use of org.vcell.util.ISize in project vcell by virtualcell.
the class Xmlproducer method getXML.
/**
* Insert the method's description here.
* Creation date: (3/3/2001 12:24:59 AM)
* @return Element
* @param param cbit.vcell.mesh.MeshSpecification
*/
private Element getXML(MeshSpecification param) {
Element meshspec = new Element(XMLTags.MeshSpecTag);
Element size = new Element(XMLTags.SizeTag);
// Add extent attributes
ISize sampling = param.getSamplingSize();
size.setAttribute(XMLTags.XAttrTag, String.valueOf(sampling.getX()));
size.setAttribute(XMLTags.YAttrTag, String.valueOf(sampling.getY()));
size.setAttribute(XMLTags.ZAttrTag, String.valueOf(sampling.getZ()));
meshspec.addContent(size);
return meshspec;
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class MathModel_SBMLExporter method addGeometry.
private static void addGeometry(Model sbmlModel, MathModel vcMathModel) {
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.getGeometry();
sbmlGeometry.setCoordinateSystem(GeometryKind.cartesian);
Geometry vcGeometry = vcMathModel.getGeometry();
//
// 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 coordCompX = sbmlGeometry.createCoordinateComponent();
coordCompX.setSpatialId("CoordCompX");
coordCompX.setType(CoordinateKind.cartesianX);
Boundary minX = coordCompX.getBoundaryMaximum();
minX.setSpatialId("Xmin");
minX.setValue(vcOrigin.getX());
Boundary maxX = coordCompX.getBoundaryMaximum();
maxX.setSpatialId("Xmax");
maxX.setValue(vcOrigin.getX() + (vcExtent.getX()));
Parameter parameterX = sbmlModel.createParameter();
// note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.X
parameterX.setId(ReservedVariable.X.getName());
SpatialSymbolReference coordXSpatialRef = new SpatialSymbolReference();
coordXSpatialRef.setSpatialRef(coordCompX.getSpatialId());
SpatialParameterPlugin parameterXSpatialPlugin = (SpatialParameterPlugin) parameterX.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
parameterXSpatialPlugin.setParamType(coordXSpatialRef);
// add y coordinate component
if (dimension == 2 || dimension == 3) {
CoordinateComponent coordCompY = sbmlGeometry.createCoordinateComponent();
coordCompY.setSpatialId("CoordCompY");
coordCompY.setType(CoordinateKind.cartesianY);
Boundary minY = coordCompY.getBoundaryMinimum();
minY.setId("Ymin");
minY.setValue(vcOrigin.getY());
Boundary maxY = coordCompY.getBoundaryMaximum();
maxY.setId("Ymax");
maxY.setValue(vcOrigin.getY() + (vcExtent.getY()));
Parameter parameterY = sbmlModel.createParameter();
// note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.Y
parameterY.setId(ReservedVariable.Y.getName());
SpatialSymbolReference coordYSpatialRef = new SpatialSymbolReference();
coordYSpatialRef.setSpatialRef(coordCompY.getSpatialId());
SpatialParameterPlugin parameterYSpatialPlugin = (SpatialParameterPlugin) parameterY.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
parameterYSpatialPlugin.setParamType(coordYSpatialRef);
}
// add z coordinate component
if (dimension == 3) {
CoordinateComponent coordCompZ = sbmlGeometry.createCoordinateComponent();
coordCompZ.setSpatialId("CoordCompZ");
coordCompZ.setType(CoordinateKind.cartesianZ);
Boundary minZ = coordCompZ.getBoundaryMinimum();
minZ.setId("Zmin");
minZ.setValue(vcOrigin.getZ());
Boundary maxZ = coordCompZ.getBoundaryMaximum();
maxZ.setId("Zmax");
maxZ.setValue(vcOrigin.getZ() + (vcExtent.getZ()));
Parameter parameterZ = sbmlModel.createParameter();
// note for exporting BioModels rather than MathModels, get ReservedSymbol from Model with Role of ReservedSymbolRole.Y
parameterZ.setId(ReservedVariable.Z.getName());
SpatialSymbolReference coordZSpatialRef = new SpatialSymbolReference();
coordZSpatialRef.setSpatialRef(coordCompZ.getSpatialId());
SpatialParameterPlugin parameterZSpatialPlugin = (SpatialParameterPlugin) parameterZ.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
parameterZSpatialPlugin.setParamType(coordZSpatialRef);
}
//
// list of domain types : subvolumes and surface classes from VC
// Also create compartments - one compartment for each geometryClass. set id and spatialDimension based on type of geometryClass.
