Example 16 with SurfaceGeometricRegion
use of cbit.vcell.geometry.surface.SurfaceGeometricRegion in project vcell by virtualcell.
the class SBMLExporter method addGeometry.
private void addGeometry() throws SbmlException {
SpatialModelPlugin mplugin = (SpatialModelPlugin) sbmlModel.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
// Creates a geometry object via SpatialModelPlugin object.
org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = mplugin.createGeometry();
sbmlGeometry.setCoordinateSystem(GeometryKind.cartesian);
sbmlGeometry.setSpatialId("vcell");
Geometry vcGeometry = getSelectedSimContext().getGeometry();
Model vcModel = getSelectedSimContext().getModel();
//
// list of CoordinateComponents : 1 if geometry is 1-d, 2 if geometry is 2-d, 3 if geometry is 3-d
//
int dimension = vcGeometry.getDimension();
Extent vcExtent = vcGeometry.getExtent();
Origin vcOrigin = vcGeometry.getOrigin();
// add x coordinate component
CoordinateComponent xComp = sbmlGeometry.createCoordinateComponent();
xComp.setSpatialId(vcModel.getX().getName());
xComp.setType(CoordinateKind.cartesianX);
final UnitDefinition sbmlUnitDef_length = getOrCreateSBMLUnit(vcModel.getUnitSystem().getLengthUnit());
xComp.setUnits(sbmlUnitDef_length);
Boundary minX = new Boundary();
xComp.setBoundaryMinimum(minX);
minX.setSpatialId("Xmin");
minX.setValue(vcOrigin.getX());
Boundary maxX = new Boundary();
xComp.setBoundaryMaximum(maxX);
maxX.setSpatialId("Xmax");
maxX.setValue(vcOrigin.getX() + (vcExtent.getX()));
org.sbml.jsbml.Parameter pX = sbmlModel.createParameter();
pX.setId(vcModel.getX().getName());
pX.setValue(0.0);
pX.setConstant(false);
pX.setUnits(sbmlUnitDef_length);
SpatialParameterPlugin spPluginPx = (SpatialParameterPlugin) pX.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
SpatialSymbolReference spSymRefPx = new SpatialSymbolReference();
spPluginPx.setParamType(spSymRefPx);
spSymRefPx.setSpatialRef(xComp.getSpatialId());
// add y coordinate component
if (dimension == 2 || dimension == 3) {
CoordinateComponent yComp = sbmlGeometry.createCoordinateComponent();
yComp.setSpatialId(vcModel.getY().getName());
yComp.setType(CoordinateKind.cartesianY);
yComp.setUnits(sbmlUnitDef_length);
Boundary minY = new Boundary();
yComp.setBoundaryMinimum(minY);
minY.setSpatialId("Ymin");
minY.setValue(vcOrigin.getY());
Boundary maxY = new Boundary();
yComp.setBoundaryMaximum(maxY);
maxY.setSpatialId("Ymax");
maxY.setValue(vcOrigin.getY() + (vcExtent.getY()));
org.sbml.jsbml.Parameter pY = sbmlModel.createParameter();
pY.setId(vcModel.getY().getName());
pY.setValue(0.0);
pY.setConstant(false);
pY.setUnits(sbmlUnitDef_length);
SpatialParameterPlugin spPluginPy = (SpatialParameterPlugin) pY.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
SpatialSymbolReference spSymRefPy = new SpatialSymbolReference();
spPluginPy.setParamType(spSymRefPy);
spSymRefPy.setSpatialRef(yComp.getSpatialId());
}
// add z coordinate component
if (dimension == 3) {
CoordinateComponent zComp = sbmlGeometry.createCoordinateComponent();
zComp.setSpatialId(vcModel.getZ().getName());
zComp.setType(CoordinateKind.cartesianZ);
zComp.setUnits(sbmlUnitDef_length);
Boundary minZ = new Boundary();
zComp.setBoundaryMinimum(minZ);
minZ.setSpatialId("Zmin");
minZ.setValue(vcOrigin.getZ());
Boundary maxZ = new Boundary();
zComp.setBoundaryMaximum(maxZ);
maxZ.setSpatialId("Zmax");
maxZ.setValue(vcOrigin.getZ() + (vcExtent.getZ()));
org.sbml.jsbml.Parameter pZ = sbmlModel.createParameter();
pZ.setId(vcModel.getZ().getName());
pZ.setValue(0.0);
pZ.setConstant(false);
pZ.setUnits(sbmlUnitDef_length);
SpatialParameterPlugin spPluginPz = (SpatialParameterPlugin) pZ.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
