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

Example 6 with ImageDataset

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

the class DefineROI_SummaryPanel method setLoadInfo.

public void setLoadInfo(final FRAPStudy frapStudy) {
    if (frapStudy != null && frapStudy.getFrapData() != null) {
        // enable components to change values
        BeanUtils.enableComponents(getInfoPanel(), true);
        BeanUtils.enableComponents(getIndexPanel(), true);
        // set info panel
        ImageDataset imgDataset = frapStudy.getFrapData().getImageDataset();
        imgXTextField.setText(NumberUtils.formatNumber(imgDataset.getExtent().getX(), 15));
        imgYTextField.setText(NumberUtils.formatNumber(imgDataset.getExtent().getY(), 15));
        FRAPData fData = frapStudy.getFrapData();
        ROI cellROI = fData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
        ROI bleachedROI = fData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
        ROI backgroundROI = fData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
        if (cellROI.getNonzeroPixelsCount() < 1) {
            cellROIUndefined.setSelected(true);
            cellROIDefined.setSelected(false);
        } else {
            cellROIUndefined.setSelected(false);
            cellROIDefined.setSelected(true);
        }
        if (bleachedROI.getNonzeroPixelsCount() < 1) {
            bleachROIUndefined.setSelected(true);
            bleachROIDefined.setSelected(false);
        } else {
            bleachROIUndefined.setSelected(false);
            bleachROIDefined.setSelected(true);
        }
        if (backgroundROI.getNonzeroPixelsCount() < 1) {
            bgROIUndefined.setSelected(true);
            bgROIDefined.setSelected(false);
        } else {
            bgROIUndefined.setSelected(false);
            bgROIDefined.setSelected(true);
        }
        // they are not editable
        imgXTextField.setEditable(false);
        imgYTextField.setEditable(false);
        cellROIDefined.setEnabled(false);
        cellROIUndefined.setEnabled(false);
        bleachROIDefined.setEnabled(false);
        bleachROIUndefined.setEnabled(false);
        bgROIDefined.setEnabled(false);
        bgROIUndefined.setEnabled(false);
        // set index panel
        startIndexCombo.removeAllItems();
        double[] timeSteps = frapStudy.getFrapData().getImageDataset().getImageTimeStamps();
        for (int i = 0; i < timeSteps.length; i++) {
            startIndexCombo.addItem(timeSteps[i] + "");
        }
        if (bleachROIDefined.isSelected()) {
            int index = (frapStudy.getStartingIndexForRecovery() == null ? FRAPDataAnalysis.calculateRecoveryIndex(frapStudy.getFrapData()) : frapStudy.getStartingIndexForRecovery());
            startIndexCombo.setSelectedIndex(index);
            startIndexAvaliableLabel.setText(START_IDX_AVAILABLE_STR);
        } else {
            startIndexCombo.setSelectedIndex(0);
            startIndexAvaliableLabel.setText(START_IDX_UNAVAILABLE_STR);
        }
    } else {
        imgXTextField.setText("");
        imgYTextField.setText("");
        cellROIDefined.setSelected(false);
        cellROIUndefined.setSelected(false);
        bleachROIDefined.setSelected(false);
        bleachROIUndefined.setSelected(false);
        bgROIDefined.setSelected(false);
        bgROIUndefined.setSelected(false);
        startIndexCombo.removeAllItems();
        startIndexCombo.addItem("     N/A     ");
        BeanUtils.enableComponents(getInfoPanel(), false);
        BeanUtils.enableComponents(getIndexPanel(), false);
    }
}

Example 7 with ImageDataset

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

the class LoadFRAPData_SummaryPanel method setLoadInfo.