//
boolean bAnalyticGeom = false;
boolean bImageGeom = false;
GeometryClass[] vcGeomClasses = vcGeometry.getGeometryClasses();
int numVCGeomClasses = vcGeomClasses.length;
for (int i = 0; i < numVCGeomClasses; i++) {
DomainType domainType = sbmlGeometry.createDomainType();
domainType.setId(vcGeomClasses[i].getName());
if (vcGeomClasses[i] instanceof SubVolume) {
if (((SubVolume) vcGeomClasses[i]) instanceof AnalyticSubVolume) {
bAnalyticGeom = true;
} else if (((SubVolume) vcGeomClasses[i]) instanceof ImageSubVolume) {
bImageGeom = true;
}
domainType.setSpatialDimensions(3);
} 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();
Compartment compartment = null;
for (int i = 0; i < vcGeometricRegions.length; i++) {
// domains
Domain domain = sbmlGeometry.createDomain();
domain.setId(vcGeometricRegions[i].getName());
compartment = sbmlModel.createCompartment();
compartment.setId("compartment" + i);
if (vcGeometricRegions[i] instanceof VolumeGeometricRegion) {
domain.setDomainType(((VolumeGeometricRegion) vcGeometricRegions[i]).getSubVolume().getName());
// domain.setImplicit(false);
compartment.setSpatialDimensions(3);
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(surfaceClass.getName());
// domain.setImplicit(true);
compartment.setSpatialDimensions(2);
// adjacent domains : 2 adjacent domain objects for each surfaceClass in VC.
// adjacent domain 1
AdjacentDomains adjDomain = sbmlGeometry.createAdjacentDomain();
adjDomain.setId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + geomRegion0.getName()));
adjDomain.setDomain1(vcSurfaceGeomReg.getName());
adjDomain.setDomain2(geomRegion0.getName());
// adjacent domain 2
adjDomain = sbmlGeometry.createAdjacentDomain();
adjDomain.setId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + geomRegion1.getName()));
adjDomain.setDomain1(vcSurfaceGeomReg.getName());
adjDomain.setDomain2(geomRegion1.getName());
}
//
// Mathmodel does not have structureMapping, hence creating compartmentMapping while creating domains.
// @TODO : how to assign unitSize for compartmentMapping?
//
SpatialCompartmentPlugin cplugin = (SpatialCompartmentPlugin) compartment.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
CompartmentMapping compMapping = cplugin.getCompartmentMapping();
String compMappingId = TokenMangler.mangleToSName(domain.getDomainType() + "_" + compartment.getId());
compMapping.setId(compMappingId);
compMapping.setDomainType(TokenMangler.mangleToSName(domain.getDomainType()));
// try {
// compMapping.setUnitSize(1.0);
// } catch (ExpressionException e) {
// e.printStackTrace(System.out);
// throw new RuntimeException("Unable to create compartment mapping for structureMapping '" + compMapping.getId() +"' : " + e.getMessage());
// }
}
AnalyticGeometry sbmlAnalyticGeom = null;
SampledFieldGeometry sbmlSFGeom = null;
// both image and analytic subvolumes?? == not handled in SBML at this time.