SpatialSymbolReference spSymRefPz = new SpatialSymbolReference();
spPluginPz.setParamType(spSymRefPz);
spSymRefPz.setSpatialRef(zComp.getSpatialId());
}
//
// list of compartmentMappings : VC structureMappings
//
GeometryContext vcGeoContext = getSelectedSimContext().getGeometryContext();
StructureMapping[] vcStrucMappings = vcGeoContext.getStructureMappings();
for (int i = 0; i < vcStrucMappings.length; i++) {
StructureMapping vcStructMapping = vcStrucMappings[i];
String structName = vcStructMapping.getStructure().getName();
Compartment comp = sbmlModel.getCompartment(TokenMangler.mangleToSName(structName));
SpatialCompartmentPlugin cplugin = (SpatialCompartmentPlugin) comp.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
GeometryClass gc = vcStructMapping.getGeometryClass();
if (!goodPointer(gc, GeometryClass.class, structName)) {
continue;
}
CompartmentMapping compMapping = new CompartmentMapping();
cplugin.setCompartmentMapping(compMapping);
String geomClassName = gc.getName();
String id = TokenMangler.mangleToSName(geomClassName + structName);
compMapping.setSpatialId(id);
compMapping.setDomainType(TokenMangler.mangleToSName(DOMAIN_TYPE_PREFIX + geomClassName));
try {
StructureMappingParameter usp = vcStructMapping.getUnitSizeParameter();
Expression e = usp.getExpression();
if (goodPointer(e, Expression.class, id)) {
compMapping.setUnitSize(e.evaluateConstant());
}
} catch (ExpressionException e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to create compartment mapping for structureMapping '" + compMapping.getId() + "' : " + e.getMessage());
}
}
//
// list of domain types : subvolumes and surface classes from VC
//
boolean bAnyAnalyticSubvolumes = false;
boolean bAnyImageSubvolumes = false;
boolean bAnyCSGSubvolumes = false;
GeometryClass[] vcGeomClasses = vcGeometry.getGeometryClasses();
int numSubVols = 0;
for (int i = 0; i < vcGeomClasses.length; i++) {
DomainType domainType = sbmlGeometry.createDomainType();
domainType.setSpatialId(DOMAIN_TYPE_PREFIX + vcGeomClasses[i].getName());
if (vcGeomClasses[i] instanceof SubVolume) {
if (((SubVolume) vcGeomClasses[i]) instanceof AnalyticSubVolume) {
bAnyAnalyticSubvolumes = true;
} else if (((SubVolume) vcGeomClasses[i]) instanceof ImageSubVolume) {
bAnyImageSubvolumes = true;
} else if (((SubVolume) vcGeomClasses[i]) instanceof CSGObject) {
bAnyCSGSubvolumes = true;
}
domainType.setSpatialDimensions(3);
numSubVols++;
} else if (vcGeomClasses[i] instanceof SurfaceClass) {
domainType.setSpatialDimensions(2);
}
}
//
// list of domains, adjacent domains : from VC geometricRegions
//
GeometrySurfaceDescription vcGSD = vcGeometry.getGeometrySurfaceDescription();
if (vcGSD.getRegionImage() == null) {
try {
vcGSD.updateAll();
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to generate region images for geometry");
}
}
GeometricRegion[] vcGeometricRegions = vcGSD.getGeometricRegions();
ISize sampleSize = vcGSD.getVolumeSampleSize();
int numX = sampleSize.getX();
int numY = sampleSize.getY();
int numZ = sampleSize.getZ();
double ox = vcOrigin.getX();
double oy = vcOrigin.getY();
double oz = vcOrigin.getZ();
RegionInfo[] regionInfos = vcGSD.getRegionImage().getRegionInfos();
for (int i = 0; i < vcGeometricRegions.length; i++) {
// domains
Domain domain = sbmlGeometry.createDomain();
domain.setSpatialId(vcGeometricRegions[i].getName());
if (vcGeometricRegions[i] instanceof VolumeGeometricRegion) {
domain.setDomainType(DOMAIN_TYPE_PREFIX + ((VolumeGeometricRegion) vcGeometricRegions[i]).getSubVolume().getName());
//
// get a list of interior points ... should probably use the distance map to find a point
// furthest inside (or several points associated with the morphological skeleton).
