diff --git a/Source/Processors/HDF5FileFormat.cpp b/Source/Processors/HDF5FileFormat.cpp
index edba56d73f0ef10b1d107fb28525d580ed36aceb..151dd915bb0a2969d3cf1ce7d292cf9fd7b62bfb 100644
--- a/Source/Processors/HDF5FileFormat.cpp
+++ b/Source/Processors/HDF5FileFormat.cpp
@@ -24,18 +24,10 @@
#include <H5Cpp.h>
#include "HDF5FileFormat.h"
-#ifndef BLOCK_XSIZE
-#define BLOCK_XSIZE 256
-#endif
-
#ifndef CHUNK_XSIZE
#define CHUNK_XSIZE 256
#endif
-#ifndef EVENT_BLOCK_XSIZE
-#define EVENT_BLOCK_XSIZE 8
-#endif
-
#ifndef EVENT_CHUNK_SIZE
#define EVENT_CHUNK_SIZE 8
#endif
@@ -230,24 +222,56 @@ HDF5RecordingData* HDF5FileBase::getDataSet(String path)
}
}
+HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int chunkX, String path)
+{
+ return createDataSet(type,1,&sizeX,chunkX,path);
+}
+
HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int sizeY, int chunkX, String path)
+{
+ int size[2];
+ size[0] = sizeX;
+ size[1] = sizeY;
+ return createDataSet(type,2,size,chunkX,path);
+}
+
+HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int sizeY, int sizeZ, int chunkX, String path)
+{
+ int size[3];
+ size[0] = sizeX;
+ size[1] = sizeY;
+ size[2] = sizeZ;
+ return createDataSet(type,2,size,chunkX,path);
+}
+
+HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int dimension, int* size, int chunkX, String path)
{
ScopedPointer<DataSet> data;
DSetCreatPropList prop;
if (!opened) return nullptr;
DataType H5type = getH5Type(type);
- hsize_t dims[2], chunk_dims[2], max_dims[2];
- dims[0] = sizeX;
- dims[1] = sizeY;
+ hsize_t dims[3], chunk_dims[3], max_dims[3];
+ dims[0] = size[0];
chunk_dims[0] = chunkX;
- chunk_dims[1] = sizeY;
max_dims[0] = H5S_UNLIMITED;
- max_dims[1] = sizeY;
+ if (dimension > 1)
+ {
+ dims[1] = size[1];
+ chunk_dims[1] = size[1];
+ max_dims[1] = size[1];
+ }
+ if (dimension > 2)
+ {
+ dims[2] = size[2];
+ chunk_dims[2] = size[2];
+ max_dims[2] = size[2];
+ }
+
try {
- DataSpace dSpace(2,dims,max_dims);
- prop.setChunk(2,chunk_dims);
+ DataSpace dSpace(dimension,dims,max_dims);
+ prop.setChunk(dimension,chunk_dims);
data = new DataSet(file->createDataSet(path.toUTF8(),H5type,dSpace,prop));
return new HDF5RecordingData(data.release());
@@ -334,18 +358,26 @@ HDF5RecordingData::HDF5RecordingData(DataSet *data)
DataSpace dSpace;
DSetCreatPropList prop;
ScopedPointer<DataSet> dSet = data;
- hsize_t dims[2], chunk[2];
+ hsize_t dims[3], chunk[3];
dSpace = dSet->getSpace();
prop = dSet->getCreatePlist();
- dSpace.getSimpleExtentDims(dims);
- prop.getChunk(2,chunk);
+ dimension = dSpace.getSimpleExtentDims(dims);
+ prop.getChunk(dimension,chunk);
+
+ this->size[0] = dims[0];
+ if (dimension > 1)
+ this->size[1] = dims[1];
+ else
+ this->size[1] = 1;
+ if (dimension > 1)
+ this->size[2] = dims[2];
+ else
+ this->size[2] = 1;
- this->xSize = dims[0];
- this->ySize = dims[1];
this->xChunkSize = chunk[0];
- this->xPos = 0;
+ this->xPos = dims[0];
this->dSet = dSet;
this->rowXPos = 0;
this->rowDataSize = 0;
@@ -357,11 +389,12 @@ HDF5RecordingData::~HDF5RecordingData()
int HDF5RecordingData::writeDataBlock(int xDataSize, HDF5FileBase::DataTypes type, void* data)
{
- hsize_t dim[2],offset[2];
+ hsize_t dim[3],offset[3];
DataSpace fSpace;
DataType nativeType;
- dim[1] = ySize;
+ dim[2] = size[2];
+ dim[1] = size[1];
dim[0] = xPos + xDataSize;
try {
//First be sure that we have enough space
@@ -369,16 +402,18 @@ int HDF5RecordingData::writeDataBlock(int xDataSize, HDF5FileBase::DataTypes typ
fSpace = dSet->getSpace();
fSpace.getSimpleExtentDims(dim);
- xSize=dim[0];
+ size[0]=dim[0];
//Create memory space
dim[0]=xDataSize;
- dim[1]=ySize;
- DataSpace mSpace(2,dim);
+ dim[1]=size[1];
+ dim[2] = size[2];
+ DataSpace mSpace(dimension,dim);
//select where to write
offset[0]=xPos;
offset[1]=0;
+ offset[2]=0;
fSpace.selectHyperslab(H5S_SELECT_SET, dim, offset);
nativeType = HDF5FileBase::getNativeType(type);
@@ -399,17 +434,18 @@ int HDF5RecordingData::writeDataBlock(int xDataSize, HDF5FileBase::DataTypes typ
int HDF5RecordingData::prepareDataBlock(int xDataSize)
{
- hsize_t dim[2];
+ hsize_t dim[3];
DataSpace fSpace;
- dim[1] = ySize;
+ dim[2] = size[2];
+ dim[1] = size[1];
dim[0] = xPos + xDataSize;
try{
dSet->extend(dim);
fSpace = dSet->getSpace();
fSpace.getSimpleExtentDims(dim);
- xSize=dim[0];
+ size[0]=dim[0];
}
catch(DataSetIException error)
{
@@ -426,13 +462,14 @@ int HDF5RecordingData::writeDataRow(int yPos, int xDataSize, HDF5FileBase::DataT
hsize_t dim[2],offset[2];
DataSpace fSpace;
DataType nativeType;
+ if (dimension > 2) return -4; //We're not going to write rows in datasets bigger than 2d.
