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

Example 6 with ROI

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

the class FRAPStudy method getROIDataGenerator.

public ROIDataGenerator getROIDataGenerator(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] roiFieldData = null;
    ROI[] rois = getFrapData().getRois();
    if (rois.length > 0) {
        Extent extent = rois[0].getRoiImages()[0].getExtent();
        ISize isize = rois[0].getISize();
        int numROIX = rois[0].getISize().getX();
        int numROIY = rois[0].getISize().getY();
        roiFieldData = new short[numROIX * numROIY];
        short regionCounter = 1;
        for (int roiIdx = FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.ordinal(); roiIdx < rois.length; roiIdx++) {
            short[] roiImg = rois[roiIdx].getPixelsXYZ();
            for (int pixelIdx = 0; pixelIdx < (numROIX * numROIY); pixelIdx++) {
                if (roiImg[pixelIdx] > 0) {
                    roiFieldData[pixelIdx] = regionCounter;
                }
            }
            regionCounter++;
        }
        // create field data
        int NumTimePoints = 1;
        // 8 rois integrated into 1 image
        int NumChannels = 1;
        short[][][] pixData = new short[NumTimePoints][NumChannels][];
        pixData[0][0] = roiFieldData;
        // get extental data id
        ExternalDataIdentifier newROIExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_SUMDATA_NAME).getExternalDataIdentifier();
        CartesianMesh cartesianMesh;
        try {
            cartesianMesh = getCartesianMesh();
            Origin origin = new Origin(0, 0, 0);
            FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = cartesianMesh;
            fdos.shortSpecData = pixData;
            fdos.specEDI = newROIExtDataID;
            fdos.varNames = new String[] { "roiSumDataVar" };
            fdos.owner = LocalWorkspace.getDefaultOwner();
            fdos.times = new double[] { 0.0 };
            fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
            fdos.origin = origin;
            fdos.extent = extent;
            fdos.isize = isize;
            localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return new ROIDataGenerator(ROI_EXTDATA_NAME, /*name*/
        new int[] { 0 }, /* volumePoints*/
        new int[0], /* membranePoints*/
        regionCounter, /*numRegions*/
        0, /*zSlice*/
        newROIExtDataID.getKey(), /* fieldDataKey, sample image*/
        new FieldFunctionArguments(FRAPStudy.ROI_SUMDATA_NAME, "roiSumDataVar", new Expression(0), VariableType.VOLUME), /*FieldFunctionArguments, sample image*/
        false);
    }
    return null;
}

Example 7 with ROI

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

the class NonGUIFRAPTest method checkExternalDataSameAsOriginal.

private static void checkExternalDataSameAsOriginal(FRAPStudy frapStudy, String testDirectoryPath) throws Exception {
    ImageDataset imageDataset = frapStudy.getFrapData().getImageDataset();
    ROI cellROI = frapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    ROI bleachROI = frapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    ROI backgroundROI = frapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
    // FileInputStream fis = new FileInputStream(getCanonicalFilename(testDirectoryPath, null));
    // BufferedInputStream bis = new BufferedInputStream(fis);
    // ZipInputStream zis = new ZipInputStream(bis);
    // ZipEntry zipEntry = null;
    // int timeIndex = 0;
    // while((zipEntry =zis.getNextEntry()) != null){
    // byte[] timePointData = new byte[(int)zipEntry.getSize()];
    // int offset = 0;
    // while((offset+= zis.read(timePointData,offset,timePointData.length-offset)) != timePointData.length){}
    // short[] shortPixels = imageDataset.getImage(0, 0, timeIndex).getPixels();
    // checkPixels(shortPixels, timePointData);
    // timeIndex++;
    // }
    // zis.close();
    ExternalDataFileContents extDataFileContents = readExternalDataContents(getCanonicalFilename(testDirectoryPath, null).getAbsolutePath(), getCanonicalFilename(testDirectoryPath, FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).getAbsolutePath(), getCanonicalFilename(testDirectoryPath, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getAbsolutePath(), getCanonicalFilename(testDirectoryPath, FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name()).getAbsolutePath());
    ImageDataset imageData = extDataFileContents.imageData;
    UShortImage[] allIDiskmages = imageData.getAllImages();
    UShortImage[] allIFrapmages = imageDataset.getAllImages();
    if (allIDiskmages.length != allIFrapmages.length) {
        throw new Exception("different number of times");
    }
    for (int i = 0; i < allIDiskmages.length; i++) {
        short[] allDiskPixels = allIDiskmages[i].getPixels();
        short[] allFrapPixels = allIFrapmages[i].getPixels();
        checkPixels(allDiskPixels, allFrapPixels);
    }
    checkPixels(extDataFileContents.cellROIData.getPixelsZ(0, 0), cellROI.getPixelsXYZ());
    checkPixels(extDataFileContents.bleachROIData.getPixelsZ(0, 0), bleachROI.getPixelsXYZ());
    checkPixels(extDataFileContents.backgroundROIData.getPixelsZ(0, 0), backgroundROI.getPixelsXYZ());
}

