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Commit 42e357bf authored by Aaron Cuevas Lopez's avatar Aaron Cuevas Lopez
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Generalize hdf5 types

parent 7986d2fc
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Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.cpp
+ 133
− 86
View file @ 42e357bf
...@@ -111,13 +111,13 @@ void HDF5FileBase::close() ...@@ -111,13 +111,13 @@ void HDF5FileBase::close()
opened = false; opened = false;
} }
int HDF5FileBase::setAttribute(DataTypes type, const void* data, String path, String name) int HDF5FileBase::setAttribute(BaseDataType type, const void* data, String path, String name)
{ {
return setAttributeArray(type, data, 1, path, name); return setAttributeArray(type, data, 1, path, name);
} }
int HDF5FileBase::setAttributeArray(DataTypes type, const void* data, int size, String path, String name) int HDF5FileBase::setAttributeArray(BaseDataType type, const void* data, int size, String path, String name)
{ {
H5Location* loc; H5Location* loc;
Group gloc; Group gloc;
...@@ -335,13 +335,13 @@ HDF5RecordingData* HDF5FileBase::getDataSet(String path) ...@@ -335,13 +335,13 @@ HDF5RecordingData* HDF5FileBase::getDataSet(String path)
} }
} }
HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int chunkX, String path) HDF5RecordingData* HDF5FileBase::createDataSet(BaseDataType type, int sizeX, int chunkX, String path)
{ {
int chunks[3] = {chunkX, 0, 0}; int chunks[3] = {chunkX, 0, 0};
return createDataSet(type,1,&sizeX,chunks,path); return createDataSet(type,1,&sizeX,chunks,path);
} }
HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int sizeY, int chunkX, String path) HDF5RecordingData* HDF5FileBase::createDataSet(BaseDataType type, int sizeX, int sizeY, int chunkX, String path)
{ {
int size[2]; int size[2];
int chunks[3] = {chunkX, 0, 0}; int chunks[3] = {chunkX, 0, 0};
...@@ -350,7 +350,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si ...@@ -350,7 +350,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si
return createDataSet(type,2,size,chunks,path); return createDataSet(type,2,size,chunks,path);
} }
HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int sizeY, int sizeZ, int chunkX, String path) HDF5RecordingData* HDF5FileBase::createDataSet(BaseDataType type, int sizeX, int sizeY, int sizeZ, int chunkX, String path)
{ {
int size[3]; int size[3];
int chunks[3] = {chunkX, 0, 0}; int chunks[3] = {chunkX, 0, 0};
...@@ -360,7 +360,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si ...@@ -360,7 +360,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si
return createDataSet(type,3,size,chunks,path); return createDataSet(type,3,size,chunks,path);
} }
HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int sizeY, int sizeZ, int chunkX, int chunkY, String path) HDF5RecordingData* HDF5FileBase::createDataSet(BaseDataType type, int sizeX, int sizeY, int sizeZ, int chunkX, int chunkY, String path)
{ {
int size[3]; int size[3];
int chunks[3] = {chunkX, chunkY, 0}; int chunks[3] = {chunkX, chunkY, 0};
...@@ -370,7 +370,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si ...@@ -370,7 +370,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si
return createDataSet(type,3,size,chunks,path); return createDataSet(type,3,size,chunks,path);
} }
HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int dimension, int* size, int* chunking, String path) HDF5RecordingData* HDF5FileBase::createDataSet(BaseDataType type, int dimension, int* size, int* chunking, String path)
{ {
ScopedPointer<DataSet> data; ScopedPointer<DataSet> data;
DSetCreatPropList prop; DSetCreatPropList prop;
...@@ -426,88 +426,135 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int dimension, in ...@@ -426,88 +426,135 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int dimension, in
} }
H5::DataType HDF5FileBase::getNativeType(DataTypes type) H5::DataType HDF5FileBase::getNativeType(BaseDataType type)
{ {
switch (type) H5::DataType baseType;
{
case I8: switch (type.type)
return PredType::NATIVE_INT8; {
break; case BaseDataType::Type::T_I8:
case I16: baseType = PredType::NATIVE_INT8;
return PredType::NATIVE_INT16; break;
break; case BaseDataType::Type::T_I16:
case I32: baseType = PredType::NATIVE_INT16;
return PredType::NATIVE_INT32; break;
break; case BaseDataType::Type::T_I32:
case I64: baseType = PredType::NATIVE_INT32;
return PredType::NATIVE_INT64; break;
break; case BaseDataType::Type::T_I64:
case U8: baseType = PredType::NATIVE_INT64;
return PredType::NATIVE_UINT8; break;
break; case BaseDataType::Type::T_U8:
case U16: baseType = PredType::NATIVE_UINT8;
return PredType::NATIVE_UINT16; break;
break; case BaseDataType::Type::T_U16:
case U32: baseType = PredType::NATIVE_UINT16;
return PredType::NATIVE_UINT32; break;
break; case BaseDataType::Type::T_U32:
case U64: baseType = PredType::NATIVE_UINT32;
return PredType::NATIVE_UINT64; break;
break; case BaseDataType::Type::T_U64:
case F32: baseType = PredType::NATIVE_UINT64;
return PredType::NATIVE_FLOAT; break;
break; case BaseDataType::Type::T_F32:
case F64: baseType = PredType::NATIVE_FLOAT;
return PredType::NATIVE_DOUBLE; break;
break; case BaseDataType::Type::T_F64:
case STR: baseType = PredType::NATIVE_DOUBLE;
return StrType(PredType::C_S1,MAX_STR_SIZE); break;
break; case BaseDataType::Type::T_STR:
} return StrType(PredType::C_S1, type.typeSize);
return PredType::NATIVE_INT32; break;
default:
baseType = PredType::NATIVE_INT32;
}
if (type.typeSize > 1)
{
hsize_t size = type.typeSize;
return ArrayType(baseType, 1, &size);
}
else return baseType;
} }
H5::DataType HDF5FileBase::getH5Type(DataTypes type) H5::DataType HDF5FileBase::getH5Type(BaseDataType type)
{ {
switch (type) H5::DataType baseType;
{
case I8: switch (type.type)
return PredType::STD_I8LE; {
break; case BaseDataType::Type::T_I8:
case I16: baseType = PredType::STD_I8LE;
return PredType::STD_I16LE; break;
break; case BaseDataType::Type::T_I16:
case I32: baseType = PredType::STD_I16LE;
return PredType::STD_I32LE; break;
break; case BaseDataType::Type::T_I32:
case I64: baseType = PredType::STD_I32LE;
return PredType::STD_I64LE; break;
break; case BaseDataType::Type::T_I64:
case U8: baseType = PredType::STD_I64LE;
return PredType::STD_U8LE; break;
break; case BaseDataType::Type::T_U8:
case U16: baseType = PredType::STD_U8LE;
return PredType::STD_U16LE; break;
break; case BaseDataType::Type::T_U16:
case U32: baseType = PredType::STD_U16LE;
return PredType::STD_U32LE; break;
break; case BaseDataType::Type::T_U32:
case U64: baseType = PredType::STD_U32LE;
return PredType::STD_U64LE; break;
break; case BaseDataType::Type::T_U64:
case F32: baseType = PredType::STD_U64LE;
return PredType::IEEE_F32LE; break;
break; case BaseDataType::Type::T_F32:
case F64: return PredType::IEEE_F32LE;
return PredType::IEEE_F64LE; break;
break; case BaseDataType::Type::T_F64:
case STR: baseType = PredType::IEEE_F64LE;
return StrType(PredType::C_S1,MAX_STR_SIZE); break;
break; case BaseDataType::Type::T_STR:
} return StrType(PredType::C_S1, type.typeSize);
return PredType::STD_I32LE; break;
default:
return PredType::STD_I32LE;
}
if (type.typeSize > 1)
{
hsize_t size = type.typeSize;
return ArrayType(baseType, 1, &size);
}
else return baseType;
} }
//BaseDataType
HDF5FileBase::BaseDataType::BaseDataType(HDF5FileBase::BaseDataType::Type t, size_t s)
: type(t), typeSize(s)
{}
HDF5FileBase::BaseDataType::BaseDataType()
: type(T_I32), typeSize(1)
{}
HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::STR(size_t size)
{
return HDF5FileBase::BaseDataType(T_STR, size);
}
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::U8 = HDF5FileBase::BaseDataType(T_U8, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::U16 = HDF5FileBase::BaseDataType(T_U16, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::U32 = HDF5FileBase::BaseDataType(T_U32, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::U64 = HDF5FileBase::BaseDataType(T_U64, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::I8 = HDF5FileBase::BaseDataType(T_I8, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::I16 = HDF5FileBase::BaseDataType(T_I16, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::I32 = HDF5FileBase::BaseDataType(T_I32, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::I64 = HDF5FileBase::BaseDataType(T_I64, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::F32 = HDF5FileBase::BaseDataType(T_F32, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::F64 = HDF5FileBase::BaseDataType(T_F64, 1);