if (bAnalyticGeom && !bImageGeom) {
sbmlAnalyticGeom = sbmlGeometry.createAnalyticGeometry();
sbmlAnalyticGeom.setId(TokenMangler.mangleToSName(vcGeometry.getName()));
} else if (bImageGeom && !bAnalyticGeom) {
// assuming image based geometry if not analytic geometry
sbmlSFGeom = sbmlGeometry.createSampledFieldGeometry();
sbmlSFGeom.setId(TokenMangler.mangleToSName(vcGeometry.getName()));
} else if (bAnalyticGeom && bImageGeom) {
throw new RuntimeException("Export to SBML of a combination of Image-based and Analytic geometries is not supported yet.");
} else if (!bAnalyticGeom && !bImageGeom) {
throw new RuntimeException("Unknown geometry type.");
}
//
for (int i = 0; i < vcGeomClasses.length; i++) {
if (vcGeomClasses[i] instanceof AnalyticSubVolume) {
// add analytiVols to sbmlAnalyticGeometry
if (sbmlAnalyticGeom != null) {
AnalyticVolume analyticVol = sbmlAnalyticGeom.createAnalyticVolume();
analyticVol.setId(vcGeomClasses[i].getName());
analyticVol.setDomainType(vcGeomClasses[i].getName());
analyticVol.setFunctionType(FunctionKind.layered);
analyticVol.setOrdinal(i);
Expression expr = ((AnalyticSubVolume) vcGeomClasses[i]).getExpression();
try {
String mathMLStr = ExpressionMathMLPrinter.getMathML(expr, true);
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());
}
} else {
throw new RuntimeException("SBML AnalyticGeometry is null.");
}
} else if (vcGeomClasses[i] instanceof ImageSubVolume) {
// add sampledVols to sbmlSFGeometry
if (sbmlSFGeom != null) {
SampledVolume sampledVol = sbmlSFGeom.createSampledVolume();
sampledVol.setId(vcGeomClasses[i].getName());
sampledVol.setDomainType(vcGeomClasses[i].getName());
sampledVol.setSampledValue(((ImageSubVolume) vcGeomClasses[i]).getPixelValue());
} else {
throw new RuntimeException("SBML SampledFieldGeometry is null.");
}
}
}
if (sbmlSFGeom != null) {
// add sampledField to sampledFieldGeometry
SampledField sampledField = sbmlGeometry.createSampledField();
VCImage vcImage = vcGeometry.getGeometrySpec().getImage();
sampledField.setId(vcImage.getName());
sampledField.setNumSamples1(vcImage.getNumX());
if (vcImage.getNumY() > 1) {
sampledField.setNumSamples2(vcImage.getNumY());
}
if (vcImage.getNumZ() > 1) {
sampledField.setNumSamples3(vcImage.getNumZ());
}
sampledField.setInterpolationType(InterpolationKind.nearestneighbor);
sampledField.setDataType(DataKind.UINT8);
// add image from vcGeometrySpec to sampledField.
try {
StringBuffer sb = new StringBuffer();
byte[] imagePixelsBytes = vcImage.getPixelsCompressed();
for (int i = 0; i < imagePixelsBytes.length; i++) {
int uint8_sample = ((int) imagePixelsBytes[i]) & 0xff;
sb.append(uint8_sample + " ");
}
sampledField.setSamplesLength(vcImage.getNumXYZ());
sampledField.setSamples(sb.toString().trim());
} catch (ImageException e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to export image from VCell to SBML : " + e.getMessage());
}
}
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class XmlReader method getMeshSpecification.
/**
* This method returns a MeshSpecification object from a XML Element.
