neurord.numeric.grid

Class ResultWriterHDF5

java.lang.Object

neurord.numeric.grid.ResultWriterHDF5

All Implemented Interfaces:

ResultWriter

public class ResultWriterHDF5
extends Object
implements ResultWriter

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ResultWriterHDF5.LoadModelResult
protected class	ResultWriterHDF5.PopulationOutput
protected class	ResultWriterHDF5.Trial

Field Summary

Fields

Modifier and Type	Field and Description
static hdf.object.h5.H5Datatype	double_t
static hdf.object.h5.H5Datatype	int_t
static org.apache.logging.log4j.Logger	log
static hdf.object.h5.H5Datatype	long_t
protected hdf.object.Group	model
protected hdf.object.h5.H5File	output
protected File	outputFile
protected hdf.object.Group	root
static hdf.object.h5.H5Datatype	short_str_t
protected Map<Integer,ResultWriterHDF5.Trial>	trials

Constructor Summary

Constructors

Constructor and Description
ResultWriterHDF5(File output, IOutputSet primary, List<? extends IOutputSet> outputSets, String[] species, VolumeGrid grid)

Method Summary

Modifier and Type	Method and Description
protected void	_init()
protected static ResultWriterHDF5.LoadModelResult	_loadModel(File filename, int trial, Double pop_from_time)
protected hdf.object.Dataset	_writeArray(String name, hdf.object.Group parent, hdf.object.h5.H5Datatype type, long[] dims, Object data)
protected void	_writeGrid(VolumeGrid vgrid, double startTime, IGridCalc source)
void	close()
void	closeTrial(IGridCalc source)
protected void	closeTrial(int trial, IGridCalc source)
protected hdf.object.h5.H5ScalarDS	createExtensibleArray(String name, hdf.object.Group parent, hdf.object.Datatype type, String TITLE, String LAYOUT, String UNITS, long... dims)
protected ResultWriterHDF5.Trial	createTrial(int trial)
protected static void	extendExtensibleArray(hdf.object.h5.H5ScalarDS ds, long howmuch)
protected static <T> T	getAttribute(hdf.object.h5.H5File h5, String path, String name)
protected static void	getGridNumbers(int[][] dst, int[] elements, int[] ispecout, IGridCalc source)
protected ResultWriterHDF5.Trial	getTrial(int trial)
void	init(String magic)
static ResultWriterHDF5.LoadModelResult	loadModel(File filename, int trial, double pop_from_time)
protected hdf.object.Group	model()
File	outputFile()
protected static void	setAttribute(hdf.object.HObject obj, String name, long value)
protected static void	setAttribute(hdf.object.HObject obj, String name, String value) Utility functions ******************
protected hdf.object.Dataset	writeArray(String name, hdf.object.Group parent, double[][] items)
protected hdf.object.Dataset	writeArray(String name, hdf.object.Group parent, int[][] items, int fill)
void	writeEventStatistics(double time, IGridCalc source)
void	writeGrid(VolumeGrid vgrid, double startTime, IGridCalc source)
protected void	writeManifest()
protected void	writeMap(hdf.object.Group element, Set<Map.Entry<Object,Object>> set)
void	writeOutputInterval(double time, IGridCalc source)
void	writeOutputScheme(int i, double time, IGridCalc source)
protected void	writeSpeciesVector(String name, String title, hdf.object.Group parent, String[] species, int[] which)
protected hdf.object.Dataset	writeVector(String name, hdf.object.Group parent, double... items)
protected hdf.object.Dataset	writeVector(String name, hdf.object.Group parent, int... items)
protected hdf.object.Dataset	writeVector(String name, hdf.object.Group parent, long... items)
protected hdf.object.Dataset	writeVector(String name, hdf.object.Group parent, String... items)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log

public static final org.apache.logging.log4j.Logger log

outputFile

protected final File outputFile

output

protected hdf.object.h5.H5File output

root

protected hdf.object.Group root

trials

protected final Map<Integer,ResultWriterHDF5.Trial> trials

double_t

public static final hdf.object.h5.H5Datatype double_t

int_t

public static final hdf.object.h5.H5Datatype int_t

long_t

public static final hdf.object.h5.H5Datatype long_t

short_str_t

public static final hdf.object.h5.H5Datatype short_str_t

model

protected hdf.object.Group model

Constructor Detail

ResultWriterHDF5

public ResultWriterHDF5(File output,
                        IOutputSet primary,
                        List<? extends IOutputSet> outputSets,
                        String[] species,
                        VolumeGrid grid)

Method Detail

init

public void init(String magic)

Specified by:

init in interface ResultWriter

_init

protected void _init()
              throws Exception

Throws:

Exception

close

public void close()