//
InteriorPoint interiorPt = domain.createInteriorPoint();
int regionID = ((VolumeGeometricRegion) vcGeometricRegions[i]).getRegionID();
boolean bFound = false;
int regInfoIndx = 0;
for (int j = 0; j < regionInfos.length; j++) {
regInfoIndx = j;
if (regionInfos[j].getRegionIndex() == regionID) {
int volIndx = 0;
for (int z = 0; z < numZ && !bFound; z++) {
for (int y = 0; y < numY && !bFound; y++) {
for (int x = 0; x < numX && !bFound; x++) {
if (regionInfos[j].isIndexInRegion(volIndx)) {
bFound = true;
double unit_z = (numZ > 1) ? ((double) z) / (numZ - 1) : 0.5;
double coordZ = oz + vcExtent.getZ() * unit_z;
double unit_y = (numY > 1) ? ((double) y) / (numY - 1) : 0.5;
double coordY = oy + vcExtent.getY() * unit_y;
double unit_x = (numX > 1) ? ((double) x) / (numX - 1) : 0.5;
double coordX = ox + vcExtent.getX() * unit_x;
interiorPt.setCoord1(coordX);
interiorPt.setCoord2(coordY);
interiorPt.setCoord3(coordZ);
}
volIndx++;
}
// end - for x
}
// end - for y
}
// end - for z
}
// end if
}
// end for regionInfos
if (!bFound) {
throw new RuntimeException("Unable to find interior point for region '" + regionInfos[regInfoIndx].toString());
}
} else if (vcGeometricRegions[i] instanceof SurfaceGeometricRegion) {
SurfaceGeometricRegion vcSurfaceGeomReg = (SurfaceGeometricRegion) vcGeometricRegions[i];
GeometricRegion geomRegion0 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[0];
GeometricRegion geomRegion1 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[1];
SurfaceClass surfaceClass = vcGSD.getSurfaceClass(((VolumeGeometricRegion) geomRegion0).getSubVolume(), ((VolumeGeometricRegion) geomRegion1).getSubVolume());
domain.setDomainType(DOMAIN_TYPE_PREFIX + surfaceClass.getName());
// adjacent domains : 2 adjacent domain objects for each surfaceClass in VC.
