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bring together ASCIIExporter related HDF5 into ASCIIExporter
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@jcschaff
jcschaff committed Apr 26, 2024
1 parent b73a652 commit e4f983c
Showing 1 changed file with 125 additions and 10 deletions.
135 changes: 125 additions & 10 deletions vcell-core/src/main/java/cbit/vcell/export/server/ASCIIExporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,6 @@
import cbit.vcell.geometry.SinglePoint;
import cbit.vcell.math.VariableType;
import cbit.vcell.simdata.DataServerImpl;
import cbit.vcell.simdata.Hdf5Utils;
import cbit.vcell.simdata.OutputContext;
import cbit.vcell.simdata.ParticleDataBlock;
import cbit.vcell.simdata.SimDataBlock;
Expand Down Expand Up @@ -75,6 +74,122 @@ public ASCIIExporter(ExportServiceImpl exportServiceImpl){
this.exportServiceImpl = exportServiceImpl;
}

/**
* Insert a dataset at the specififed group where the data are doubles (as a java List)
*
* @param hdf5GroupID the id of the group to apply the dataset to
* @param dataspaceName name of the dataset
* @param dims dimentional meansurements
* @param data the data to fill the dataset
* @throws NullPointerException (unsure how this occurs)
* @throws HDF5Exception if the hdf5 library encounters something unusual
*/
public static void insertDoubles(int hdf5GroupID,String dataspaceName,long[] dims,List<Double> data) throws NullPointerException, HDF5Exception {
double[] hdfData = org.apache.commons.lang.ArrayUtils.toPrimitive(((ArrayList<Double>)data).toArray(new Double[0]));
int hdf5DataspaceID = H5.H5Screate_simple(dims.length, dims, null);
int hdf5DatasetID = H5.H5Dcreate(hdf5GroupID, dataspaceName,HDF5Constants.H5T_NATIVE_DOUBLE, hdf5DataspaceID,HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Dwrite_double(hdf5DatasetID, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, hdfData);
H5.H5Dclose(hdf5DatasetID);
H5.H5Sclose(hdf5DataspaceID);
}

/**
* Insert a dataset at the specififed group where the data are doubles (as an array)
*
* @param hdf5GroupID the id of the group to apply the dataset to
* @param dataspaceName name of the dataset
* @param dims dimentional meansurements
* @param data the data to fill the dataset
* @throws NullPointerException (unsure how this occurs)
* @throws HDF5Exception if the hdf5 library encounters something unusual
*/
public static void insertDoubles(int hdf5GroupID,String dataspaceName,long[] dims,double[] data) throws NullPointerException, HDF5Exception {
int hdf5DataspaceID = H5.H5Screate_simple(dims.length, dims, null);
int hdf5DatasetID = H5.H5Dcreate(hdf5GroupID, dataspaceName,HDF5Constants.H5T_NATIVE_DOUBLE, hdf5DataspaceID,HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Dwrite_double(hdf5DatasetID, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, (double[])data);
H5.H5Dclose(hdf5DatasetID);
H5.H5Sclose(hdf5DataspaceID);
}

/**
* Insert a dataset at the specififed group where the data are integers
*
* @param hdf5GroupID the id of the group to apply the dataset to
* @param dataspaceName name of the dataset
* @param dims dimentional meansurements
* @param data the data to fill the dataset
* @throws NullPointerException (unsure how this occurs)
* @throws HDF5Exception if the hdf5 library encounters something unusual
*/
public static void insertInts(int hdf5GroupID,String dataspaceName,long[] dims,int[] data) throws NullPointerException, HDF5Exception {
int hdf5DataspaceID = H5.H5Screate_simple(dims.length, dims, null);
int hdf5DatasetID = H5.H5Dcreate(hdf5GroupID, dataspaceName,HDF5Constants.H5T_NATIVE_INT, hdf5DataspaceID,HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Dwrite_int(hdf5DatasetID, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, (int[])data);
H5.H5Dclose(hdf5DatasetID);
H5.H5Sclose(hdf5DataspaceID);
}

/**
* Insert a dataset at the specififed group where the data are strings
*
* @param hdf5GroupID the id of the group to apply the dataset to
* @param datasetName name of the dataset
* @param dims dimentional meansurements
* @param data the data to fill the dataset
* @throws NullPointerException (unsure how this occurs)
* @throws HDF5Exception if the hdf5 library encounters something unusual
*/
public static void insertStrings(int hdf5GroupID,String datasetName,long[] dims,List<String> data) throws NullPointerException, HDF5Exception {
int largestStrLen = 0;
for(int i=0;i<data.size();i++) {
largestStrLen = Math.max(largestStrLen, data.get(i).length());
}
byte[] bytes = new byte[largestStrLen*data.size()];
int index = 0;
for(int i=0;i<data.size();i++) {
System.arraycopy(data.get(i).getBytes(), 0, bytes, index, data.get(i).length());
index+= largestStrLen;
}
int h5tcs1 = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
H5.H5Tset_size(h5tcs1, largestStrLen);
int hdf5DataspaceID = H5.H5Screate_simple(dims.length, dims, null);
int hdf5DatasetID = H5.H5Dcreate(hdf5GroupID, datasetName,h5tcs1, hdf5DataspaceID,HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
//final byte[] bytes = allStringSB.toString().getBytes();
H5.H5Dwrite(hdf5DatasetID, h5tcs1, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, bytes);
H5.H5Tclose(h5tcs1);
H5.H5Dclose(hdf5DatasetID);
H5.H5Sclose(hdf5DataspaceID);
}

