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combine Hdf5Reader into ChomboFileReader
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@jcschaff
jcschaff committed Apr 24, 2024
1 parent a2fb9d6 commit 46727a8
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Showing 2 changed files with 213 additions and 226 deletions.
244 changes: 213 additions & 31 deletions vcell-core/src/main/java/org/vcell/vis/io/ChomboFileReader.java
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Original file line number Diff line number Diff line change
@@ -1,10 +1,15 @@
package org.vcell.vis.io;

import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;

import javax.swing.tree.DefaultMutableTreeNode;

import ncsa.hdf.object.h5.H5CompoundDS;
import ncsa.hdf.object.h5.H5ScalarDS;
import org.vcell.vis.chombo.ChomboBoundaries;
import org.vcell.vis.chombo.ChomboBoundaries.BorderCellInfo;
import org.vcell.vis.chombo.ChomboBoundaries.MeshMetrics;
Expand Down Expand Up @@ -34,7 +39,78 @@ public class ChomboFileReader {
private static final String MESH_ATTR_DIMENSION = "dimension";
private static final String MESH_ATTR_ORIGIN = "origin";
private static final String MESH_ATTR_EXTENT = "extent";



/**
* Z = boolean
[B = byte
[S = short
[I = int
[J = long
[F = float
[D = double
[C = char
[L = any non-primitives(Object)
* @author schaff
*
*/
static abstract class DataColumn {
private String colName;
public DataColumn(String name){
this.colName = name;
}
public abstract int getNumRows();
public abstract double getValue(int index);
}

static class IntColumn extends DataColumn {
int[] data;
public IntColumn(String name, int[] data){
super(name);
this.data = data;
}
@Override
public int getNumRows(){
return data.length;
}
@Override
public double getValue(int index){
return data[index];
}
}

static class LongColumn extends DataColumn {
long[] data;
public LongColumn(String name, long[] data){
super(name);
this.data = data;
}
@Override
public int getNumRows(){
return data.length;
}
@Override
public double getValue(int index){
return data[index];
}
}

static class DoubleColumn extends DataColumn {
double[] data;
public DoubleColumn(String name, double[] data){
super(name);
this.data = data;
}
@Override
public int getNumRows(){
return data.length;
}
@Override
public double getValue(int index){
return data[index];
}
}

private static ChomboMeshData readMesh(String meshFileName, String vol0FileName) throws Exception{

ChomboMesh chomboMesh = new ChomboMesh();
Expand All @@ -52,11 +128,11 @@ private static ChomboMeshData readMesh(String meshFileName, String vol0FileName)

DefaultMutableTreeNode meshRootNode = (DefaultMutableTreeNode)meshFile.getRootNode();
Group meshRootGroup = (Group)meshRootNode.getUserObject();
Group meshGroup = Hdf5Reader.getChildGroup(meshRootGroup,"mesh");
Group meshGroup = getChildGroup(meshRootGroup,"mesh");

chomboMesh.setDimension(Hdf5Reader.getIntAttribute(meshGroup,MESH_ATTR_DIMENSION));
chomboMesh.setExtent(Hdf5Reader.getVect3DAttribute(meshGroup,MESH_ATTR_EXTENT,1.0));
chomboMesh.setOrigin(Hdf5Reader.getVect3DAttribute(meshGroup,MESH_ATTR_ORIGIN,0.0));
chomboMesh.setDimension(getIntAttribute(meshGroup,MESH_ATTR_DIMENSION));
chomboMesh.setExtent(getVect3DAttribute(meshGroup,MESH_ATTR_EXTENT,1.0));
chomboMesh.setOrigin(getVect3DAttribute(meshGroup,MESH_ATTR_ORIGIN,0.0));

// it's very wasteful here, but what can I do?
CartesianMeshChombo cartesianMeshChombo = CartesianMeshChombo.readMeshFile(new File(meshFileName));
Expand All @@ -65,10 +141,10 @@ private static ChomboMeshData readMesh(String meshFileName, String vol0FileName)
chomboMesh.addFeaturePhase(fpv.feature, fpv.iphase);
}

