exception {
    CartesianMesh cartesianMesh = null;
    ImageDataset imgDataSet = getFrapData().getImageDataset();
    Extent extent = imgDataSet.getExtent();
    ISize isize = imgDataSet.getISize();
    Origin origin = new Origin(0, 0, 0);
    if (getBioModel() == null) {
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
    } else {
        RegionImage regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        if (regionImage == null) {
            getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().updateAll();
            regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        }
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    }
    return cartesianMesh;
}

Example 28 with ImageDataset

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

the class FRAPWorkspace method loadFRAPDataFromMultipleFiles.

public static FRAPStudy loadFRAPDataFromMultipleFiles(File[] inputFiles, ClientTaskStatusSupport clientTaskStatusSupport, boolean isTimeSeries, double timeInterval) throws Exception {
    FRAPStudy newFrapStudy = new FRAPStudy();
    FRAPData newFrapData = null;
    newFrapStudy.setXmlFilename(null);
    ImageDataset imageDataset;
    imageDataset = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDatasetFromMultiFiles(inputFiles, clientTaskStatusSupport, isTimeSeries, timeInterval);
    newFrapData = 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() });
    newFrapStudy.setFrapData(newFrapData);
    return newFrapStudy;
}

Example 29 with ImageDataset

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

the class MicroscopyXmlReader method getFrapData.

/**
 * 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 FRAPData getFrapData(Element param, ClientTaskStatusSupport progressListener) throws XmlParseException {
    Element imageDatasetElement = param.getChild(MicroscopyXMLTags.ImageDatasetTag);
    ImageDataset imageDataset = null;
    if (imageDatasetElement != null) {
        imageDataset = getImageDataset(imageDatasetElement, progressListener);
    }
    @SuppressWarnings("unchecked") List<Element> roiList = param.getChildren(MicroscopyXMLTags.ROITag);
    ROI[] rois = null;
    int numROIs = roiList.size();
    if (numROIs > 0) {
        rois = new ROI[numROIs];
        Iterator<Element> roiIter = roiList.iterator();
        int index = 0;
        while (roiIter.hasNext()) {
            Element roiElement = roiIter.next();
            rois[index++] = getROI(roiElement);
        }
    }
    // reorder ROIs according to the order of FRAPData.VFRAP_ROI_ENUM
    ROI[] reorderedROIs = AnnotatedImageDataset.reorderROIs(rois);
    FRAPData frapData = new FRAPData(imageDataset, reorderedROIs);
    // After loading all the ROI rings, the progress should set to 100.
    if (progressListener != null) {
        progressListener.setProgress(100);
    }
    return frapData;
}

Example 30 with ImageDataset

use of cbit.vcell.VirtualMicroscopy.ImageDataset 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;
}