Example 8 with ROI

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

the class AnnotatedImageDataset method setCurrentlyDisplayedROI.

public void setCurrentlyDisplayedROI(ROI argCurrentlyDisplayedROI, boolean bSave) {
    ROI oldDisplayedROI = this.currentlyDisplayedROI;
    this.currentlyDisplayedROI = argCurrentlyDisplayedROI;
    if (bSave) {
        propertyChangeSupport.firePropertyChange(FRAPSingleWorkspace.PROPERTY_CHANGE_CURRENTLY_DISPLAYED_ROI_WITH_SAVE, oldDisplayedROI, currentlyDisplayedROI);
    } else {
        propertyChangeSupport.firePropertyChange(FRAPSingleWorkspace.PROPERTY_CHANGE_CURRENTLY_DISPLAYED_ROI_WITHOUT_SAVE, oldDisplayedROI, currentlyDisplayedROI);
    }
}

Example 9 with ROI

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

the class FRAPData method refreshDependentROIs.

protected void refreshDependentROIs() {
    UShortImage cellROI_2D = null;
    UShortImage bleachedROI_2D = null;
    UShortImage dilatedROI_2D_1 = null;
    UShortImage dilatedROI_2D_2 = null;
    UShortImage dilatedROI_2D_3 = null;
    UShortImage dilatedROI_2D_4 = null;
    UShortImage dilatedROI_2D_5 = null;
    UShortImage erodedROI_2D_0 = null;
    UShortImage erodedROI_2D_1 = null;
    UShortImage erodedROI_2D_2 = null;
    try {
        cellROI_2D = convertToUShortImage(binarize(getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).getRoiImages()[0]), getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).getRoiImages()[0].getOrigin(), getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).getRoiImages()[0].getExtent());
        bleachedROI_2D = convertToUShortImage(AndDescriptor.create(binarize(getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getRoiImages()[0]), binarize(cellROI_2D), null).createInstance(), getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getRoiImages()[0].getOrigin(), getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getRoiImages()[0].getExtent());
        // writeUShortFile(cellROI_2D, new File("D:\\developer\\eclipse\\workspace\\cellROI_2D.bmp"));
        // writeUShortFile(bleachedROI_2D, new File("D:\\developer\\eclipse\\workspace\\bleachedROI_2D.bmp"));
        dilatedROI_2D_1 = fastDilate(bleachedROI_2D, 4, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(8), cellROI_2D,false);
        dilatedROI_2D_2 = fastDilate(bleachedROI_2D, 10, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(16), cellROI_2D,false);
        dilatedROI_2D_3 = fastDilate(bleachedROI_2D, 18, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(24), cellROI_2D,false);
        dilatedROI_2D_4 = fastDilate(bleachedROI_2D, 28, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(32), cellROI_2D,false);
        dilatedROI_2D_5 = fastDilate(bleachedROI_2D, 40, cellROI_2D);
        // erodeDilate(bleachedROI_2D, createCircularBinaryKernel(40), cellROI_2D,false);
        erodedROI_2D_0 = new UShortImage(bleachedROI_2D);
        // The erode always causes problems if eroding without checking the bleached length and hight.
        // we have to check the min length of the bleahed area to make sure erode within the length.
        Rectangle bleachRect = bleachedROI_2D.getNonzeroBoundingBox();
        int minLen = Math.min(bleachRect.height, bleachRect.width);
        if ((minLen / 2.0) < 5) {
            erodedROI_2D_1 = erodeDilate(bleachedROI_2D, createCircularBinaryKernel(1), bleachedROI_2D, true);
            erodedROI_2D_2 = erodeDilate(bleachedROI_2D, createCircularBinaryKernel(2), bleachedROI_2D, true);
        } else {
            erodedROI_2D_1 = erodeDilate(bleachedROI_2D, createCircularBinaryKernel(2), bleachedROI_2D, true);
            erodedROI_2D_2 = erodeDilate(bleachedROI_2D, createCircularBinaryKernel(5), bleachedROI_2D, true);
        }
        UShortImage reverseErodeROI_2D_1 = new UShortImage(erodedROI_2D_1);
        reverseErodeROI_2D_1.reverse();
        erodedROI_2D_0.and(reverseErodeROI_2D_1);
        UShortImage reverseErodeROI_2D_2 = new UShortImage(erodedROI_2D_2);
        reverseErodeROI_2D_2.reverse();
        erodedROI_2D_1.and(reverseErodeROI_2D_2);
        UShortImage reverseDilateROI_2D_4 = new UShortImage(dilatedROI_2D_4);
        reverseDilateROI_2D_4.reverse();
        dilatedROI_2D_5.and(reverseDilateROI_2D_4);
        UShortImage reverseDilateROI_2D_3 = new UShortImage(dilatedROI_2D_3);
        // writeUShortFile(dilatedROI_2D_3, new File("D:\\developer\\eclipse\\workspace\\dilatedROI_2D_3.bmp"));
        reverseDilateROI_2D_3.reverse();
        // writeUShortFile(reverseDilateROI_2D_3, new File("D:\\developer\\eclipse\\workspace\\dilatedROI_2D_3_reverse.bmp"));
