Examples with RegionImage cbit.vcell.geometry.RegionImage used on opensource projects

Example 36 with RegionImage

use of cbit.vcell.geometry.RegionImage in project vcell by virtualcell.

the class FRAPStudy method getCartesianMesh.

public CartesianMesh getCartesianMesh() throws Exception {
    CartesianMesh cartesianMesh = null;
    ImageDataset imgDataSet = getFrapData().getImageDataset();
    Extent extent = imgDataSet.getExtent();
    ISize isize = imgDataSet.getISize();
    Origin origin = new Origin(0, 0, 0);
    if (getBioModel() == null) {
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
    } else {
        RegionImage regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        if (regionImage == null) {
            getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().updateAll();
            regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        }
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    }
    return cartesianMesh;
}

Example 37 with RegionImage

use of cbit.vcell.geometry.RegionImage in project vcell by virtualcell.

the class FRAPStudy method getPSFFieldData.

public static FieldDataIdentifierSpec getPSFFieldData(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] psfFieldData = null;
    psfFieldData = new short[9];
    psfFieldData[4] = (short) 1;
    // create field data
    int NumTimePoints = 1;
    // 8 rois integrated into 1 image
    int NumChannels = 1;
    short[][][] pixData = new short[NumTimePoints][NumChannels][1];
    pixData[0][0] = psfFieldData;
    // get extental data id
    ExternalDataIdentifier newPsfExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.PSF_DATA_NAME).getExternalDataIdentifier();
    CartesianMesh cartesianMesh;
    try {
        Origin origin = new Origin(0, 0, 0);
        Extent ext = new Extent(1, 1, 1);
        ISize isize = new ISize(3, 3, 1);
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, ext, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], ext, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
        FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
        fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
        fdos.cartesianMesh = cartesianMesh;
        fdos.shortSpecData = pixData;
        fdos.specEDI = newPsfExtDataID;
        fdos.varNames = new String[] { "psfVar" };
        fdos.owner = LocalWorkspace.getDefaultOwner();
        fdos.times = new double[] { 0.0 };
        fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
        fdos.origin = origin;
        fdos.extent = ext;
        fdos.isize = isize;
        localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        FieldFunctionArguments psfFieldFunc = new FieldFunctionArguments(PSF_DATA_NAME, "psfVar", new Expression(0.0), VariableType.VOLUME);
        FieldDataIdentifierSpec fdis = new FieldDataIdentifierSpec(psfFieldFunc, newPsfExtDataID);
        return fdis;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return null;
    }
}

Example 38 with RegionImage

use of cbit.vcell.geometry.RegionImage in project vcell by virtualcell.

the class TopLevelWindowManager method addWorkspaceGeomSizeSelection.