//Hdf5Reader.DataColumn[] metricsColumns = Hdf5Reader.getDataTable(meshGroup,METRICS_DATASET);
//DataColumn[] metricsColumns = getDataTable(meshGroup,METRICS_DATASET);
if (chomboMesh.getDimension()==2){
Hdf5Reader.DataColumn[] segmentColumns = Hdf5Reader.getDataTable(meshGroup,"segments");
Hdf5Reader.DataColumn[] verticesColumns = Hdf5Reader.getDataTable(meshGroup,"vertices");
DataColumn[] segmentColumns = getDataTable(meshGroup,"segments");
DataColumn[] verticesColumns = getDataTable(meshGroup,"vertices");
ChomboBoundaries boundaries = chomboMesh.getBoundaries();
int numVertices = verticesColumns[0].getNumRows();
int numSegments = segmentColumns[0].getNumRows();
Expand All @@ -85,7 +161,7 @@ private static ChomboMeshData readMesh(String meshFileName, String vol0FileName)
boundaries.addSegment(new ChomboBoundaries.Segment(chomboIndex, v1, v2));
}
}else if (chomboMesh.getDimension()==3){
Hdf5Reader.DataColumn[] surfaceTriangleColumns = Hdf5Reader.getDataTable(meshGroup,"surface triangles");
DataColumn[] surfaceTriangleColumns = getDataTable(meshGroup,"surface triangles");
ChomboBoundaries boundaries = chomboMesh.getBoundaries();
int numTriangles = surfaceTriangleColumns[0].getNumRows();
for (int row=0;row<numTriangles;row++){
Expand All @@ -108,7 +184,7 @@ private static ChomboMeshData readMesh(String meshFileName, String vol0FileName)
SurfaceTriangle surfaceTriangle = new SurfaceTriangle(index, face, p0_index,p1_index,p2_index);
boundaries.addSurfaceTriangle(surfaceTriangle);
}
Hdf5Reader.DataColumn[] metricsColumns = Hdf5Reader.getDataTable(meshGroup,"membrane elements");
DataColumn[] metricsColumns = getDataTable(meshGroup,"membrane elements");
MeshMetrics meshMetrics = boundaries.getMeshMetrics();
int numMeshMetrics = metricsColumns[0].getNumRows();
for (int row=0;row<numMeshMetrics;row++){
Expand Down Expand Up @@ -145,44 +221,44 @@ private static ChomboMeshData readMesh(String meshFileName, String vol0FileName)
DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode)vol0File.getRootNode();
Group rootGroup = (Group)rootNode.getUserObject();

Group level0Group = Hdf5Reader.getChildGroup(rootGroup, "level_0");
double time = Hdf5Reader.getDoubleAttribute(level0Group, "time");
Group level0Group = getChildGroup(rootGroup, "level_0");
double time = getDoubleAttribute(level0Group, "time");
ChomboMeshData chomboMeshData = new ChomboMeshData(chomboMesh, time);