        // writeUShortFile(dilatedROI_2D_4, new File("D:\\developer\\eclipse\\workspace\\dilatedROI_2D_4.bmp"));
        dilatedROI_2D_4.and(reverseDilateROI_2D_3);
        // writeUShortFile(dilatedROI_2D_4, new File("D:\\developer\\eclipse\\workspace\\dilatedROI_2D_4_anded.bmp"));
        UShortImage reverseDilateROI_2D_2 = new UShortImage(dilatedROI_2D_2);
        reverseDilateROI_2D_2.reverse();
        dilatedROI_2D_3.and(reverseDilateROI_2D_2);
        UShortImage reverseDilateROI_2D_1 = new UShortImage(dilatedROI_2D_1);
        reverseDilateROI_2D_1.reverse();
        dilatedROI_2D_2.and(reverseDilateROI_2D_1);
        UShortImage reverseBleach_2D = new UShortImage(bleachedROI_2D);
        reverseBleach_2D.reverse();
        dilatedROI_2D_1.and(reverseBleach_2D);
    } catch (ImageException e) {
        e.printStackTrace(System.out);
    }
    ROI roiBleachedRing1_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name());
    if (roiBleachedRing1_2D == null) {
        roiBleachedRing1_2D = new ROI(erodedROI_2D_2, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name());
        addReplaceRoi(roiBleachedRing1_2D);
    } else {
        System.arraycopy(erodedROI_2D_2.getPixels(), 0, roiBleachedRing1_2D.getRoiImages()[0].getPixels(), 0, erodedROI_2D_2.getPixels().length);
    }
    ROI roiBleachedRing2_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name());
    if (roiBleachedRing2_2D == null) {
        roiBleachedRing2_2D = new ROI(erodedROI_2D_1, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name());
        addReplaceRoi(roiBleachedRing2_2D);
    } else {
        System.arraycopy(erodedROI_2D_1.getPixels(), 0, roiBleachedRing2_2D.getRoiImages()[0].getPixels(), 0, erodedROI_2D_1.getPixels().length);
    }
    ROI roiBleachedRing3_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name());
    if (roiBleachedRing3_2D == null) {
        roiBleachedRing3_2D = new ROI(erodedROI_2D_0, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name());
        addReplaceRoi(roiBleachedRing3_2D);
    } else {
        System.arraycopy(erodedROI_2D_0.getPixels(), 0, roiBleachedRing3_2D.getRoiImages()[0].getPixels(), 0, erodedROI_2D_0.getPixels().length);
    }
    ROI roiBleachedRing4_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name());
    if (roiBleachedRing4_2D == null) {
        roiBleachedRing4_2D = new ROI(dilatedROI_2D_1, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name());
        addReplaceRoi(roiBleachedRing4_2D);
    } else {
        System.arraycopy(dilatedROI_2D_1.getPixels(), 0, roiBleachedRing4_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_1.getPixels().length);
    }
    ROI roiBleachedRing5_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name());
    if (roiBleachedRing5_2D == null) {
        roiBleachedRing5_2D = new ROI(dilatedROI_2D_2, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name());
        addReplaceRoi(roiBleachedRing5_2D);
    } else {
        System.arraycopy(dilatedROI_2D_2.getPixels(), 0, roiBleachedRing5_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_2.getPixels().length);
    }
    ROI roiBleachedRing6_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name());
    if (roiBleachedRing6_2D == null) {
        roiBleachedRing6_2D = new ROI(dilatedROI_2D_3, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name());
        addReplaceRoi(roiBleachedRing6_2D);
    } else {
        System.arraycopy(dilatedROI_2D_3.getPixels(), 0, roiBleachedRing6_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_3.getPixels().length);
    }
    ROI roiBleachedRing7_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name());
    if (roiBleachedRing7_2D == null) {
        roiBleachedRing7_2D = new ROI(dilatedROI_2D_4, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name());
        addReplaceRoi(roiBleachedRing7_2D);
    } else {
        System.arraycopy(dilatedROI_2D_4.getPixels(), 0, roiBleachedRing7_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_4.getPixels().length);
    }
    ROI roiBleachedRing8_2D = getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name());
    if (roiBleachedRing8_2D == null) {
        roiBleachedRing8_2D = new ROI(dilatedROI_2D_5, FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name());
        addReplaceRoi(roiBleachedRing8_2D);
    } else {
        System.arraycopy(dilatedROI_2D_5.getPixels(), 0, roiBleachedRing8_2D.getRoiImages()[0].getPixels(), 0, dilatedROI_2D_5.getPixels().length);
    }
}