// adjacent domain 1
GeometricRegion adjGeomRegion0 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[0];
GeometricRegion adjGeomRegion1 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[1];
AdjacentDomains adjDomain = new AdjacentDomains();
adjDomain.setSpatialId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + adjGeomRegion0.getName()));
adjDomain.setDomain1(vcSurfaceGeomReg.getName());
adjDomain.setDomain2(adjGeomRegion0.getName());
sbmlGeometry.addAdjacentDomain(adjDomain);
// adj domain 2
adjDomain = new AdjacentDomains();
adjDomain.setSpatialId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + adjGeomRegion1.getName()));
adjDomain.setDomain1(vcSurfaceGeomReg.getName());
adjDomain.setDomain2(adjGeomRegion1.getName());
sbmlGeometry.addAdjacentDomain(adjDomain);
}
}
//
if (bAnyAnalyticSubvolumes && !bAnyImageSubvolumes && !bAnyCSGSubvolumes) {
AnalyticGeometry sbmlAnalyticGeomDefinition = sbmlGeometry.createAnalyticGeometry();
sbmlAnalyticGeomDefinition.setSpatialId(TokenMangler.mangleToSName("Analytic_" + vcGeometry.getName()));
sbmlAnalyticGeomDefinition.setIsActive(true);
for (int i = 0; i < vcGeomClasses.length; i++) {
if (vcGeomClasses[i] instanceof AnalyticSubVolume) {
AnalyticVolume analyticVol = sbmlAnalyticGeomDefinition.createAnalyticVolume();
analyticVol.setSpatialId(vcGeomClasses[i].getName());
analyticVol.setDomainType(DOMAIN_TYPE_PREFIX + vcGeomClasses[i].getName());
analyticVol.setFunctionType(FunctionKind.layered);
analyticVol.setOrdinal(numSubVols - (i + 1));
Expression expr = ((AnalyticSubVolume) vcGeomClasses[i]).getExpression();
try {
String mathMLStr = ExpressionMathMLPrinter.getMathML(expr, true, MathType.BOOLEAN);
ASTNode mathMLNode = ASTNode.readMathMLFromString(mathMLStr);
analyticVol.setMath(mathMLNode);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Error converting VC subvolume expression to mathML" + e.getMessage());
}
}
}
}
//
if (!bAnyAnalyticSubvolumes && !bAnyImageSubvolumes && bAnyCSGSubvolumes) {
CSGeometry sbmlCSGeomDefinition = new CSGeometry();
sbmlGeometry.addGeometryDefinition(sbmlCSGeomDefinition);
sbmlCSGeomDefinition.setSpatialId(TokenMangler.mangleToSName("CSG_" + vcGeometry.getName()));
for (int i = 0; i < vcGeomClasses.length; i++) {
if (vcGeomClasses[i] instanceof CSGObject) {
CSGObject vcellCSGObject = (CSGObject) vcGeomClasses[i];
org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = new org.sbml.jsbml.ext.spatial.CSGObject();
sbmlCSGeomDefinition.addCSGObject(sbmlCSGObject);
sbmlCSGObject.setSpatialId(vcellCSGObject.getName());
sbmlCSGObject.setDomainType(DOMAIN_TYPE_PREFIX + vcellCSGObject.getName());
// the ordinal should the the least for the default/background subVolume
sbmlCSGObject.setOrdinal(numSubVols - (i + 1));
org.sbml.jsbml.ext.spatial.CSGNode sbmlcsgNode = getSBMLCSGNode(vcellCSGObject.getRoot());
sbmlCSGObject.setCSGNode(sbmlcsgNode);
}
}
}
//
// add "Segmented" and "DistanceMap" SampledField Geometries
//
final boolean bVCGeometryIsImage = bAnyImageSubvolumes && !bAnyAnalyticSubvolumes && !bAnyCSGSubvolumes;
// 55if (bAnyAnalyticSubvolumes || bAnyImageSubvolumes || bAnyCSGSubvolumes){
if (bVCGeometryIsImage) {
//
// add "Segmented" SampledFieldGeometry
//
SampledFieldGeometry segmentedImageSampledFieldGeometry = sbmlGeometry.createSampledFieldGeometry();
segmentedImageSampledFieldGeometry.setSpatialId(TokenMangler.mangleToSName("SegmentedImage_" + vcGeometry.getName()));
segmentedImageSampledFieldGeometry.setIsActive(true);
// 55boolean bVCGeometryIsImage = bAnyImageSubvolumes && !bAnyAnalyticSubvolumes && !bAnyCSGSubvolumes;
Geometry vcImageGeometry = null;
{
if (bVCGeometryIsImage) {
// make a resampled image;
if (dimension == 3) {
try {
ISize imageSize = vcGeometry.getGeometrySpec().getDefaultSampledImageSize();
vcGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
vcImageGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), vcGeometry, imageSize);
} catch (Throwable e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to convert the original analytic or constructed solid geometry to image-based geometry : " + e.getMessage());
}
} else {
try {
vcGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, false);
GeometrySpec origGeometrySpec = vcGeometry.getGeometrySpec();
VCImage newVCImage = origGeometrySpec.getSampledImage().getCurrentValue();
//
// construct the new geometry with the sampled VCImage.
