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WIP: CSG round trip to SBML #424

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c5067af
WIP: CSG round trip to SBML
jcschaff Sep 27, 2022
e1717fb
WIP: CSG + Analytic SBML export
jcschaff Oct 24, 2022
22ecde7
WIP
jcschaff Dec 2, 2022
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15 changes: 14 additions & 1 deletion vcell-core/src/main/java/cbit/vcell/geometry/CSGObject.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,9 @@
package cbit.vcell.geometry;

import org.vcell.util.Compare;
import org.vcell.util.Extent;
import org.vcell.util.Matchable;
import org.vcell.util.Origin;
import org.vcell.util.document.KeyValue;

import cbit.image.ImageException;
Expand All @@ -33,7 +35,18 @@ public CSGObject(CSGObject csgObj) {
root = csgObj.root.clone();
}

public boolean compareEqual(Matchable obj) {
public static CSGObject createBackgroundObject(Origin vcOrigin, Extent vcExtent, String name, int handle) {
CSGPrimitive cube = new CSGPrimitive("background", CSGPrimitive.PrimitiveType.CUBE);
CSGScale scale = new CSGScale("scale",new Vect3d(2*vcExtent.getX(),2*vcExtent.getY(), 2*vcExtent.getZ()));
CSGTranslation translation = new CSGTranslation("translate", new Vect3d(-vcOrigin.getX(), -vcOrigin.getY(), -vcOrigin.getZ()));
scale.setChild(translation);
translation.setChild(cube);
CSGObject csgObject = new CSGObject(null ,name, handle);
csgObject.setRoot(scale);
return csgObject;
}

public boolean compareEqual(Matchable obj) {
if (!compareEqual0(obj)){
return false;
}
Expand Down
2 changes: 1 addition & 1 deletion vcell-core/src/main/java/cbit/vcell/model/Kinetics.java
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Expand Up @@ -905,7 +905,7 @@ private final void cleanupParameters() throws ModelException, ExpressionExceptio
try {
exp.bindExpression(reactionStep);
}catch (ExpressionBindingException e){
logger.error("error binding expression '"+exp.infix()+"': "+e.getMessage(), e);
logger.warn("error binding expression '"+exp.infix()+"': "+e.getMessage());
}
}
}
Expand Down
115 changes: 90 additions & 25 deletions vcell-core/src/main/java/org/vcell/sbml/vcell/SBMLExporter.java
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Expand Up @@ -20,6 +20,9 @@
import cbit.vcell.field.FieldFunctionArguments;
import cbit.vcell.field.FieldUtilities;
import cbit.vcell.geometry.CSGObject;
import cbit.vcell.geometry.CSGPrimitive;
import cbit.vcell.geometry.CSGScale;
import cbit.vcell.geometry.CSGTranslation;
import cbit.vcell.geometry.Geometry;
import cbit.vcell.geometry.*;
import cbit.vcell.geometry.RegionImage.RegionInfo;
Expand Down Expand Up @@ -53,6 +56,7 @@
import cbit.vcell.parser.ExpressionMathMLPrinter;
import cbit.vcell.parser.ExpressionMathMLPrinter.MathType;
import cbit.vcell.parser.SymbolTableEntry;
import cbit.vcell.render.Vect3d;
import cbit.vcell.solver.AnnotatedFunction;
import cbit.vcell.solver.Simulation;
import cbit.vcell.solver.SimulationSymbolTable;
Expand All @@ -75,7 +79,7 @@
import org.vcell.sbml.UnsupportedSbmlExportException;
import org.vcell.sbml.vcell.SBMLSymbolMapping.SBaseWrapper;
import org.vcell.util.*;
import org.vcell.util.document.VCellSoftwareVersion;
import org.vcell.vis.core.Vect3D;