Example 10 with ROI

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

the class DefineROI_RoiForErrorPanel method refreshROIImage.

public void refreshROIImage() {
    FRAPData frapData = frapWorkspace.getWorkingFrapStudy().getFrapData();
    ROI[] allROIs = getAllROIs();
    Color[] allColors = getAllROIColors();
    ArrayList<ROI> plottedROIs = new ArrayList<ROI>();
    ArrayList<Color> plottedColors = new ArrayList<Color>();
    ArrayList<String> tempSelectedROIs = new ArrayList<String>();
    if (roi_bleachedCheckBox.isEnabled() && roi_bleachedCheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    }
    if (roi_bleached_ring1CheckBox.isEnabled() && roi_bleached_ring1CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING1]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING1]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name());
    }
    if (roi_bleached_ring2CheckBox.isEnabled() && roi_bleached_ring2CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING2]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING2]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name());
    }
    if (roi_bleached_ring3CheckBox.isEnabled() && roi_bleached_ring3CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING3]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING3]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name());
    }
    if (roi_bleached_ring4CheckBox.isEnabled() && roi_bleached_ring4CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING4]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING4]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name());
    }
    if (roi_bleached_ring5CheckBox.isEnabled() && roi_bleached_ring5CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING5]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING5]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name());
    }
    if (roi_bleached_ring6CheckBox.isEnabled() && roi_bleached_ring6CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING6]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING6]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name());
    }
    if (roi_bleached_ring7CheckBox.isEnabled() && roi_bleached_ring7CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING7]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING7]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name());
    }
    if (roi_bleached_ring8CheckBox.isEnabled() && roi_bleached_ring8CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING8]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING8]);
        tempSelectedROIs.add(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name());
    }
    // save selected ROI names
    refreshSelectedROIs(tempSelectedROIs);
    // show ROI image
    ROI[] plottedROIArray = new ROI[plottedROIs.size()];
    plottedROIArray = plottedROIs.toArray(plottedROIArray);
    Color[] plottedColorArray = new Color[plottedColors.size()];
    plottedColorArray = plottedColors.toArray(plottedColorArray);
    roiImagePanel.refreshROIImage(plottedROIArray, plottedColorArray, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()), Color.white);
}