//
vcImageGeometry = new Geometry(vcGeometry.getName() + "_asImage", newVCImage);
vcImageGeometry.getGeometrySpec().setExtent(vcGeometry.getExtent());
vcImageGeometry.getGeometrySpec().setOrigin(vcGeometry.getOrigin());
vcImageGeometry.setDescription(vcGeometry.getDescription());
vcImageGeometry.getGeometrySurfaceDescription().setFilterCutoffFrequency(vcGeometry.getGeometrySurfaceDescription().getFilterCutoffFrequency());
vcImageGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to convert the original analytic or constructed solid geometry to image-based geometry : " + e.getMessage());
}
}
GeometryClass[] vcImageGeomClasses = vcImageGeometry.getGeometryClasses();
for (int j = 0; j < vcImageGeomClasses.length; j++) {
if (vcImageGeomClasses[j] instanceof ImageSubVolume) {
SampledVolume sampledVol = segmentedImageSampledFieldGeometry.createSampledVolume();
sampledVol.setSpatialId(vcGeomClasses[j].getName());
sampledVol.setDomainType(DOMAIN_TYPE_PREFIX + vcGeomClasses[j].getName());
sampledVol.setSampledValue(((ImageSubVolume) vcImageGeomClasses[j]).getPixelValue());
}
}
// add sampledField to sampledFieldGeometry
SampledField segmentedImageSampledField = sbmlGeometry.createSampledField();
VCImage vcImage = vcImageGeometry.getGeometrySpec().getImage();
segmentedImageSampledField.setSpatialId("SegmentedImageSampledField");
segmentedImageSampledField.setNumSamples1(vcImage.getNumX());
segmentedImageSampledField.setNumSamples2(vcImage.getNumY());
segmentedImageSampledField.setNumSamples3(vcImage.getNumZ());
segmentedImageSampledField.setInterpolationType(InterpolationKind.nearestneighbor);
segmentedImageSampledField.setCompression(CompressionKind.uncompressed);
segmentedImageSampledField.setDataType(DataKind.UINT8);
segmentedImageSampledFieldGeometry.setSampledField(segmentedImageSampledField.getId());
try {
byte[] vcImagePixelsBytes = vcImage.getPixels();
// imageData.setCompression("");
StringBuffer sb = new StringBuffer();
for (int i = 0; i < vcImagePixelsBytes.length; i++) {
int uint8_sample = ((int) vcImagePixelsBytes[i]) & 0xff;
sb.append(uint8_sample + " ");
}
segmentedImageSampledField.setSamplesLength(vcImage.getNumXYZ());
segmentedImageSampledField.setSamples(sb.toString().trim());
} catch (ImageException e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to export image from VCell to SBML : " + e.getMessage());
}
}
}
/*
//
// add "DistanceMap" SampledFieldGeometry if there are exactly two subvolumes (else need more fields) and geometry is 3d.
//
if (numSubVols==2 && dimension == 3){
SignedDistanceMap[] distanceMaps = null;
try {
distanceMaps = DistanceMapGenerator.computeDistanceMaps(vcImageGeometry, vcImageGeometry.getGeometrySpec().getImage(), false, false);
} catch (ImageException e) {
e.printStackTrace(System.out);
System.err.println("Unable to export distance map sampled field from VCell to SBML : " + e.getMessage());
// throw new RuntimeException("Unable to export distance map sampled field from VCell to SBML : " + e.getMessage());
// don't want to throw an exception and stop export because distance map geometry couldn't be exported.
// just 'return' from method (since this is the last thing that is being done in this method).
return;
}
//
// the two distanceMaps should be redundant (one is negation of the other) ... so choose first one for field.