public void setLoadInfo(final FRAPStudy frapStudy) {
    if (frapStudy != null && frapStudy.getFrapData() != null) {
        BeanUtils.enableComponents(getTimePanel(), true);
        BeanUtils.enableComponents(getTimePanel(), true);
        // title
        loadInfo.setText(loadSuccessInfo);
        // time
        sTimeCombo.removeAllItems();
        eTimeCombo.removeAllItems();
        double[] timeSteps = frapStudy.getFrapData().getImageDataset().getImageTimeStamps();
        for (int i = 0; i < timeSteps.length; i++) {
            sTimeCombo.addItem(timeSteps[i] + "");
            eTimeCombo.addItem(timeSteps[i] + "");
        }
        sTimeCombo.setSelectedIndex(0);
        eTimeCombo.setSelectedIndex(timeSteps.length - 1);
        totTimeLabel.setText((timeSteps[timeSteps.length - 1] - timeSteps[0]) + "");
        ImageDataset imgDataset = frapStudy.getFrapData().getImageDataset();
        int numXPixels = imgDataset.getAllImages()[0].getNumX();
        int numYPixels = imgDataset.getAllImages()[0].getNumY();
        numXPixelsValLabel.setText(numXPixels + "");
        numYPixelsValLabel.setText(numYPixels + "");
        double pixelSizeX = imgDataset.getExtent().getX() / numXPixels;
        double pixelSizeY = imgDataset.getExtent().getY() / numYPixels;
        imgPixelSizeX.setText(NumberUtils.formatNumber(pixelSizeX, 10));
        imgPixelSizeY.setText(NumberUtils.formatNumber(pixelSizeY, 10));
    } else {
        // title
        loadInfo.setText(loadFailedInfo);
        // time
        sTimeCombo.removeAllItems();
        sTimeCombo.addItem("     N/A     ");
        eTimeCombo.removeAllItems();
        eTimeCombo.addItem("     N/A     ");
        totTimeLabel.setText("");
        numXPixelsValLabel.setText("");
        numYPixelsValLabel.setText("");
        imgPixelSizeX.setText("");
        imgPixelSizeY.setText("");
        BeanUtils.enableComponents(getSizePanel(), false);
        BeanUtils.enableComponents(getTimePanel(), false);
    }
}

Example 8 with ImageDataset

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

the class ROIMultiPaintManager method initImageDataSet.

private void initImageDataSet(short[][] dataToSegmentChannels, ISize uncroppedISize) throws Exception {
    initImageDataSetChannels = new ImageDataset[(dataToSegmentChannels != null ? dataToSegmentChannels.length : 1)];
    for (int c = 0; c < initImageDataSetChannels.length; c++) {
        UShortImage[] zImageSet = new UShortImage[uncroppedISize.getZ()];
        for (int i = 0; i < zImageSet.length; i++) {
            short[] shortData = new short[uncroppedISize.getX() * uncroppedISize.getY()];
            if (dataToSegmentChannels != null) {
                System.arraycopy(dataToSegmentChannels[c], shortData.length * i, shortData, 0, shortData.length);
            }
            zImageSet[i] = new UShortImage(shortData, DEFAULT_ORIGIN, DEFAULT_EXTENT, uncroppedISize.getX(), uncroppedISize.getY(), 1);
        }
        initImageDataSetChannels[c] = new ImageDataset(zImageSet, new double[] { 0.0 }, uncroppedISize.getZ());
    }
}

Example 9 with ImageDataset

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

the class ExportRawTimeSeriesToVFrapOp method exportToVFRAP.

public void exportToVFRAP(File vfrapFile, ImageTimeSeries<UShortImage> imageTimeSeries, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    Xmlproducer vcellXMLProducer = new Xmlproducer(false);
    boolean bSaveCompressed = true;
    ImageDataset imageData = new ImageDataset(imageTimeSeries.getAllImages(), imageTimeSeries.getImageTimeStamps(), imageTimeSeries.getSizeZ());
    Element root = new Element(MicroscopyXMLTags.FRAPStudyTag);
    Element next = new Element(MicroscopyXMLTags.FRAPDataTag);
    root.addContent(next);
    Element imageDataXML = MicroscopyXmlproducer.getXML(imageData, vcellXMLProducer, clientTaskStatusSupport, bSaveCompressed);
    next.addContent(imageDataXML);
    java.io.FileOutputStream fileOutStream = new java.io.FileOutputStream(vfrapFile);
    BufferedOutputStream bufferedStream = new BufferedOutputStream(fileOutStream);
    // XmlUtil.writeXmlToStream(root, false, bufferedStream);
    XMLOutputter xmlOut = new XMLOutputter(Format.getPrettyFormat());
    xmlOut.getFormat().setTextMode(Format.TextMode.PRESERVE);
    xmlOut.output(root, bufferedStream);
    bufferedStream.flush();
    fileOutStream.flush();
    fileOutStream.close();
}

Example 10 with ImageDataset

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

the class ImportRawTimeSeriesFromExperimentImageOp method importRawTimeSeries.

public ImageTimeSeries<UShortImage> importRawTimeSeries(File expTimeSeriesFile) throws Exception {
    ClientTaskStatusSupport clientTaskStatusSupport = null;
    ImageDataset rawTimeData = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(expTimeSeriesFile.getAbsolutePath(), clientTaskStatusSupport);
    ImageTimeSeries<UShortImage> imageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, rawTimeData.getAllImages(), rawTimeData.getImageTimeStamps(), 1);
    return imageTimeSeries;
}