* Creation date: (5/22/2001 12:05:21 PM)
* @return cbit.vcell.mesh.MeshSpecification
* @param param org.jdom.Element
*/
private MeshSpecification getMeshSpecification(Element param, Geometry geometry) throws XmlParseException {
// *** create new MeshSpecification ***
MeshSpecification meshSpec = new MeshSpecification(geometry);
// get ISize
Element size = param.getChild(XMLTags.SizeTag, vcNamespace);
int x = Integer.parseInt(size.getAttributeValue(XMLTags.XAttrTag));
int y = Integer.parseInt(size.getAttributeValue(XMLTags.YAttrTag));
int z = Integer.parseInt(size.getAttributeValue(XMLTags.ZAttrTag));
ISize newsize = new ISize(x, y, z);
// set ISize
try {
meshSpec.setSamplingSize(newsize);
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace();
throw new XmlParseException("A PropertyVetoException was fired when setting the ISize object to a new MeshSpecification", e);
}
return meshSpec;
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class Xmlproducer method getXML.
private Element getXML(GeometrySurfaceDescription param) throws XmlParseException {
Element gsd = new Element(XMLTags.SurfaceDescriptionTag);
// add attributes
ISize isize = param.getVolumeSampleSize();
if (isize == null) {
throw new XmlParseException("Unable to retrieve dimensions for surface descriptions for Geometry: " + param.getGeometry().getName());
}
gsd.setAttribute(XMLTags.NumSamplesXAttrTag, String.valueOf(isize.getX()));
gsd.setAttribute(XMLTags.NumSamplesYAttrTag, String.valueOf(isize.getY()));
gsd.setAttribute(XMLTags.NumSamplesZAttrTag, String.valueOf(isize.getZ()));
Double coFrequency = param.getFilterCutoffFrequency();
if (coFrequency == null) {
throw new XmlParseException("Unable to retrieve cutoff frequency for surface descriptions for Geometry: " + param.getGeometry().getName());
}
double cutoffFrequency = coFrequency.doubleValue();
gsd.setAttribute(XMLTags.CutoffFrequencyAttrTag, String.valueOf(cutoffFrequency));
// add subelements
GeometricRegion[] geomRegions = param.getGeometricRegions();
if (geomRegions != null) {
for (int i = 0; i < geomRegions.length; i++) {
if (geomRegions[i] instanceof SurfaceGeometricRegion) {
SurfaceGeometricRegion sgr = (SurfaceGeometricRegion) geomRegions[i];
Element membraneRegion = new Element(XMLTags.MembraneRegionTag);
membraneRegion.setAttribute(XMLTags.NameAttrTag, sgr.getName());
GeometricRegion[] adjacents = sgr.getAdjacentGeometricRegions();
if (adjacents == null || adjacents.length != 2) {
throw new XmlParseException("Wrong number of adjacent regions for surface descriptions for location: " + sgr.getName() + " in Geometry: " + param.getGeometry().getName());
}
membraneRegion.setAttribute(XMLTags.VolumeRegion_1AttrTag, adjacents[0].getName());
membraneRegion.setAttribute(XMLTags.VolumeRegion_2AttrTag, adjacents[1].getName());
double size = sgr.getSize();
if (size != -1) {
membraneRegion.setAttribute(XMLTags.SizeAttrTag, String.valueOf(size));
VCUnitDefinition unit = sgr.getSizeUnit();
if (unit != null) {
membraneRegion.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
}
}
gsd.addContent(membraneRegion);
} else if (geomRegions[i] instanceof VolumeGeometricRegion) {
VolumeGeometricRegion vgr = (VolumeGeometricRegion) geomRegions[i];
Element volumeRegion = new Element(XMLTags.VolumeRegionTag);
volumeRegion.setAttribute(XMLTags.NameAttrTag, vgr.getName());
volumeRegion.setAttribute(XMLTags.RegionIDAttrTag, String.valueOf(vgr.getRegionID()));
volumeRegion.setAttribute(XMLTags.SubVolumeAttrTag, vgr.getSubVolume().getName());
double size = vgr.getSize();
if (size != -1) {
volumeRegion.setAttribute(XMLTags.SizeAttrTag, String.valueOf(size));
VCUnitDefinition unit = vgr.getSizeUnit();
if (unit != null) {
volumeRegion.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
}
}
gsd.addContent(volumeRegion);
}
}
}
return gsd;
}
use of org.vcell.util.ISize 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;
}
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