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

Example 16 with ISize

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

the class ClientDocumentManager method saveAsNew.

/**
 * Insert the method's description here.
 * Creation date: (2/5/01 4:58:40 PM)
 */
public VCImage saveAsNew(VCImage vcImage, java.lang.String newName) throws DataAccessException {
    try {
        String vcImageXML = null;
        try {
            vcImageXML = XmlHelper.imageToXML(vcImage);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        String savedVCImageXML = sessionManager.getUserMetaDbServer().saveVCImageAs(new BigString(vcImageXML), newName).toString();
        VCImage savedVCImage = null;
        try {
            savedVCImage = XmlHelper.XMLToImage(savedVCImageXML);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        savedVCImage.refreshDependencies();
        KeyValue savedKey = savedVCImage.getVersion().getVersionKey();
        if (xmlHash.get(savedKey) == null) {
            xmlHash.put(savedKey, savedVCImageXML);
        }
        try {
            ISize size = new ISize(savedVCImage.getNumX(), savedVCImage.getNumY(), savedVCImage.getNumZ());
            GIFImage browseData = BrowseImage.makeBrowseGIFImage(savedVCImage);
            VCImageInfo savedVCImageInfo = new VCImageInfo(savedVCImage.getVersion(), size, savedVCImage.getExtent(), browseData, VCellSoftwareVersion.fromSystemProperty());
            imgInfoHash.put(savedKey, savedVCImageInfo);
            fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, savedVCImageInfo));
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
        return savedVCImage;
    } catch (RemoteProxyException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(VCellErrorMessages.FAIL_SAVE_MESSAGE + "\n\n" + e.getMessage());
    }
}

Example 17 with ISize

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

the class ClientDocumentManager method updateGeometryRelatedHashes.

private void updateGeometryRelatedHashes(Geometry savedGeometry) {
    if (savedGeometry == null || (savedGeometry.getVersion() != null && geoInfoHash.get(savedGeometry.getVersion().getVersionKey()) != null)) {
        return;
    }
    KeyValue imageRef = (savedGeometry.getGeometrySpec().getImage() != null) ? (savedGeometry.getGeometrySpec().getImage().getKey()) : (null);
    if (imageRef != null && imgInfoHash.get(imageRef) == null) {
        VCImage savedVCImage = savedGeometry.getGeometrySpec().getImage();
        ISize size = new ISize(savedVCImage.getNumX(), savedVCImage.getNumY(), savedVCImage.getNumZ());
        VCImageInfo savedVCImageInfo = new VCImageInfo(savedVCImage.getVersion(), size, savedVCImage.getExtent(), null, VCellSoftwareVersion.fromSystemProperty());
        imgInfoHash.put(savedVCImage.getVersion().getVersionKey(), savedVCImageInfo);
    }
    GeometryInfo savedGeometryInfo = new GeometryInfo(savedGeometry.getVersion(), savedGeometry.getDimension(), savedGeometry.getExtent(), savedGeometry.getOrigin(), imageRef, VCellSoftwareVersion.fromSystemProperty());
    geoInfoHash.put(savedGeometry.getVersion().getVersionKey(), savedGeometryInfo);
    fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, geoInfoHash.get(savedGeometry.getVersion().getVersionKey())));
}

Example 18 with ISize

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

the class GeometrySpec method calulateResetSamplingSize.

public static ISize calulateResetSamplingSize(int dim, Extent extent, long total) {
    long numX = 1;
    long numY = 1;
    long numZ = 1;
    switch(dim) {
        case 1:
            {
                numX = total;
                numY = 1;
                numZ = 1;
                break;
            }
        case 2:
            {
                // 
                // choose so that the aspect ratio is correct
                // 
                // so x * y = total    and x/y = extentX/extentY = xyRatio
                // 
                // thus  y = sqrt(total/xyRatio);
                // x = total/y;
                // 
                double aspectRatio = extent.getX() / extent.getY();
                numY = Math.max(3, Math.round(Math.sqrt(total / aspectRatio)));
                numX = Math.max(3, Math.round(total / numY));
                numZ = 1;
                break;
            }
        case 3:
            {
                // 
                // choose so that the aspect ratio is correct
                // 
                // x * y * z = total
                // z / x = extentZ/extentX = zxRatio
                // z / y = extentZ/extentY = zyRatio
                // 
                // thus  z = pow(total*zxRatio*zyRatio,1/3)
                // x = z/zxRatio;
                // y = z/zyRatio;
                // 
                double aspectRatioZX = extent.getZ() / extent.getX();
                double aspectRatioZY = extent.getZ() / extent.getY();
                numZ = Math.max(3, Math.round(Math.pow(total * aspectRatioZX * aspectRatioZY, 1.0 / 3.0)));
                numX = Math.max(3, Math.round(numZ / aspectRatioZX));
                numY = Math.max(3, Math.round(numZ / aspectRatioZY));
                break;
            }
    }
    ISize samplingSize = new ISize((int) numX, (int) numY, (int) numZ);
    return samplingSize;
}

