Examples with Origin org.vcell.util.Origin used on opensource projects

Example 6 with Origin

use of org.vcell.util.Origin 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 Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class Image method crop.

static Image crop(Image origImage, Rectangle rect) throws ImageException {
    Object inArray = origImage.getPixelArray();
    Object outArray = Array.newInstance(inArray.getClass().getComponentType(), rect.width * rect.height * origImage.getNumZ());
    for (int k = 0; k < origImage.getNumZ(); k++) {
        for (int j = 0; j < rect.height; j++) {
            for (int i = 0; i < rect.width; i++) {
                int inIndex = rect.x + i + (j + rect.y) * origImage.getNumX() + k * origImage.getNumX() * origImage.getNumY();
                int outIndex = i + j * rect.width + (k * rect.width * rect.height);
                Array.set(outArray, outIndex, Array.get(inArray, inIndex));
            }
        }
    }
    Extent croppedExtent = null;
    if (origImage.getExtent() != null) {
        croppedExtent = new Extent(origImage.getExtent().getX() * rect.width / origImage.getNumX(), origImage.getExtent().getY() * rect.height / origImage.getNumY(), origImage.getExtent().getZ());
    }
    Origin croppedOrigin = null;
    if (origImage.getOrigin() != null) {
        croppedOrigin = new Origin(calcOriginPosition(origImage.getOrigin().getX(), rect.x, origImage.getExtent().getX(), origImage.getNumX()), calcOriginPosition(origImage.getOrigin().getY(), rect.y, origImage.getExtent().getY(), origImage.getNumY()), // origImage.getOrigin().getY()+(rect.y*(origImage.getExtent().getY()/origImage.getNumY())),
        origImage.getExtent().getZ());
    }
    if (origImage instanceof UShortImage) {
        return new UShortImage((short[]) outArray, croppedOrigin, croppedExtent, rect.width, rect.height, origImage.getNumZ());
    } else if (origImage instanceof ByteImage) {
        return new ByteImage((byte[]) outArray, croppedOrigin, croppedExtent, rect.width, rect.height, origImage.getNumZ());
    } else if (origImage instanceof FloatImage) {
        return new FloatImage((float[]) outArray, croppedOrigin, croppedExtent, rect.width, rect.height, origImage.getNumZ());
    }
    throw new ImageException("Crop if Image type " + origImage.getClass().getName() + " not implemented.");
}

Example 8 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class DistanceMapGenerator method computeDistanceMaps.