//
double[] signedDistances = distanceMaps[0].getSignedDistances();
SampledFieldGeometry distanceMapSampledFieldGeometry = sbmlGeometry.createSampledFieldGeometry();
distanceMapSampledFieldGeometry.setSpatialId(TokenMangler.mangleToSName("DistanceMap_"+vcGeometry.getName()));
SampledField distanceMapSampledField = distanceMapSampledFieldGeometry.createSampledField();
distanceMapSampledField.setSpatialId("DistanceMapSampledField");
distanceMapSampledField.setNumSamples1(distanceMaps[0].getSamplesX().length);
distanceMapSampledField.setNumSamples2(distanceMaps[0].getSamplesY().length);
distanceMapSampledField.setNumSamples3(distanceMaps[0].getSamplesZ().length);
distanceMapSampledField.setDataType("real");
System.err.println("do we need distanceMapSampleField.setDataType()?");
distanceMapSampledField.setInterpolationType("linear");
ImageData distanceMapImageData = distanceMapSampledField.createImageData();
distanceMapImageData.setDataType("int16");
System.err.println("should be:\n distanceMapImageData.setDataType(\"float32\")");
// distanceMapImageData.setCompression("");
double maxAbsValue = 0;
for (int i = 0; i < signedDistances.length; i++) {
maxAbsValue = Math.max(maxAbsValue,Math.abs(signedDistances[i]));
}
if (maxAbsValue==0.0){
throw new RuntimeException("computed distance map all zeros");
}
double scale = (Short.MAX_VALUE-1)/maxAbsValue;
int[] scaledIntegerDistanceMap = new int[signedDistances.length];
for (int i = 0; i < signedDistances.length; i++) {
scaledIntegerDistanceMap[i] = (int)(scale * signedDistances[i]);
}
distanceMapImageData.setSamples(scaledIntegerDistanceMap, signedDistances.length);
System.err.println("should be:\n distanceMapImageData.setSamples((float[])signedDistances,signedDistances.length)");
SampledVolume sampledVol = distanceMapSampledFieldGeometry.createSampledVolume();
sampledVol.setSpatialId(distanceMaps[0].getInsideSubvolumeName());
sampledVol.setDomainType(DOMAIN_TYPE_PREFIX+distanceMaps[0].getInsideSubvolumeName());
sampledVol.setSampledValue(255);
sampledVol = distanceMapSampledFieldGeometry.createSampledVolume();
sampledVol.setSpatialId(distanceMaps[1].getInsideSubvolumeName());
sampledVol.setDomainType(DOMAIN_TYPE_PREFIX+distanceMaps[1].getInsideSubvolumeName());
sampledVol.setSampledValue(1);
}
*/
}
//
// add "SurfaceMesh" ParametricGeometry
//
// if (bAnyAnalyticSubvolumes || bAnyImageSubvolumes || bAnyCSGSubvolumes){
// ParametricGeometry sbmlParametricGeomDefinition = sbmlGeometry.createParametricGeometry();
// sbmlParametricGeomDefinition.setSpatialId(TokenMangler.mangleToSName("SurfaceMesh_"+vcGeometry.getName()));
// xxxx
// }
}
Also used :
Origin(org.vcell.util.Origin)
CompartmentMapping(org.sbml.jsbml.ext.spatial.CompartmentMapping)
Compartment(org.sbml.jsbml.Compartment)
SpatialParameterPlugin(org.sbml.jsbml.ext.spatial.SpatialParameterPlugin)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
AnalyticGeometry(org.sbml.jsbml.ext.spatial.AnalyticGeometry)
ExpressionException(cbit.vcell.parser.ExpressionException)
Boundary(org.sbml.jsbml.ext.spatial.Boundary)
GeometrySpec(cbit.vcell.geometry.GeometrySpec)
DomainType(org.sbml.jsbml.ext.spatial.DomainType)
SampledVolume(org.sbml.jsbml.ext.spatial.SampledVolume)
SubVolume(cbit.vcell.geometry.SubVolume)
ImageSubVolume(cbit.vcell.geometry.ImageSubVolume)
AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume)
GeometryContext(cbit.vcell.mapping.GeometryContext)
SpatialCompartmentPlugin(org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin)
CoordinateComponent(org.sbml.jsbml.ext.spatial.CoordinateComponent)
SimulationContext(cbit.vcell.mapping.SimulationContext)
SpeciesContext(cbit.vcell.model.SpeciesContext)
GeometryContext(cbit.vcell.mapping.GeometryContext)
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