/**
* Insert an attribute at the specified group where the data are a single value
*
* @param hdf5GroupID the id of the group to apply the attribute to
* @param attributeName name of the attribute
* @param data the data to place
* @throws NullPointerException (unsure how this occurs)
* @throws HDF5Exception if the hdf5 library encounters something unusual
*/
public static void insertAttribute(int hdf5GroupID,String attributeName,String data) throws NullPointerException, HDF5Exception {
//insertAttributes(hdf5GroupID, dataspaceName, new ArrayList<String>(Arrays.asList(new String[] {data})));
//String[] attr = data.toArray(new String[0]);

String attr = data + '\u0000';

//https://support.hdfgroup.org/ftp/HDF5/examples/misc-examples/vlstra.c
int h5attrcs1 = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
H5.H5Tset_size (h5attrcs1, attr.length() /*HDF5Constants.H5T_VARIABLE*/);
int dataspace_id = -1;
//dataspace_id = H5.H5Screate_simple(dims.length, dims,null);
dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
int attribute_id = H5.H5Acreate(hdf5GroupID, attributeName, h5attrcs1, dataspace_id, HDF5Constants.H5P_DEFAULT,HDF5Constants.H5P_DEFAULT);
H5.H5Awrite(attribute_id, h5attrcs1, attr.getBytes());
H5.H5Sclose(dataspace_id);
H5.H5Aclose(attribute_id);
H5.H5Tclose(h5attrcs1);
}


/**
* @throws IOException
* @deprecated
Expand Down Expand Up @@ -531,8 +646,8 @@ private List<ExportOutput> exportPDEData(OutputContext outputContext, long jobID
for(int st = beginTimeIndex; st <= endTimeIndex; st++){
subTimes[st - beginTimeIndex] = allTimes[st];
}
Hdf5Utils.insertDoubles(hdf5GroupID, PCS.TIMES.name(), new long[]{subTimes.length}, subTimes);//Hdf5Utils.writeHDF5Dataset(hdf5GroupID, PCS.TIMES.name(), new long[] {subTimes.length}, subTimes,false);
Hdf5Utils.insertInts(hdf5GroupID, PCS.TIMEBOUNDS.name(), new long[]{2}, new int[]{beginTimeIndex, endTimeIndex});//Hdf5Utils.writeHDF5Dataset(hdf5GroupID, PCS.TIMEBOUNDS.name(), new long[] {2}, new int[] {beginTimeIndex,endTimeIndex},false);
insertDoubles(hdf5GroupID, PCS.TIMES.name(), new long[]{subTimes.length}, subTimes);//UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupID, PCS.TIMES.name(), new long[] {subTimes.length}, subTimes,false);
insertInts(hdf5GroupID, PCS.TIMEBOUNDS.name(), new long[]{2}, new int[]{beginTimeIndex, endTimeIndex});//UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupID, PCS.TIMEBOUNDS.name(), new long[] {2}, new int[] {beginTimeIndex,endTimeIndex},false);
}