public static SubvolumeSignedDistanceMap[] computeDistanceMaps(Geometry geometry, VCImage subvolumeHandleImage, boolean bCellCentered, boolean insideOnly) throws ImageException {
    double[] samplesX = new double[subvolumeHandleImage.getNumX()];
    double[] samplesY = new double[subvolumeHandleImage.getNumY()];
    double[] samplesZ = new double[subvolumeHandleImage.getNumZ()];
    ISize sampleSize = new ISize(subvolumeHandleImage.getNumX(), subvolumeHandleImage.getNumY(), subvolumeHandleImage.getNumZ());
    byte[] pixels = subvolumeHandleImage.getPixels();
    boolean[] ignoreMask = new boolean[sampleSize.getXYZ()];
    Origin origin = geometry.getOrigin();
    Extent extent = geometry.getExtent();
    RayCaster.sampleXYZCoordinates(sampleSize, origin, extent, samplesX, samplesY, samplesZ, bCellCentered);
    ArrayList<SubvolumeSignedDistanceMap> distanceMaps = new ArrayList<SubvolumeSignedDistanceMap>();
    int count = 0;
    for (SubVolume subVolume : geometry.getGeometrySpec().getSubVolumes()) {
        // 
        // find surfaces that bound the current SubVolume
        // 
        ArrayList<Surface> surfaces = new ArrayList<Surface>();
        for (GeometricRegion geometricRegion : geometry.getGeometrySurfaceDescription().getGeometricRegions()) {
            if (geometricRegion instanceof SurfaceGeometricRegion) {
                SurfaceGeometricRegion surfaceGeometricRegion = (SurfaceGeometricRegion) geometricRegion;
                for (GeometricRegion adjacentRegion : ((SurfaceGeometricRegion) geometricRegion).getAdjacentGeometricRegions()) {
                    if (adjacentRegion instanceof VolumeGeometricRegion && ((VolumeGeometricRegion) adjacentRegion).getSubVolume() == subVolume) {
                        surfaces.add(geometry.getGeometrySurfaceDescription().getSurfaceCollection().getSurface(surfaceGeometricRegion));
                    }
                }
            }
        }
        // find unsigned distances in a narrow band for surfaces that bound this SubVolume (expensive)
        // values outside the band are assumed to be initialized to MAX_NUMBER
        long t1 = System.currentTimeMillis();
        double[] distanceMap = localUnsignedDistanceMap(surfaces, samplesX, samplesY, samplesZ, 3);
        long t2 = System.currentTimeMillis();
        System.out.println("          Distance to triangle:   " + (int) ((t2 - t1) / 1000) + " sec.");
        // extend signed distance map using fast marching method from narrow band to all points.
        // will do it in 2 steps, positive growth first towards inside, then change the sign of the whole
        // distance map, then positive growth towards the exterior
        // this way, the interior distances will end negative and the exterior distances positive
        // 2 step growth saves memory and reduces the number of elements present at any given time in the binary
        // heap (binary heap manipulation is the most time consuming factor and it depends on the # of elements)
        Arrays.fill(ignoreMask, true);
        int subvolumeHandle = subVolume.getHandle();
        for (int i = 0; i < ignoreMask.length; i++) {
            if (pixels[i] == subvolumeHandle) {
                // inside
                ignoreMask[i] = false;
            } else {
                // outside
                if (distanceMap[i] < MAX_NUMBER) {
                    // make negative the part of narrow band which is outside
                    distanceMap[i] = -distanceMap[i];
                }
            }
        }
        // // step 1, we compute distances for the points "inside"
        // // the points outside are cold (we don't compute their distances this step)
        double deltaX = samplesX[1] - samplesX[0];
        double deltaY = samplesY[1] - samplesY[0];
        double deltaZ = samplesZ[1] - samplesZ[0];
        FastMarchingMethodHA fmm = new FastMarchingMethodHA(samplesX.length, samplesY.length, samplesZ.length, deltaX, deltaY, deltaZ, distanceMap, ignoreMask);
        fmm.march();
        if (!insideOnly) {
            // sign change of the half-completed distance map, the "interior" will become negative as it should be
            for (int i = 0; i < distanceMap.length; i++) {
                if (distanceMap[i] < MAX_NUMBER) {
                    distanceMap[i] = -distanceMap[i];
                }
            }
            // step 2, we compute distances for the points "outside"
            // no cold points (points we don't care about) this time, they are already frozen
            fmm = new FastMarchingMethodHA(samplesX.length, samplesY.length, samplesZ.length, deltaX, deltaY, deltaZ, distanceMap, null);
            fmm.march();
        } else {
            // sign change of the half-completed distance map, the "interior" will become negative as it should be
            for (int i = 0; i < distanceMap.length; i++) {
                if (distanceMap[i] < MAX_NUMBER) {
                    if (pixels[i] != subvolumeHandle) {
                        // need to filter out the part of the narrow band which is not inside
                        distanceMap[i] = MAX_NUMBER;
                    } else {
                        distanceMap[i] = -distanceMap[i];
                    }
                }
            }
        }
        // try {		// save some points in a VisIt compatible format
        // int xm = samplesX.length;
        // int ym = samplesY.length;
        // BufferedWriter out = new BufferedWriter(new FileWriter("c:\\TEMP\\2D_circle" + count + ".3D"));
        // out.write("x y z value\n");
        // 
        // for(int j=0; j<distanceMap.length; j++) {
        // int x = getX(j,xm,ym);
        // int y = getY(j,xm,ym);
        // int z = getZ(j,xm,ym);
        // if(distanceMap[j] < MAX_NUMBER) {
        // if((j%2 == 0 || j%3 == 0)  && (distanceMap[j] <= -2)) {
        // out.write(x + " " + y + " " + z + " " + (int)(distanceMap[j]*10) + "\n");
        // } else if((j%17 == 0 || j%23 == 0) && (distanceMap[j] <= 0.5) && (distanceMap[j] > -2)) {
        // out.write(x + " " + y + " " + z + " " + (int)(distanceMap[j]*10) + "\n");
        // } else if((j%31 == 0 || j%41 == 0) && (distanceMap[j] > 0.5)) {
        // out.write(x + " " + y + " " + z + " " + (int)(distanceMap[j]*10) + "\n");
        // }
        // }
        // if(distanceMap[j] < MAX_NUMBER) {
        // if(j%2 == 0) {
        // out.write(x + " " + y + " " + z + " " + (int)(distanceMap[j]*100) + "\n");
        // }
        // }
        // if(x==50 && y==50 && z==25) {		// on the surface
        // out.write(x + " " + y + " " + z + " " + (int)(distanceMap[j]*100) + "\n");
        // }
        // if(x==0 && y==0 && z==0) {
        // out.write(x + " " + y + " " + z + " " + 0 + "\n");
        // }
        // if(x==100 && y==100 && z==100) {
        // out.write(x + " " + y + " " + z + " " + 0 + "\n");
        // }
        // 
        // }
        // out.close();
        // } catch (IOException e) {
        // }
        SubvolumeSignedDistanceMap subvolumeSignedDistanceMap = new SubvolumeSignedDistanceMap(subVolume, samplesX, samplesY, samplesZ, distanceMap);
        distanceMaps.add(subvolumeSignedDistanceMap);
        count++;
    }
    return distanceMaps.toArray(new SubvolumeSignedDistanceMap[distanceMaps.size()]);
}

Example 9 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class RayCaster method sampleGeometry.