if (xDataSize != rowDataSize) return -2;
- if ((yPos < 0 ) || (yPos >= ySize)) return -3;
+ if ((yPos < 0 ) || (yPos >= size[1])) return -3;
try {
dim[0] = xDataSize;
dim[1] = 1;
- DataSpace mSpace(2,dim);
+ DataSpace mSpace(dimension,dim);
fSpace = dSet->getSpace();
offset[0] = rowXPos;
@@ -492,11 +529,11 @@ void KWDFile::startNewRecording(int recordingNumber, int nChannels, HDF5Recordin
String recordPath = String("/recordings/")+String(recordingNumber);
CHECK_ERROR(createGroup(recordPath));
CHECK_ERROR(setAttributeStr(info->name,recordPath,String("name")));
- CHECK_ERROR(setAttribute(I64,&(info->start_time),recordPath,String("start_time")));
+ CHECK_ERROR(setAttribute(U64,&(info->start_time),recordPath,String("start_time")));
// CHECK_ERROR(setAttribute(U32,&(info->start_sample),recordPath,String("start_sample")));
CHECK_ERROR(setAttribute(F32,&(info->sample_rate),recordPath,String("sample_rate")));
CHECK_ERROR(setAttribute(U32,&(info->bit_depth),recordPath,String("bit_depth")));
- recdata = createDataSet(I16,BLOCK_XSIZE,nChannels,CHUNK_XSIZE,recordPath+"/data");
+ recdata = createDataSet(I16,0,nChannels,CHUNK_XSIZE,recordPath+"/data");
if (!recdata.get())
std::cerr << "Error creating data set" << std::endl;
curChan = nChannels;
@@ -570,9 +607,9 @@ int KWIKFile::createFileStructure()
if(createGroup(path)) return -1;
path += "/events";
if(createGroup(path)) return -1;
- dSet = createDataSet(U64,EVENT_BLOCK_XSIZE,1,EVENT_BLOCK_XSIZE,path + "/time_samples");
+ dSet = createDataSet(U64,0,EVENT_CHUNK_SIZE,path + "/time_samples");
if (!dSet) return -1;
- dSet = createDataSet(U16,EVENT_BLOCK_XSIZE,1,EVENT_BLOCK_XSIZE,path + "/recording");
+ dSet = createDataSet(U16,0,EVENT_CHUNK_SIZE,path + "/recording");
if (!dSet) return -1;
}
if(setAttribute(U16,(void*)&ver,"/","kwik_version")) return -1;
@@ -586,7 +623,7 @@ void KWIKFile::startNewRecording(int recordingNumber, HDF5RecordingInfo* info)
String recordPath = String("/recordings/")+String(recordingNumber);
CHECK_ERROR(createGroup(recordPath));
CHECK_ERROR(setAttributeStr(info->name,recordPath,String("name")));
- CHECK_ERROR(setAttribute(I64,&(info->start_time),recordPath,String("start_time")));
+ CHECK_ERROR(setAttribute(U64,&(info->start_time),recordPath,String("start_time")));
// CHECK_ERROR(setAttribute(U32,&(info->start_sample),recordPath,String("start_sample")));
CHECK_ERROR(setAttribute(F32,&(info->sample_rate),recordPath,String("sample_rate")));
CHECK_ERROR(setAttribute(U32,&(info->bit_depth),recordPath,String("bit_depth")));
diff --git a/Source/Processors/HDF5FileFormat.h b/Source/Processors/HDF5FileFormat.h
index a5cda0ff9cf88480d4cd6efa92e04eea3659c164..a17396bec9467b67615e8d2f3d06b04bee55dd8d 100644
--- a/Source/Processors/HDF5FileFormat.h
+++ b/Source/Processors/HDF5FileFormat.h
@@ -67,7 +67,11 @@ protected:
HDF5RecordingData* getDataSet(String path);
//create dataset extendable on X dimension.
+ HDF5RecordingData* createDataSet(DataTypes type, int dimension, int* size, int chunkX, String path);
+ //Easier aliases
+ HDF5RecordingData* createDataSet(DataTypes type, int sizeX, int chunkX, String path);
HDF5RecordingData* createDataSet(DataTypes type, int sizeX, int sizeY, int chunkX, String path);
+ HDF5RecordingData* createDataSet(DataTypes type, int sizeX, int sizeY, int sizeZ, int chunkX, String path);
bool readyToOpen;
@@ -93,8 +97,8 @@ public:
private:
int xPos;
int xChunkSize;
- int ySize;
- int xSize;
+ int size[3];
+ int dimension;
int rowXPos;
int rowDataSize;
ScopedPointer<H5::DataSet> dSet;