import javax.xml.stream.XMLStreamException;
import java.beans.PropertyVetoException;
Expand Down Expand Up @@ -2243,7 +2247,8 @@ private void addGeometry() throws SbmlException {
if (vcGeomClasses[i] instanceof AnalyticSubVolume) {
AnalyticSubVolume vcAnalyticSubVolume = (AnalyticSubVolume) vcGeomClasses[i];
// need to avoid id name clash with structures (compartments)
AnalyticVolume analyticVol = sbmlAnalyticGeomDefinition.createAnalyticVolume(TokenMangler.mangleToSName("AnalyticVol_"+vcAnalyticSubVolume.getName()));
String id = TokenMangler.mangleToSName("AnalyticVol_" + vcAnalyticSubVolume.getName());
AnalyticVolume analyticVol = sbmlAnalyticGeomDefinition.createAnalyticVolume(id);
// analyticVol.setSpatialId(vcGeomClasses[i].getName());
analyticVol.setDomainType(DOMAIN_TYPE_PREFIX+vcAnalyticSubVolume.getName());
analyticVol.setFunctionType(FunctionKind.layered);
Expand All @@ -2262,9 +2267,46 @@ private void addGeometry() throws SbmlException {
addGeometrySamplingAnnotation(dimension, vcGSD, sbmlAnalyticGeomDefinition);
}
//
// add CSGeometry
// add CSGeometry without any AnalyticSubVolumes
//
if (!bAnyAnalyticSubvolumes && !bAnyImageSubvolumes && bAnyCSGSubvolumes){
// if (!bAnyAnalyticSubvolumes && !bAnyImageSubvolumes && bAnyCSGSubvolumes){
if (!bAnyImageSubvolumes && bAnyCSGSubvolumes){
CSGeometry sbmlCSGeomDefinition = sbmlGeometry.createCSGeometry();
sbmlCSGeomDefinition.setSpatialId(TokenMangler.mangleToSName("CSG_"+vcGeometry.getName()));
sbmlCSGeomDefinition.setIsActive(true);
for (int i = 0; i < vcGeomClasses.length; i++) {
if (vcGeomClasses[i] instanceof CSGObject) {
CSGObject vcellCSGObject = (CSGObject)vcGeomClasses[i];
String id = TokenMangler.mangleToSName("CSGObject_" + vcellCSGObject.getName());
org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = sbmlCSGeomDefinition.createCSGObject(id);
sbmlCSGObject.setDomainType(DOMAIN_TYPE_PREFIX+vcellCSGObject.getName());
sbmlCSGObject.setOrdinal(vcellCSGObject.getHandle()); // numSubVols - (i+1)); // the ordinal should be the least for the default/background subVolume
org.sbml.jsbml.ext.spatial.CSGNode sbmlcsgNode = getSBMLCSGNode(vcellCSGObject.getRoot());
sbmlcsgNode.setParent(sbmlCSGObject);
sbmlCSGObject.setCSGNode(sbmlcsgNode);
}else if (vcGeomClasses[i] instanceof AnalyticSubVolume && ((AnalyticSubVolume)vcGeomClasses[i]).getExpression().isOne()) {
AnalyticSubVolume analyticSubVolume = (AnalyticSubVolume)vcGeomClasses[i];
String id = TokenMangler.mangleToSName("CSGObject_" + analyticSubVolume.getName());
org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = sbmlCSGeomDefinition.createCSGObject(id);
sbmlCSGObject.setDomainType(DOMAIN_TYPE_PREFIX+analyticSubVolume.getName());
sbmlCSGObject.setOrdinal(analyticSubVolume.getHandle()); // the ordinal should be the least for the default/background subVolume
CSGObject backgroundObject = CSGObject.createBackgroundObject(vcOrigin, vcExtent, analyticSubVolume.getName(), analyticSubVolume.getHandle());
org.sbml.jsbml.ext.spatial.CSGNode sbmlcsgNode = getSBMLCSGNode(backgroundObject.getRoot());
sbmlcsgNode.setParent(sbmlCSGObject);
sbmlCSGObject.setCSGNode(sbmlcsgNode);
}
}
addGeometrySamplingAnnotation(dimension, vcGSD, sbmlCSGeomDefinition);
}
//
// add CSGeometry with a single AnalyticSubVolume as the background
//
List<AnalyticSubVolume> analyticSubVolumes = Arrays.stream(vcGeometry.getGeometrySpec().getSubVolumes())
.filter(sv -> sv instanceof AnalyticSubVolume)
.map(sv -> (AnalyticSubVolume)sv).collect(Collectors.toList());
if (analyticSubVolumes.size()==1 && analyticSubVolumes.get(0).getExpression().isOne() && !bAnyImageSubvolumes && bAnyCSGSubvolumes){
AnalyticSubVolume backgroundAnalyticSubVolume = analyticSubVolumes.get(0);

CSGeometry sbmlCSGeomDefinition = new CSGeometry();
sbmlGeometry.addGeometryDefinition(sbmlCSGeomDefinition);
sbmlCSGeomDefinition.setSpatialId(TokenMangler.mangleToSName("CSG_"+vcGeometry.getName()));
Expand All @@ -2275,9 +2317,28 @@ private void addGeometry() throws SbmlException {
sbmlCSGeomDefinition.addCSGObject(sbmlCSGObject);
sbmlCSGObject.setSpatialId(vcellCSGObject.getName());
sbmlCSGObject.setDomainType(DOMAIN_TYPE_PREFIX+vcellCSGObject.getName());
sbmlCSGObject.setOrdinal(numSubVols - (i+1)); // the ordinal should the the least for the default/background subVolume
sbmlCSGObject.setOrdinal(numSubVols - (i+1)); // the ordinal should the the least for the default/background subVolume
org.sbml.jsbml.ext.spatial.CSGNode sbmlcsgNode = getSBMLCSGNode(vcellCSGObject.getRoot());
sbmlCSGObject.setCSGNode(sbmlcsgNode);
}else if (vcGeomClasses[i] == backgroundAnalyticSubVolume){
org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = new org.sbml.jsbml.ext.spatial.CSGObject();
sbmlCSGeomDefinition.addCSGObject(sbmlCSGObject);
sbmlCSGObject.setSpatialId(backgroundAnalyticSubVolume.getName());
sbmlCSGObject.setDomainType(DOMAIN_TYPE_PREFIX+backgroundAnalyticSubVolume.getName());
sbmlCSGObject.setOrdinal(numSubVols - (i+1)); // the ordinal should the the least for the default/background subVolume
CSGPrimitive cube = new CSGPrimitive("background_cube", CSGPrimitive.PrimitiveType.CUBE);
CSGScale cubeScale = new CSGScale("background_scale", new Vect3d(
vcExtent.getX()/2.0,
vcExtent.getY()/2.0,
vcExtent.getZ()/2.0));
CSGTranslation cubeTranslate = new CSGTranslation("background_translate",new Vect3d(
vcOrigin.getX() + vcExtent.getX()/2.0,
vcOrigin.getX() + vcExtent.getY()/2.0,
vcOrigin.getZ() + vcExtent.getZ()/2.0));
cubeScale.setChild(cube);
cubeTranslate.setChild(cubeScale);
org.sbml.jsbml.ext.spatial.CSGNode sbmlcsgNode = getSBMLCSGNode(cubeTranslate);
sbmlCSGObject.setCSGNode(sbmlcsgNode);
}
}
addGeometrySamplingAnnotation(dimension, vcGSD, sbmlCSGeomDefinition);
Expand Down Expand Up @@ -2435,6 +2496,10 @@ private void addGeometry() throws SbmlException {
}
*/
}