Example 19 with ISize

use of org.vcell.util.ISize 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 20 with ISize

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

the class GeometrySurfaceDescription method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    if (evt.getSource() == this && evt.getPropertyName().equals("volumeSampleSize")) {
        ISize oldValue = (ISize) evt.getOldValue();
        ISize newValue = (ISize) evt.getNewValue();
        if (!oldValue.compareEqual(newValue)) {
            try {
                // nobody listens to this, updateAll() will propagate changes
                getRegionImage0().setDirty();
                getSurfaceCollection0().setDirty();
                fieldGeometricRegions.setDirty();
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (evt.getSource() == this && evt.getPropertyName().equals("filterCutoffFrequency")) {
        Double oldValue = (Double) evt.getOldValue();
        Double newValue = (Double) evt.getNewValue();
        if (!oldValue.equals(newValue)) {
            try {
                getSurfaceCollection0().setDirty();
                fieldGeometricRegions.setDirty();
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (evt.getSource() == this && evt.getPropertyName().equals(PROPERTY_NAME_GEOMETRIC_REGIONS)) {
        refreshSurfaceClasses();
    }
    if (evt.getSource() == getGeometry().getGeometrySpec() && (evt.getPropertyName().equals("extent") || evt.getPropertyName().equals("origin"))) {
        Matchable oldExtentOrOrigin = (Matchable) evt.getOldValue();
        Matchable newExtentOrOrigin = (Matchable) evt.getNewValue();
        if (!Compare.isEqual(oldExtentOrOrigin, newExtentOrOrigin)) {
            try {
                // nobody listens to this, updateAll() will propagate changes
                getRegionImage0().setDirty();
                getSurfaceCollection0().setDirty();
                fieldGeometricRegions.setDirty();
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (evt.getSource() instanceof AnalyticSubVolume && evt.getPropertyName().equals("expression")) {
        Expression oldExpression = (Expression) evt.getOldValue();
        Expression newExpression = (Expression) evt.getNewValue();
        if (!Compare.isEqual(oldExpression, newExpression)) {
            try {
                // nobody listens to this, updateAll() will propagate changes
                getRegionImage0().setDirty();
                getSurfaceCollection0().setDirty();
                fieldGeometricRegions.setDirty();
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (evt.getSource() instanceof CSGObject && evt.getPropertyName().equals(CSGObject.PROPERTY_NAME_ROOT)) {
        try {
            // nobody listens to this, updateAll() will propagate changes
            getRegionImage0().setDirty();
            getSurfaceCollection0().setDirty();
            fieldGeometricRegions.setDirty();
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
    }
    if (evt.getSource() instanceof SubVolume && evt.getPropertyName().equals("name")) {
        String oldName = (String) evt.getOldValue();
        String newName = (String) evt.getNewValue();
        if (!Compare.isEqual(oldName, newName)) {
            try {
                fieldGeometricRegions.setDirty();
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (evt.getSource() == getGeometry().getGeometrySpec() && evt.getPropertyName().equals("subVolumes")) {
        SubVolume[] oldValue = (SubVolume[]) evt.getOldValue();
        SubVolume[] newValue = (SubVolume[]) evt.getNewValue();
        // 
        for (int i = 0; oldValue != null && i < oldValue.length; i++) {
            oldValue[i].removePropertyChangeListener(this);
        }
        for (int i = 0; newValue != null && i < newValue.length; i++) {
            newValue[i].addPropertyChangeListener(this);
        }
        // 
        if (oldValue == null || newValue == null || !Compare.isEqualStrict(oldValue, newValue)) {
            try {
                // nobody listens to this, updateAll() will propagate changes
                getRegionImage0().setDirty();
                getSurfaceCollection0().setDirty();
                fieldGeometricRegions.setDirty();
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        } else if (fieldGeometricRegions.getCurrentValue() != null && oldValue != newValue) {
            // 
            for (int i = 0; i < newValue.length; i++) {
                SubVolume subVolume = newValue[i];
                for (int j = 0; j < fieldGeometricRegions.getCurrentValue().length; j++) {
                    if (fieldGeometricRegions.getCurrentValue()[j] instanceof VolumeGeometricRegion) {
                        VolumeGeometricRegion volumeRegion = (VolumeGeometricRegion) fieldGeometricRegions.getCurrentValue()[j];
                        // 
                        if (volumeRegion.getSubVolume().compareEqual(subVolume) && volumeRegion.getSubVolume() != subVolume) {
                            volumeRegion.setSubVolume(subVolume);
                        }
                    }
                }
            }
        }
    }
}