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

Example 6 with CoordinateIndex

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

the class MathTestingUtilities method resample1DSpatialSimple.

/**
 * Insert the method's description here.
 * Creation date: (10/27/2003 5:07:42 PM)
 * @return double[]
 * @param data double[]
 * @param sourceMesh cbit.vcell.solvers.CartesianMesh
 * @param targetMesh cbit.vcell.solvers.CartesianMesh
 */
public static double[] resample1DSpatialSimple(double[] sourceData, CartesianMesh sourceMesh, CartesianMesh refMesh) {
    if (sourceData.length != sourceMesh.getNumVolumeElements()) {
        throw new RuntimeException("must be volume data, data length doesn't match number of volume elements");
    }
    // for volume samples:
    // 
    // loop through volumeIndexes from refMesh
    // Coordinate refCoordinate = refMesh.getCoordinate(volumeIndex);
    // Coordinate fractionalIndex = sourceMesh.getFractionCoordinateIndex(Coordinate refCoordinate);
    // ....interpolate in z
    // start with integer portion of fractionIndex
    double[] resampledData = new double[refMesh.getSizeX()];
    for (int i = 0; i < resampledData.length; i++) {
        Coordinate refCoordinate = refMesh.getCoordinateFromVolumeIndex(i);
        Coordinate fractionalIndex = sourceMesh.getFractionalCoordinateIndex(refCoordinate);
        int ceil_x;
        int floor_x;
        if (fractionalIndex.getX() < 0) {
            floor_x = 0;
            ceil_x = 1;
        } else if (fractionalIndex.getX() > sourceMesh.getSizeX() - 1) {
            floor_x = sourceMesh.getSizeX() - 2;
            ceil_x = sourceMesh.getSizeX() - 1;
        } else {
            ceil_x = (int) Math.ceil(fractionalIndex.getX());
            floor_x = (int) Math.floor(fractionalIndex.getX());
        }
        double fract_x = fractionalIndex.getX() - floor_x;
        // ***** SHOULD Y,Z BE 0 OR 1 ???? *****
        CoordinateIndex coord_1 = new CoordinateIndex(floor_x, 0, 0);
        CoordinateIndex coord_2 = new CoordinateIndex(ceil_x, 0, 0);
        int volIndx1 = sourceMesh.getVolumeIndex(coord_1);
        int volIndx2 = sourceMesh.getVolumeIndex(coord_2);
        // Interpolate in X - final resampledSourceData value
        resampledData[i] = sourceData[volIndx1] + fract_x * (sourceData[volIndx2] - sourceData[volIndx1]);
    }
    return resampledData;
}

Example 7 with CoordinateIndex

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

the class MeshDisplayAdapter method determineOrder.

/**
 * Insert the method's description here.
 * Creation date: (9/2/00 4:44:31 PM)
 * @return boolean
 */
private int determineOrder(MembraneElement from, MembraneElement to, int normalAxis) {
    CoordinateIndex ciFrom = null;
    CoordinateIndex ciTo = null;
    if (from.getOutsideVolumeIndex() == to.getOutsideVolumeIndex()) {
        // Inside Corner
        ciFrom = mesh.getCoordinateIndexFromVolumeIndex(from.getInsideVolumeIndex());
        ciTo = mesh.getCoordinateIndexFromVolumeIndex(to.getInsideVolumeIndex());
    } else if (from.getInsideVolumeIndex() == to.getInsideVolumeIndex()) {
        // Outside Corner
        ciFrom = mesh.getCoordinateIndexFromVolumeIndex(from.getOutsideVolumeIndex());
        ciTo = mesh.getCoordinateIndexFromVolumeIndex(to.getOutsideVolumeIndex());
    } else {
        // Edge, can be either inside or outside, doesn't matter
        ciFrom = mesh.getCoordinateIndexFromVolumeIndex(from.getInsideVolumeIndex());
        ciTo = mesh.getCoordinateIndexFromVolumeIndex(to.getInsideVolumeIndex());
    }
    int[] deltaXYZ = new int[3];
    deltaXYZ[Coordinate.X_AXIS] = ciTo.x - ciFrom.x;
    deltaXYZ[Coordinate.Y_AXIS] = ciTo.y - ciFrom.y;
    deltaXYZ[Coordinate.Z_AXIS] = ciTo.z - ciFrom.z;
    int toMembranePlane = getParalellAxis(to, normalAxis);
    boolean bP0 = (deltaXYZ[toMembranePlane] < 0);
    int fromMembranePlane = getParalellAxis(from, normalAxis);
    boolean bPrepend = (deltaXYZ[fromMembranePlane] < 0);
    return (0x00 | (bPrepend ? ORDER_PREPEND : 0) | (bP0 ? ORDER_P0 : 0));
}