Specified by:

close in interface ResultWriter

outputFile

public File outputFile()

Specified by:

outputFile in interface ResultWriter

writeManifest

protected void writeManifest()
                      throws Exception

Throws:

Exception

model

protected hdf.object.Group model()
                          throws Exception

Throws:

Exception

getTrial

protected ResultWriterHDF5.Trial getTrial(int trial)
                                   throws Exception

Throws:

Exception

createTrial

protected ResultWriterHDF5.Trial createTrial(int trial)
                                      throws Exception

Throws:

Exception

closeTrial

protected void closeTrial(int trial,
                          IGridCalc source)
                   throws Exception

Throws:

Exception

closeTrial

public void closeTrial(IGridCalc source)

Specified by:

closeTrial in interface ResultWriter

writeGrid

public void writeGrid(VolumeGrid vgrid,
                      double startTime,
                      IGridCalc source)

Specified by:

writeGrid in interface ResultWriter

_writeGrid

protected void _writeGrid(VolumeGrid vgrid,
                          double startTime,
                          IGridCalc source)
                   throws Exception

Throws:

Exception

writeOutputInterval

public void writeOutputInterval(double time,
                                IGridCalc source)

Specified by:

writeOutputInterval in interface ResultWriter

writeOutputScheme

public void writeOutputScheme(int i,
                              double time,
                              IGridCalc source)

Specified by:

writeOutputScheme in interface ResultWriter

writeEventStatistics

public void writeEventStatistics(double time,
                                 IGridCalc source)

Specified by:

writeEventStatistics in interface ResultWriter

_loadModel

protected static ResultWriterHDF5.LoadModelResult _loadModel(File filename,
                                                             int trial,
                                                             Double pop_from_time)
                                                      throws Exception

Throws:

Exception

loadModel

public static ResultWriterHDF5.LoadModelResult loadModel(File filename,
                                                         int trial,
                                                         double pop_from_time)

setAttribute

protected static void setAttribute(hdf.object.HObject obj,
                                   String name,
                                   String value)
                            throws Exception

Utility functions ******************

Throws:

Exception

setAttribute

protected static void setAttribute(hdf.object.HObject obj,
                                   String name,
                                   long value)
                            throws Exception

Throws:

Exception

getAttribute

protected static <T> T getAttribute(hdf.object.h5.H5File h5,
                                    String path,
                                    String name)
                             throws Exception

Throws:

Exception

_writeArray

protected hdf.object.Dataset _writeArray(String name,
                                         hdf.object.Group parent,
                                         hdf.object.h5.H5Datatype type,
                                         long[] dims,
                                         Object data)
                                  throws Exception

Throws:

Exception

writeArray

protected hdf.object.Dataset writeArray(String name,
                                        hdf.object.Group parent,
                                        double[][] items)
                                 throws Exception

Throws:

Exception

writeArray

protected hdf.object.Dataset writeArray(String name,
                                        hdf.object.Group parent,
                                        int[][] items,
                                        int fill)
                                 throws Exception

Throws:

Exception

writeVector

protected hdf.object.Dataset writeVector(String name,
                                         hdf.object.Group parent,
                                         String... items)
                                  throws Exception

Throws:

Exception

writeMap

protected void writeMap(hdf.object.Group element,
                        Set<Map.Entry<Object,Object>> set)
                 throws Exception

Throws:

Exception

writeVector

protected hdf.object.Dataset writeVector(String name,
                                         hdf.object.Group parent,
                                         double... items)
                                  throws Exception

Throws:

Exception

writeVector

protected hdf.object.Dataset writeVector(String name,
                                         hdf.object.Group parent,
                                         int... items)
                                  throws Exception

Throws:

Exception

writeVector

protected hdf.object.Dataset writeVector(String name,
                                         hdf.object.Group parent,
                                         long... items)
                                  throws Exception

Throws:

Exception

writeSpeciesVector

protected void writeSpeciesVector(String name,
                                  String title,
                                  hdf.object.Group parent,
                                  String[] species,
                                  int[] which)
                           throws Exception

Throws:

Exception

createExtensibleArray

protected hdf.object.h5.H5ScalarDS createExtensibleArray(String name,
                                                         hdf.object.Group parent,
                                                         hdf.object.Datatype type,
                                                         String TITLE,
                                                         String LAYOUT,
                                                         String UNITS,
                                                         long... dims)
                                                  throws Exception

Throws:

Exception

extendExtensibleArray

protected static void extendExtensibleArray(hdf.object.h5.H5ScalarDS ds,
                                            long howmuch)
                                     throws Exception

Throws:

Exception

getGridNumbers

protected static void getGridNumbers(int[][] dst,
                                     int[] elements,
                                     int[] ispecout,
                                     IGridCalc source)