switch(geometrySpecs.getModeID()){
Expand Down Expand Up @@ -846,20 +961,20 @@ private FileDataContainerID getCurveTimeSeries(int hdf5GroupVarID, PointsCurvesS
if(hdf5GroupVarID != -1){
try {
int hdf5GroupCurveID = H5.H5Gcreate(hdf5GroupVarID, getSpatialSelectionDescription(curve), HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
Hdf5Utils.insertInts(hdf5GroupCurveID, PCS.CURVEINDEXES.name(), new long[]{((int[]) treePCS.get(PCS.CURVEINDEXES)).length}, (int[]) treePCS.get(PCS.CURVEINDEXES));//Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEINDEXES.name(), new long[] {((int[])treePCS.get(PCS.CURVEINDEXES)).length}, (int[])treePCS.get(PCS.CURVEINDEXES),false);
Hdf5Utils.insertDoubles(hdf5GroupCurveID, PCS.CURVEDISTANCES.name(), new long[]{((double[]) treePCS.get(PCS.CURVEDISTANCES)).length}, (double[]) treePCS.get(PCS.CURVEDISTANCES));//Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEDISTANCES.name(), new long[] {((double[])treePCS.get(PCS.CURVEDISTANCES)).length}, (double[])treePCS.get(PCS.CURVEDISTANCES),false);
insertInts(hdf5GroupCurveID, PCS.CURVEINDEXES.name(), new long[]{((int[]) treePCS.get(PCS.CURVEINDEXES)).length}, (int[]) treePCS.get(PCS.CURVEINDEXES));//UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEINDEXES.name(), new long[] {((int[])treePCS.get(PCS.CURVEINDEXES)).length}, (int[])treePCS.get(PCS.CURVEINDEXES),false);
insertDoubles(hdf5GroupCurveID, PCS.CURVEDISTANCES.name(), new long[]{((double[]) treePCS.get(PCS.CURVEDISTANCES)).length}, (double[]) treePCS.get(PCS.CURVEDISTANCES));//UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEDISTANCES.name(), new long[] {((double[])treePCS.get(PCS.CURVEDISTANCES)).length}, (double[])treePCS.get(PCS.CURVEDISTANCES),false);
if(treePCS.get(PCS.CURVECROSSMEMBRINDEX) != null){
Hdf5Utils.insertInts(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name(), new long[]{((int[]) treePCS.get(PCS.CURVECROSSMEMBRINDEX)).length}, (int[]) treePCS.get(PCS.CURVECROSSMEMBRINDEX));//Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name(), new long[] {((int[])treePCS.get(PCS.CURVECROSSMEMBRINDEX)).length}, (int[])treePCS.get(PCS.CURVECROSSMEMBRINDEX),false);
insertInts(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name(), new long[]{((int[]) treePCS.get(PCS.CURVECROSSMEMBRINDEX)).length}, (int[]) treePCS.get(PCS.CURVECROSSMEMBRINDEX));//UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name(), new long[] {((int[])treePCS.get(PCS.CURVECROSSMEMBRINDEX)).length}, (int[])treePCS.get(PCS.CURVECROSSMEMBRINDEX),false);
ArrayList<Integer> crossPoints = new ArrayList<Integer>();
for(int i = 0; i < crossingMembraneIndexes.length; i++){
if(crossingMembraneIndexes[i] != -1){
crossPoints.add(i);
}
}
String attrText = PCS.CURVEVALS.name() + " columns " + crossPoints.get(0) + " and " + crossPoints.get(1) + " are added points of interpolation near membrane";
Hdf5Utils.insertAttribute(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name() + " Info", attrText); //Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name()+" Info", null, attrText,true);
insertAttribute(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name() + " Info", attrText); //UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name()+" Info", null, attrText,true);
}
Hdf5Utils.insertDoubles(hdf5GroupCurveID, PCS.CURVEVALS.name(), new long[]{endIndex - beginIndex + 1, ((int[]) treePCS.get(PCS.CURVEINDEXES)).length}, (ArrayList<Double>) treePCS.get(PCS.CURVEVALS));//Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEVALS.name(), new long[] {endIndex-beginIndex+1,((int[])treePCS.get(PCS.CURVEINDEXES)).length}, (ArrayList<Double>)treePCS.get(PCS.CURVEVALS),false);
insertDoubles(hdf5GroupCurveID, PCS.CURVEVALS.name(), new long[]{endIndex - beginIndex + 1, ((int[]) treePCS.get(PCS.CURVEINDEXES)).length}, (ArrayList<Double>) treePCS.get(PCS.CURVEVALS));//UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEVALS.name(), new long[] {endIndex-beginIndex+1,((int[])treePCS.get(PCS.CURVEINDEXES)).length}, (ArrayList<Double>)treePCS.get(PCS.CURVEVALS),false);
H5.H5Gclose(hdf5GroupCurveID);
} catch(Exception e){
throw new DataAccessException(e.getMessage(), e);
Expand Down Expand Up @@ -1054,9 +1169,9 @@ private FileDataContainerID getPointsTimeSeries(PointsCurvesSlices pcs, int hdf5
}
if(hdf5GroupID != -1){
long[] dimsCoord = new long[]{1, pointSpatialSelections.length};
Hdf5Utils.insertStrings(hdf5GroupID, PCS.POINTINFO.name(), dimsCoord, (ArrayList<String>) pcs.data.get(PCS.POINTINFO));//Hdf5Utils.writeHDF5Dataset(hdf5GroupID, PCS.POINTINFO.name(), dimsCoord, pcs.data.get(PCS.POINTINFO),false);
insertStrings(hdf5GroupID, PCS.POINTINFO.name(), dimsCoord, (ArrayList<String>) pcs.data.get(PCS.POINTINFO));//UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupID, PCS.POINTINFO.name(), dimsCoord, pcs.data.get(PCS.POINTINFO),false);
long[] dimsValues = new long[]{hdfTimes.length, pointSpatialSelections.length};
Hdf5Utils.insertDoubles(hdf5GroupID, PCS.POINTVALS.name(), dimsValues, hdfValues);//Hdf5Utils.writeHDF5Dataset(hdf5GroupID, PCS.POINTVALS.name(), dimsValues, hdfValues,false);
insertDoubles(hdf5GroupID, PCS.POINTVALS.name(), dimsValues, hdfValues);//UiTableExporterToHDF5.writeHDF5Dataset(hdf5GroupID, PCS.POINTVALS.name(), dimsValues, hdfValues,false);
}
}

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