if (sbmlGeometry.getListOfGeometryDefinitions().size()==0){
throw new SbmlException("did not export any SBML geometry definitions for this spatial application");
}
//
// add "SurfaceMesh" ParametricGeometry
//
Expand Down Expand Up @@ -2475,31 +2540,31 @@ private boolean goodPointer(Object obj, Class<?> clzz, String sourceName) {
}

private static org.sbml.jsbml.ext.spatial.CSGNode getSBMLCSGNode(cbit.vcell.geometry.CSGNode vcCSGNode) {
String csgNodeName = vcCSGNode.getName();
String csgNodeName = "CSGObjectNode_"+vcCSGNode.getName();
if (vcCSGNode instanceof cbit.vcell.geometry.CSGPrimitive){
cbit.vcell.geometry.CSGPrimitive vcCSGprimitive = (cbit.vcell.geometry.CSGPrimitive)vcCSGNode;
org.sbml.jsbml.ext.spatial.CSGPrimitive sbmlPrimitive = new org.sbml.jsbml.ext.spatial.CSGPrimitive();
sbmlPrimitive.setSpatialId(csgNodeName);
switch (vcCSGprimitive.getType()){
case SPHERE: {
sbmlPrimitive.setPrimitiveType(SBMLSpatialConstants.SOLID_SPHERE);
break;
}
case CONE: {
sbmlPrimitive.setPrimitiveType(SBMLSpatialConstants.SOLID_CONE);
break;
}
case CUBE: {
sbmlPrimitive.setPrimitiveType(SBMLSpatialConstants.SOLID_CUBE);
break;
}
case CYLINDER: {
sbmlPrimitive.setPrimitiveType(SBMLSpatialConstants.SOLID_CYLINDER);
break;
}
default: {
throw new RuntimeException("unsupported primitive type "+vcCSGprimitive.getType());
}
case SPHERE: {
sbmlPrimitive.setPrimitiveType(PrimitiveKind.sphere);
break;
}
case CONE: {
sbmlPrimitive.setPrimitiveType(PrimitiveKind.cone);
break;
}
case CUBE: {
sbmlPrimitive.setPrimitiveType(PrimitiveKind.cube);
break;
}
case CYLINDER: {
sbmlPrimitive.setPrimitiveType(PrimitiveKind.cylinder);
break;
}
default: {
throw new RuntimeException("unsupported primitive type "+vcCSGprimitive.getType());
}
}
return sbmlPrimitive;
}else if (vcCSGNode instanceof cbit.vcell.geometry.CSGPseudoPrimitive){
Expand Down
2 changes: 1 addition & 1 deletion vcell-core/src/main/java/org/vcell/sbml/vcell/SBMLImporter.java
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Expand Up @@ -4026,7 +4026,7 @@ private static void addGeometry(org.sbml.jsbml.Model sbmlModel, BioModel vcBioMo
// CSGObject[] vcCSGSubVolumes = new CSGObject[n];
for (int i = 0; i < n; i++) {
org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = sbmlCSGs.get(i);
CSGObject vcellCSGObject = new CSGObject(null, sbmlCSGObject.getSpatialId(), i);
CSGObject vcellCSGObject = new CSGObject(null, sbmlCSGObject.getDomainType(), i);
if (domainTypeId_to_handle_map.get(sbmlCSGObject.getDomainType()) != null){
vcellCSGObject.setHandle(domainTypeId_to_handle_map.get(sbmlCSGObject.getDomainType()));
}
Expand Down
12 changes: 0 additions & 12 deletions vcell-core/src/main/java/org/vcell/sbml/vcell/SBMLSpatialConstants.java
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