int numComponents = Hdf5Reader.getIntAttribute(rootGroup, "num_components");
int numLevels = Hdf5Reader.getIntAttribute(rootGroup, "num_levels");
int numComponents = getIntAttribute(rootGroup, "num_components");
int numLevels = getIntAttribute(rootGroup, "num_levels");
int fractionComponentIndex = -1;
for (int i=0;i<numComponents;i++){
String compName = Hdf5Reader.getStringAttribute(rootGroup, "component_"+i);
String compName = getStringAttribute(rootGroup, "component_"+i);
chomboMeshData.addComponentName(compName);
if (compName.equals("fraction-0")){
fractionComponentIndex = i;
chomboMeshData.setFraction0ComponentIndex(fractionComponentIndex);
}
}
for (int i=0;i<numLevels;i++){
Group levelGroup = Hdf5Reader.getChildGroup(rootGroup, "level_"+i);
Group levelGroup = getChildGroup(rootGroup, "level_"+i);
int refinement = 2;
if (i==0){
refinement = 1;
}
ChomboLevel chomboLevel = new ChomboLevel(chomboMesh, i, refinement);
Hdf5Reader.DataColumn[] boxColumns = Hdf5Reader.getDataTable(levelGroup, "boxes");
DataColumn[] boxColumns = getDataTable(levelGroup, "boxes");
int[] lo_i, lo_j, lo_k, hi_i, hi_j, hi_k;
if (chomboMesh.getDimension()==2){
lo_i = ((Hdf5Reader.IntColumn)boxColumns[0]).data;
lo_j = ((Hdf5Reader.IntColumn)boxColumns[1]).data;
hi_i = ((Hdf5Reader.IntColumn)boxColumns[2]).data;
hi_j = ((Hdf5Reader.IntColumn)boxColumns[3]).data;
lo_i = ((IntColumn)boxColumns[0]).data;
lo_j = ((IntColumn)boxColumns[1]).data;
hi_i = ((IntColumn)boxColumns[2]).data;
hi_j = ((IntColumn)boxColumns[3]).data;
lo_k = new int[boxColumns[0].getNumRows()];
hi_k = new int[boxColumns[0].getNumRows()];
}else{
lo_i = ((Hdf5Reader.IntColumn)boxColumns[0]).data;
lo_j = ((Hdf5Reader.IntColumn)boxColumns[1]).data;
lo_k = ((Hdf5Reader.IntColumn)boxColumns[2]).data;
hi_i = ((Hdf5Reader.IntColumn)boxColumns[3]).data;
hi_j = ((Hdf5Reader.IntColumn)boxColumns[4]).data;
hi_k = ((Hdf5Reader.IntColumn)boxColumns[5]).data;
lo_i = ((IntColumn)boxColumns[0]).data;
lo_j = ((IntColumn)boxColumns[1]).data;
lo_k = ((IntColumn)boxColumns[2]).data;
hi_i = ((IntColumn)boxColumns[3]).data;
hi_j = ((IntColumn)boxColumns[4]).data;
hi_k = ((IntColumn)boxColumns[5]).data;
}
for (int b=0; b<boxColumns[0].getNumRows(); b++){
ChomboBox chomboBox = new ChomboBox(chomboLevel,lo_i[b],hi_i[b],lo_j[b],hi_j[b],lo_k[b],hi_k[b],chomboMesh.getDimension());
Expand All @@ -192,9 +268,9 @@ private static ChomboMeshData readMesh(String meshFileName, String vol0FileName)
//
// read the variables
//
Hdf5Reader.DataColumn[] data = Hdf5Reader.getDataTable(levelGroup,"data:datatype=0");
Hdf5Reader.DataColumn[] offsets = Hdf5Reader.getDataTable(levelGroup,"data:offsets=0");
ChomboLevelData chomboLevelData = new ChomboLevelData(i,fractionComponentIndex,((Hdf5Reader.DoubleColumn)data[0]).data,((Hdf5Reader.LongColumn)offsets[0]).data);
DataColumn[] data = getDataTable(levelGroup,"data:datatype=0");
DataColumn[] offsets = getDataTable(levelGroup,"data:offsets=0");
ChomboLevelData chomboLevelData = new ChomboLevelData(i,fractionComponentIndex,((DoubleColumn)data[0]).data,((LongColumn)offsets[0]).data);
chomboMeshData.addLevelData(chomboLevelData);
}