GeometricRegion(cbit.vcell.geometry.surface.GeometricRegion)
SpatialSymbolReference(org.sbml.jsbml.ext.spatial.SpatialSymbolReference)
AnalyticVolume(org.sbml.jsbml.ext.spatial.AnalyticVolume)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
SampledField(org.sbml.jsbml.ext.spatial.SampledField)
Domain(org.sbml.jsbml.ext.spatial.Domain)
AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume)
GeometryClass(cbit.vcell.geometry.GeometryClass)
ImageException(cbit.image.ImageException)
GeometrySurfaceDescription(cbit.vcell.geometry.surface.GeometrySurfaceDescription)
Extent(org.vcell.util.Extent)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
ISize(org.vcell.util.ISize)
CSGeometry(org.sbml.jsbml.ext.spatial.CSGeometry)
RegionInfo(cbit.vcell.geometry.RegionImage.RegionInfo)
VCImage(cbit.image.VCImage)
StructureMapping(cbit.vcell.mapping.StructureMapping)
GeometryThumbnailImageFactoryAWT(cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT)
ASTNode(org.sbml.jsbml.ASTNode)
CSGObject(cbit.vcell.geometry.CSGObject)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
UnitDefinition(org.sbml.jsbml.UnitDefinition)
ImageSubVolume(cbit.vcell.geometry.ImageSubVolume)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
SampledFieldGeometry(org.sbml.jsbml.ext.spatial.SampledFieldGeometry)
SpatialModelPlugin(org.sbml.jsbml.ext.spatial.SpatialModelPlugin)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
XMLStreamException(javax.xml.stream.XMLStreamException)
SbmlException(org.vcell.sbml.SbmlException)
ImageException(cbit.image.ImageException)
SBMLException(org.sbml.jsbml.SBMLException)
ExpressionException(cbit.vcell.parser.ExpressionException)
AdjacentDomains(org.sbml.jsbml.ext.spatial.AdjacentDomains)
Geometry(cbit.vcell.geometry.Geometry)
SampledFieldGeometry(org.sbml.jsbml.ext.spatial.SampledFieldGeometry)
AnalyticGeometry(org.sbml.jsbml.ext.spatial.AnalyticGeometry)
CSGeometry(org.sbml.jsbml.ext.spatial.CSGeometry)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
Example 17 with SurfaceGeometricRegion
use of cbit.vcell.geometry.surface.SurfaceGeometricRegion in project vcell by virtualcell.
the class SBMLImporter method getAssociatedSurfaceGeometricRegion.
private SurfaceGeometricRegion getAssociatedSurfaceGeometricRegion(GeometrySurfaceDescription vcGsd, Vector<VolumeGeometricRegion> volGeomRegionsVector) {
GeometricRegion[] geomeRegions = vcGsd.getGeometricRegions();
// adjVolGeomRegionsVector should have only 2 elements - the 2 adj
// volGeomRegions for any surfaceRegion.
VolumeGeometricRegion[] volGeomRegionsArray = volGeomRegionsVector.toArray(new VolumeGeometricRegion[0]);
for (int i = 0; i < geomeRegions.length; i++) {
if (geomeRegions[i] instanceof SurfaceGeometricRegion) {
SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) geomeRegions[i];
GeometricRegion[] adjVolGeomRegs = surfaceRegion.getAdjacentGeometricRegions();
// if the 2 arrays do not have 2 elements each, throw exception
if (volGeomRegionsArray.length != 2 && adjVolGeomRegs.length != 2) {
throw new SBMLImportException("There should be 2 adjacent geometric regions for surfaceRegion '" + surfaceRegion.getName() + "'");
}
// winner! - return surfaceRegion
if ((adjVolGeomRegs[0].compareEqual(volGeomRegionsArray[0]) && adjVolGeomRegs[1].compareEqual(volGeomRegionsArray[1])) || (adjVolGeomRegs[0].compareEqual(volGeomRegionsArray[1]) && adjVolGeomRegs[1].compareEqual(volGeomRegionsArray[0]))) {
return surfaceRegion;
}
}
}
return null;
}
Also used :
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
GeometricRegion(cbit.vcell.geometry.surface.GeometricRegion)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
Example 18 with SurfaceGeometricRegion
use of cbit.vcell.geometry.surface.SurfaceGeometricRegion in project vcell by virtualcell.