public static VCImage sampleGeometry(Geometry geometry, ISize sampleSize, boolean bCellCentered) throws ImageException, PropertyVetoException, GeometryException, ExpressionException {
    int numX = sampleSize.getX();
    int numY = sampleSize.getY();
    int numZ = sampleSize.getZ();
    Origin origin = geometry.getOrigin();
    Extent extent = geometry.getExtent();
    SurfaceCollection surfaceCollection = geometry.getGeometrySurfaceDescription().getSurfaceCollection();
    int surfaceCount = surfaceCollection.getSurfaceCount();
    // 
    if (surfaceCount == 0 && geometry.getGeometrySpec().getNumSubVolumes() == 1) {
        byte[] pixels = new byte[numX * numY * numZ];
        SubVolume subVolume = geometry.getGeometrySpec().getSubVolumes()[0];
        Arrays.fill(pixels, (byte) subVolume.getHandle());
        VCImageUncompressed vcImage = new VCImageUncompressed(null, pixels, extent, numX, numY, numZ);
        return vcImage;
    }
    VolumeSamples volumeSamples = volumeSampleSurface(surfaceCollection, sampleSize, origin, extent, bCellCentered);
    // for each mask bit, find union of masks which contain that bit ... iterate until no change.
    HashSet<Long> uniqueMasks = volumeSamples.getUniqueMasks();
    ArrayList<Long> consensusMaskArray = new ArrayList<Long>(uniqueMasks);
    // boolean bChanged = true;
    // while (bChanged){
    // bChanged = false;
    // for (int i=0;i<consensusMaskArray.size();i++){
    // for (int j=i+1;j<consensusMaskArray.size();j++){
    // if ((((long)consensusMaskArray.get(i)) & ((long)consensusMaskArray.get(j))) != 0L && (((long)consensusMaskArray.get(i))!=((long)consensusMaskArray.get(j)))){
    // long merged = consensusMaskArray.get(i) | consensusMaskArray.get(j);
    // if ((((merged<<1) & merged)==0L) &&  (((merged>>1) & merged)==0L)){
    // System.out.println("++++++++++++++++++++++++++++++++ merged "+Long.toBinaryString(consensusMaskArray.get(i))+" with "+Long.toBinaryString(consensusMaskArray.get(j))+" to get "+Long.toBinaryString(merged));
    // consensusMaskArray.set(i, merged);
    // consensusMaskArray.set(j, merged);
    // bChanged = true;
    // }
    // }
    // }
    // }
    // }
    /*
		for (Long l : consensusMaskArray) {
			System.out.println("++++++++++++++++++++++++++++++++ final mask "+Long.toBinaryString(l));
		}
		*/
    HashSet<Long> consensusSet = new HashSet<Long>(consensusMaskArray);
    byte[] pixels = new byte[numX * numY * numZ];
    setSurfaceMasks(geometry.getGeometrySurfaceDescription().getSurfaceCollection());
    for (long mask : consensusSet) {
        // for this consensus mask, find the subvolume that is associated
        SubVolume subvolume = getSubvolume(geometry, mask);
        if (subvolume == null) {
            throw new RuntimeException("could not reconcile volume samples with original geometry");
        }
        byte pixelValue = (byte) subvolume.getHandle();
        for (int i = 0; i < volumeSamples.getNumXYZ(); i++) {
            if ((volumeSamples.getMask(i) & mask) != 0) {
                pixels[i] = (byte) pixelValue;
            }
        }
    }
    VCImageUncompressed vcImage = new VCImageUncompressed(null, pixels, extent, numX, numY, numZ);
    return vcImage;
}

Example 10 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class RayCasterBitSet method createGeometryFromSTL.

public static Geometry createGeometryFromSTL(GeometryThumbnailImageFactory geometryThumbnailImageFactory, File stlFile, int numSamples) throws ImageException, PropertyVetoException, GeometryException, ExpressionException, IOException {
    SurfaceCollection surfaceCollection = StlReader.readStl(stlFile);
    Node[] nodes = surfaceCollection.getNodes();
    double minX = Double.MAX_VALUE;
    double maxX = -Double.MAX_VALUE;
    double minY = Double.MAX_VALUE;
    double maxY = -Double.MAX_VALUE;
    double minZ = Double.MAX_VALUE;
    double maxZ = -Double.MAX_VALUE;
    for (Node node : nodes) {
        double nx = node.getX();
        double ny = node.getY();
        double nz = node.getZ();
        minX = Math.min(minX, nx);
        maxX = Math.max(maxX, nx);
        minY = Math.min(minY, ny);
        maxY = Math.max(maxY, ny);
        minZ = Math.min(minZ, nz);
        maxZ = Math.max(maxZ, nz);
    }
    Extent extent = new Extent((maxX - minX) * 1.4, (maxY - minY) * 1.4, (maxZ - minZ) * 1.4);
    Origin origin = new Origin(minX - 0.2 * extent.getX(), minY - 0.2 * extent.getY(), minZ - 0.2 * extent.getZ());
    ISize sampleSize = GeometrySpec.calulateResetSamplingSize(3, extent, numSamples);
    Geometry geometry = createGeometry(geometryThumbnailImageFactory, surfaceCollection, origin, extent, sampleSize);
    return geometry;
}