Example 8 with CoordinateIndex

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

the class SpatialSelectionVolume method getMeshIndexFromU.

private int getMeshIndexFromU(double u) {
    Coordinate wc = getSamplingWorldCoordinate(u);
    CoordinateIndex ci = getCoordinateIndexFromWC(wc);
    return getMesh().getVolumeIndex(ci);
}

Example 9 with CoordinateIndex

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

the class ROIMultiPaintManager method generateHighlightROIInfo.

private static HighlightROIInfo generateHighlightROIInfo(byte debugValue, BufferedImage[] roiArr, RegionImage regionImage, RegionAction regionAction, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    HighlightROIInfo highlightROIInfo = new HighlightROIInfo();
    // Create lookup map to speedup highlighting operation for large dataset
    RegionImage.RegionInfo[] selectedRegionMap = new RegionImage.RegionInfo[regionAction.getAllRegionInfos().length];
    Iterator<RegionImage.RegionInfo> selectedIter = regionAction.getSelectedRegionInfos().iterator();
    while (selectedIter.hasNext()) {
        RegionImage.RegionInfo nextRegion = selectedIter.next();
        selectedRegionMap[nextRegion.getRegionIndex()] = nextRegion;
    }
    byte[] shortEncodedRegionIndexes = regionImage.getShortEncodedRegionIndexImage();
    final int XSIZE = roiArr[0].getWidth();
    if (regionAction.getAction() == RegionAction.REGION_ACTION_HIGHLIGHT) {
        highlightROIInfo.highlightROI = createEmptyROI(new ISize(roiArr[0].getWidth(), roiArr[0].getHeight(), roiArr.length));
    }
    int allIndex = 0;
    final int ZMAX = roiArr.length - 1;
    final int XMAX = roiArr[0].getWidth() - 1;
    final int YMAX = roiArr[0].getHeight() - 1;
    for (int z = 0; z < roiArr.length; z++) {
        if (clientTaskStatusSupport != null && clientTaskStatusSupport.isInterrupted()) {
            return null;
        }
        int index = 0;
        byte[] zSlice = ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData();
        for (int y = 0; y < roiArr[0].getHeight(); y++) {
            for (int x = 0; x < XSIZE; x++) {
                int regionIndex = (shortEncodedRegionIndexes[allIndex] & 0x000000FF) | (shortEncodedRegionIndexes[allIndex + 1] & 0x000000FF) << 8;
                if (selectedRegionMap[regionIndex] != null) {
                    RegionInfo currentRegionInfo = selectedRegionMap[regionIndex];
                    if (regionAction.getAction() == RegionAction.REGION_ACTION_CHECKNEIGHBORSONLY) {
                        // Find neighbors
                        int[] neighbors = new int[6];
                        Arrays.fill(neighbors, -1);
                        if (z > 0) {
                            // top neighbor
                            neighbors[0] = 0x000000FF & ((DataBufferByte) roiArr[z - 1].getRaster().getDataBuffer()).getData()[index];
                        }
                        if (z < ZMAX) {
                            // bottom neighbor
                            neighbors[1] = 0x000000FF & ((DataBufferByte) roiArr[z + 1].getRaster().getDataBuffer()).getData()[index];
                        }
                        if (x > 0) {
                            // left neighbor
                            neighbors[2] = 0x000000FF & ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData()[index - 1];
                        }
                        if (x < XMAX) {
                            // right neighbor
                            neighbors[3] = 0x000000FF & ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData()[index + 1];
                        }
                        if (y > 0) {
                            // front neighbor
                            neighbors[4] = 0x000000FF & ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData()[index - XSIZE];
                        }
                        if (y < YMAX) {
                            // back neighbor
                            neighbors[5] = 0x000000FF & ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData()[index + XSIZE];
                        }
                        if (!highlightROIInfo.neighborsForRegionsMap.containsKey(currentRegionInfo)) {
                            highlightROIInfo.neighborsForRegionsMap.put(currentRegionInfo, new TreeSet<Integer>());
                        }
                        TreeSet<Integer> neighborTreeSet = highlightROIInfo.neighborsForRegionsMap.get(currentRegionInfo);
                        for (int i = 0; i < neighbors.length; i++) {
                            if (neighbors[i] != -1 && neighbors[i] != currentRegionInfo.getPixelValue()) {
                                neighborTreeSet.add(neighbors[i]);
                            }
                        }
                        if (!highlightROIInfo.coordIndexForRegionsMap.containsKey(currentRegionInfo)) {
                            highlightROIInfo.coordIndexForRegionsMap.put(currentRegionInfo, new CoordinateIndex(x, y, z));
                        }
                    } else if (regionAction.getAction() == RegionAction.REGION_ACTION_HIGHLIGHT) {
                        highlightROIInfo.highlightROI.getRoiImages()[z].getPixels()[index] = 1;
                    } else if (regionAction.getAction() == RegionAction.REGION_ACTION_MERGESELECTEDWITHNEIGHBORS) {
                        int numNeighbors = regionAction.getNeighborsForRegionMap().get(currentRegionInfo).size();
                        if (/*!regionAction.bLeaveMultiNeighborUnchanged || */
                        numNeighbors == 1) {
                            zSlice[index] = (byte) regionAction.getNeighborsForRegionMap().get(currentRegionInfo).first().intValue();
                        } else {
                            boolean hasBG = false;
                            Integer randomNeighbor = null;
                            Iterator<Integer> pixelValIter = regionAction.getNeighborsForRegionMap().get(currentRegionInfo).iterator();
                            while (pixelValIter.hasNext()) {
                                Integer pixelValue = pixelValIter.next();
                                if (pixelValue == 0) {
                                    hasBG = true;
                                    break;
                                } else {
                                    randomNeighbor = pixelValue;
                                }
                            }
                            if (hasBG) {
                                // merge with background
                                zSlice[index] = 0;
                            } else {
                                // merge with random
                                zSlice[index] = randomNeighbor.byteValue();
                            }
                        }
                    }
                }
                index++;
                allIndex += 2;
            }
        }
    }
    return highlightROIInfo;
}