Expand Down Expand Up @@ -234,7 +310,7 @@ private static void readMembraneVarData(ChomboMeshData chomboMeshData, Group roo
{
try
{
Group vcellGroup = Hdf5Reader.getChildGroup(rootGroup, group);
Group vcellGroup = getChildGroup(rootGroup, group);
if (vcellGroup != null)
{
List<HObject> children = vcellGroup.getMemberList();
Expand Down Expand Up @@ -267,4 +343,110 @@ private static void readMembraneVarData(ChomboMeshData chomboMeshData, Group roo
}
}
}

private static Attribute getAttribute(Group group, String name) throws Exception{
List<Attribute> attributes = group.getMetadata();
for (Attribute attr : attributes){
if (attr.getName().equals(name)){
return attr;
}
}
throw new RuntimeException("failed to find attribute "+name);
}

private static double getDoubleAttribute(Group group, String name) throws Exception{
Attribute attr = getAttribute(group,name);
return ((double[])attr.getValue())[0];
}

private static float getFloatAttribute(Group group, String name) throws Exception{
Attribute attr = getAttribute(group,name);
return ((float[])attr.getValue())[0];
}

private static int getIntAttribute(Group group, String name) throws Exception{
Attribute attr = getAttribute(group,name);
return ((int[])attr.getValue())[0];
}

private static String getStringAttribute(Group group, String name) throws Exception{
Attribute attr = getAttribute(group,name);
return ((String[])attr.getValue())[0];
}

private static Vect3D getVect3DAttribute(Group group, String name, double defaultZ) throws Exception{
String str = getStringAttribute(group, name);
return parseAttrString(str,defaultZ);
}

private static Group getChildGroup(Group group, String name){
List<HObject> memberList = group.getMemberList();
for (HObject member : memberList) {
if (member.getName().equals(name)){
if (member instanceof Group) {
return (Group)member;
}else{
throw new RuntimeException("expecting type Group for group member '"+name+"'");
}
}
}
throw new RuntimeException("child group '"+name+"' not found");
}

private static DataColumn[] getDataTable(Group group, String name) throws Exception{
List<HObject> memberList = group.getMemberList();
for (HObject member : memberList) {
if (member.getName().equals(name)){
if (member instanceof H5CompoundDS) {
H5CompoundDS compoundDataSet = (H5CompoundDS) member;
Vector columnValueArrays = (Vector)compoundDataSet.read();
String[] columnNames = compoundDataSet.getMemberNames();
ArrayList<DataColumn> dataColumns = new ArrayList<DataColumn>();
for (int c=0;c<columnNames.length;c++){
Object column = columnValueArrays.get(c);
if (column instanceof int[]){
dataColumns.add(new IntColumn(columnNames[c], (int[])columnValueArrays.get(c)));
}else if (column instanceof double[]){
dataColumns.add(new DoubleColumn(columnNames[c], (double[])columnValueArrays.get(c)));
}else{
throw new RuntimeException("unexpected type '"+column.getClass().getName()+"' for group member '"+name+"'");
}
}
return dataColumns.toArray(new DataColumn[0]);
}else if (member instanceof H5ScalarDS){
H5ScalarDS compoundDataSet = (H5ScalarDS) member;
Object column = compoundDataSet.read();
if (column instanceof int[]){
return new DataColumn[] { new IntColumn("col", (int[])column) };
}else if (column instanceof double[]){
return new DataColumn[] { new DoubleColumn("col", (double[])column) };
}else if (column instanceof long[]){
return new DataColumn[] { new LongColumn("col", (long[])column) };
}else{
throw new RuntimeException("unexpected type '"+column.getClass().getName()+"' for group member '"+name+"'");
}
}else{
throw new RuntimeException("expecting type H5CompoundDS for group member '"+name+"', found type "+member.getClass().getName());
}
}
}
throw new RuntimeException("group member '"+name+"' not found");
}

private static Vect3D parseAttrString(String attrString, double defaultZ){
StringTokenizer st = new StringTokenizer(attrString, "{,} ");
List<Double> valueList = new ArrayList<Double>();
while (st.hasMoreTokens())
{
String token = st.nextToken();
valueList.add(Double.parseDouble(token));
}
if (valueList.size()==2){
return new Vect3D(valueList.get(0),valueList.get(1),defaultZ);
}else if (valueList.size()==3){
return new Vect3D(valueList.get(0),valueList.get(1),valueList.get(2));
}else{
throw new RuntimeException("cannot parse, unexpected array size "+valueList.size());
}
}
}
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