the class GeometricRegionTable method getSurfaceRegion.
/**
* This method was created in VisualAge.
* @return cbit.vcell.model.ReactionParticipant
* @param rset java.sql.ResultSet
*/
public SurfaceGeometricRegion getSurfaceRegion(java.sql.ResultSet rset, VolumeGeometricRegion[] volumeRegions, VCUnitSystem unitSystem) throws java.sql.SQLException, DataAccessException {
String _name = rset.getString(this.name.toString());
double _size = rset.getBigDecimal(this.size.toString()).doubleValue();
String _sizeUnitSymbol = rset.getString(this.sizeUnit.toString());
cbit.vcell.units.VCUnitDefinition _sizeUnit = unitSystem.getInstance(_sizeUnitSymbol);
//
// get neighboring regions
//
String _volRegion1Name = rset.getString(VOLUME1_NAME_COLUMN);
String _volRegion2Name = rset.getString(VOLUME2_NAME_COLUMN);
VolumeGeometricRegion _volumeRegion1 = null;
VolumeGeometricRegion _volumeRegion2 = null;
for (int i = 0; i < volumeRegions.length; i++) {
if (volumeRegions[i].getName().equals(_volRegion1Name)) {
_volumeRegion1 = volumeRegions[i];
}
if (volumeRegions[i].getName().equals(_volRegion2Name)) {
_volumeRegion2 = volumeRegions[i];
}
}
SurfaceGeometricRegion surfaceRegion = new SurfaceGeometricRegion(_name, _size, _sizeUnit);
surfaceRegion.addAdjacentGeometricRegion(_volumeRegion1);
_volumeRegion1.addAdjacentGeometricRegion(surfaceRegion);
surfaceRegion.addAdjacentGeometricRegion(_volumeRegion2);
_volumeRegion2.addAdjacentGeometricRegion(surfaceRegion);
return surfaceRegion;
}
Also used :
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
Aggregations
SurfaceGeometricRegion (cbit.vcell.geometry.surface.SurfaceGeometricRegion)18
VolumeGeometricRegion (cbit.vcell.geometry.surface.VolumeGeometricRegion)18
GeometricRegion (cbit.vcell.geometry.surface.GeometricRegion)17
SubVolume (cbit.vcell.geometry.SubVolume)9
GeometrySurfaceDescription (cbit.vcell.geometry.surface.GeometrySurfaceDescription)9
SurfaceClass (cbit.vcell.geometry.SurfaceClass)7
ISize (org.vcell.util.ISize)7
ImageException (cbit.image.ImageException)5
AnalyticSubVolume (cbit.vcell.geometry.AnalyticSubVolume)5
ExpressionException (cbit.vcell.parser.ExpressionException)5
PropertyVetoException (java.beans.PropertyVetoException)5
ArrayList (java.util.ArrayList)5
Geometry (cbit.vcell.geometry.Geometry)4
GeometrySpec (cbit.vcell.geometry.GeometrySpec)4
ImageSubVolume (cbit.vcell.geometry.ImageSubVolume)4
Surface (cbit.vcell.geometry.surface.Surface)4
SurfaceCollection (cbit.vcell.geometry.surface.SurfaceCollection)4
VCImage (cbit.image.VCImage)3
GeometryClass (cbit.vcell.geometry.GeometryClass)3
RegionInfo (cbit.vcell.geometry.RegionImage.RegionInfo)3