Example 10 with CoordinateIndex

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

the class ROIMultiPaintManager method padCropDataset.

private void padCropDataset() {
    int xm = 0;
    int ym = 0;
    int zm = 0;
    int xp = 0;
    int yp = 0;
    int zp = 0;
    String result = null;
    do {
        try {
            result = DialogUtils.showInputDialog0(overlayEditorPanelJAI, "Enter the number of pixels to add or crop (negative number) at each border: (xlow,ylow,zlow,xhigh,yhigh,zhigh)", xm + "," + ym + "," + zm + "," + xp + "," + yp + "," + zp);
            if (result != null) {
                final String SEP = ",";
                result = result.trim();
                StringTokenizer st = new StringTokenizer(result, SEP);
                xm = Integer.parseInt(st.nextToken());
                ym = Integer.parseInt(st.nextToken());
                zm = Integer.parseInt(st.nextToken());
                xp = Integer.parseInt(st.nextToken());
                yp = Integer.parseInt(st.nextToken());
                zp = Integer.parseInt(st.nextToken());
                if (st.hasMoreElements() || result.endsWith(SEP)) {
                    throw new Exception("Some input was not parsed, check input.");
                }
                break;
            }
        } catch (UtilCancelException e) {
            throw UserCancelException.CANCEL_GENERIC;
        } catch (Exception e) {
            DialogUtils.showErrorDialog(overlayEditorPanelJAI, "Error parsing '" + result + "' Resetting to valid values.  Enter 6 comma separated integers.");
        }
    } while (true);
    final CoordinateIndex low = new CoordinateIndex(xm, ym, zm);
    final CoordinateIndex high = new CoordinateIndex(xp, yp, zp);
    final AsynchClientTask padTask = new AsynchClientTask("Changeing borders...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            resizeImpl(ResizeInfo.createPadCropResizeInfo(getImageDataSetChannel().getISize(), low, high), getClientTaskStatusSupport());
        }
    };
    final AsynchClientTask updatePanelTask = getUpdateDisplayAfterCropTask();
    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { padTask, updatePanelTask }, false, false, null, true);
}