private void addWorkspaceGeomSizeSelection(final Hashtable<String, Object> hash, Geometry sourceGeom) throws Exception {
    if (TopLevelWindowManager.this instanceof DocumentWindowManager) {
        Simulation[] simulations = null;
        SimulationContext[] simContexts = null;
        SimulationContext selectedSC = null;
        ArrayList<Object[]> allRows = new ArrayList<Object[]>();
        ArrayList<ISize> iSizes = new ArrayList<ISize>();
        if (this instanceof BioModelWindowManager) {
            BioModelWindowManager bmwm = ((BioModelWindowManager) this);
            // System.out.println(bmwm);
            if (bmwm.getDocumentEditor() instanceof cbit.vcell.client.desktop.biomodel.BioModelEditor) {
                cbit.vcell.client.desktop.biomodel.BioModelEditor bme = (cbit.vcell.client.desktop.biomodel.BioModelEditor) bmwm.getDocumentEditor();
                // System.out.println(bme);
                selectedSC = bme.getSelectedSimulationContext();
            // System.out.println(selectedSC);
            }
        }
        if (((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument() instanceof BioModel) {
            simContexts = ((BioModel) ((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument()).getSimulationContexts();
        } else if (((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument() instanceof MathModel) {
            simulations = ((MathModel) ((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument()).getSimulations();
        }
        String[] simColumnNames = null;
        if (simContexts != null) {
            simColumnNames = new String[] { "x", "y", "z", "appName", "simName" };
        } else {
            simColumnNames = new String[] { "x", "y", "z", "simName" };
        }
        ArrayList<Object[]> simRows = new ArrayList<Object[]>();
        ArrayList<CartesianMesh> meshes = new ArrayList<CartesianMesh>();
        for (int j = 0; j < (simContexts == null ? 1 : simContexts.length); j++) {
            Geometry geom = null;
            if (simContexts != null) {
                if (simContexts[j] != selectedSC) {
                    continue;
                }
                simulations = simContexts[j].getSimulations();
                geom = simContexts[j].getGeometry();
            } else {
                geom = ((MathModel) ((DocumentWindowManager) TopLevelWindowManager.this).getVCDocument()).getGeometry();
            }
            // ISize defaultSamplesize = geom.getGeometrySpec().getDefaultSampledImageSize();
            if (simulations != null && simulations.length > 0) {
                for (int i = 0; i < simulations.length; i++) {
                    Object[] row = new Object[simColumnNames.length];
                    // }
                    if (simulations[i].getMeshSpecification() != null && simulations[i].getMeshSpecification() != null) {
                        row = new Object[simColumnNames.length];
                        ISize samplingSize = simulations[i].getMeshSpecification().getSamplingSize();
                        row[0] = samplingSize.getX();
                        row[1] = samplingSize.getY();
                        row[2] = samplingSize.getZ();
                        row[3] = (simContexts != null ? simContexts[j].getName() : simulations[i].getName());
                        if (simContexts != null) {
                            row[4] = simulations[i].getName();
                        }
                        simRows.add(row);
                        VCImageUncompressed vcImageUnc = new VCImageUncompressed(null, new byte[samplingSize.getXYZ()], geom.getExtent(), samplingSize.getX(), samplingSize.getY(), samplingSize.getZ());
                        CartesianMesh simpleMesh = CartesianMesh.createSimpleCartesianMesh(geom.getOrigin(), geom.getExtent(), samplingSize, new RegionImage(vcImageUnc, geom.getDimension(), geom.getExtent(), geom.getOrigin(), RegionImage.NO_SMOOTHING));
                        meshes.add(simpleMesh);
                    }
                }
            }
        }
        for (int i = 0; i < simRows.size(); i++) {
            ISize iSize = meshes.get(i).getISize();
            iSizes.add(iSize);
            allRows.add(new Object[] { iSize.getX(), iSize.getY(), iSize.getZ(), "Simulation=" + (simColumnNames.length == 4 ? simRows.get(i)[3] : simRows.get(i)[3] + ":" + simRows.get(i)[4]) });
        }
        // if(allRows.size() > 0) {
        if (simRows.size() > 0) {
            Object[][] rowData = simRows.toArray(new Object[0][]);
            int[] selections = DialogUtils.showComponentOKCancelTableList(TopLevelWindowManager.this.getComponent(), "Select Simulation for Geom Size", simColumnNames, rowData, ListSelectionModel.SINGLE_SELECTION);
            if (selections != null && selections.length == 1) {
                // ImageSizeInfo imagesizeInfo = new ImageSizeInfo("internal",meshes.get(selections[0]).getISize(),1,new double[] {0},0);
                ImageSizeInfo imagesizeInfo = new ImageSizeInfo("internal", iSizes.get(selections[0]), 1, new double[] { 0 }, 0);
                hash.put(ClientRequestManager.NEW_IMAGE_SIZE_INFO, imagesizeInfo);
                VCImage image = null;
                if (sourceGeom.getGeometrySpec().getImage() == null) {
                    image = sourceGeom.getGeometrySpec().createSampledImage(iSizes.get(selections[0]));
                } else {
                    image = sourceGeom.getGeometrySpec().getImage();
                }
                // 
                ISize samplingSize = new ISize(image.getNumX(), image.getNumY(), image.getNumZ());
                VCImageUncompressed vcImageUnc = new VCImageUncompressed(null, new byte[samplingSize.getXYZ()], sourceGeom.getExtent(), samplingSize.getX(), samplingSize.getY(), samplingSize.getZ());
                CartesianMesh sourceMesh = CartesianMesh.createSimpleCartesianMesh(sourceGeom.getOrigin(), sourceGeom.getExtent(), samplingSize, new RegionImage(vcImageUnc, sourceGeom.getDimension(), sourceGeom.getExtent(), sourceGeom.getOrigin(), RegionImage.NO_SMOOTHING));
                hash.put("newMesh", meshes.get(selections[0]));
                hash.put("sourceMesh", sourceMesh);
            }
        }
    }
}