const HDF5FileBase::BaseDataType HDF5FileBase::BaseDataType::DSTR = HDF5FileBase::BaseDataType(T_STR, DEFAULT_STR_SIZE);
//H5RecordingData
HDF5RecordingData::HDF5RecordingData(DataSet* data) HDF5RecordingData::HDF5RecordingData(DataSet* data)
{ {
DataSpace dSpace; DataSpace dSpace;
...@@ -543,12 +590,12 @@ HDF5RecordingData::~HDF5RecordingData() ...@@ -543,12 +590,12 @@ HDF5RecordingData::~HDF5RecordingData()
//Safety //Safety
dSet->flush(H5F_SCOPE_GLOBAL); dSet->flush(H5F_SCOPE_GLOBAL);
} }
int HDF5RecordingData::writeDataBlock(int xDataSize, HDF5FileBase::DataTypes type, const void* data) int HDF5RecordingData::writeDataBlock(int xDataSize, HDF5FileBase::BaseDataType type, const void* data)
{ {
return writeDataBlock(xDataSize,size[1],type,data); return writeDataBlock(xDataSize,size[1],type,data);
} }
int HDF5RecordingData::writeDataBlock(int xDataSize, int yDataSize, HDF5FileBase::DataTypes type, const void* data) int HDF5RecordingData::writeDataBlock(int xDataSize, int yDataSize, HDF5FileBase::BaseDataType type, const void* data)
{ {
hsize_t dim[3],offset[3]; hsize_t dim[3],offset[3];
DataSpace fSpace; DataSpace fSpace;
...@@ -602,7 +649,7 @@ int HDF5RecordingData::writeDataBlock(int xDataSize, int yDataSize, HDF5FileBase ...@@ -602,7 +649,7 @@ int HDF5RecordingData::writeDataBlock(int xDataSize, int yDataSize, HDF5FileBase
} }
int HDF5RecordingData::writeDataRow(int yPos, int xDataSize, HDF5FileBase::DataTypes type, const void* data) int HDF5RecordingData::writeDataRow(int yPos, int xDataSize, HDF5FileBase::BaseDataType type, const void* data)
{ {
hsize_t dim[2],offset[2]; hsize_t dim[2],offset[2];
DataSpace fSpace; DataSpace fSpace;
......
Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.h
+ 36
− 15
View file @ 42e357bf
...@@ -33,7 +33,7 @@ ...@@ -33,7 +33,7 @@
#define CHUNK_XSIZE 2048 #define CHUNK_XSIZE 2048
#endif #endif
#define MAX_STR_SIZE 256 #define DEFAULT_STR_SIZE 256
namespace H5 namespace H5
{ {
...@@ -59,18 +59,39 @@ public: ...@@ -59,18 +59,39 @@ public:
virtual String getFileName() = 0; virtual String getFileName() = 0;
bool isOpen() const; bool isOpen() const;
bool isReadyToOpen() const; bool isReadyToOpen() const;
typedef enum DataTypes { U8, U16, U32, U64, I8, I16, I32, I64, F32, F64, STR} DataTypes; class COMMON_LIB BaseDataType {
public:
static H5::DataType getNativeType(DataTypes type); enum Type { T_U8, T_U16, T_U32, T_U64, T_I8, T_I16, T_I32, T_I64, T_F32, T_F64, T_STR };
static H5::DataType getH5Type(DataTypes type); BaseDataType();
BaseDataType(Type, size_t);
Type type;
size_t typeSize;
//handy accessors
static const BaseDataType U8;
static const BaseDataType U16;
static const BaseDataType U32;
static const BaseDataType U64;
static const BaseDataType I8;
static const BaseDataType I16;
static const BaseDataType I32;
static const BaseDataType I64;
static const BaseDataType F32;
static const BaseDataType F64;
static const BaseDataType DSTR;
static BaseDataType STR(size_t size);
};
static H5::DataType getNativeType(BaseDataType type);
static H5::DataType getH5Type(BaseDataType type);
protected: protected:
virtual int createFileStructure() = 0; virtual int createFileStructure() = 0;
int setAttribute(DataTypes type, const void* data, String path, String name); int setAttribute(BaseDataType type, const void* data, String path, String name);
int setAttributeStr(const String& value, String path, String name); int setAttributeStr(const String& value, String path, String name);
int setAttributeArray(DataTypes type, const void* data, int size, String path, String name); int setAttributeArray(BaseDataType type, const void* data, int size, String path, String name);
int setAttributeStrArray(const StringArray& data, String path, String name); int setAttributeStrArray(const StringArray& data, String path, String name);
int createGroup(String path); int createGroup(String path);
int createGroupIfDoesNotExist(String path); int createGroupIfDoesNotExist(String path);
...@@ -78,10 +99,10 @@ protected: ...@@ -78,10 +99,10 @@ protected:
HDF5RecordingData* getDataSet(String path); HDF5RecordingData* getDataSet(String path);
//aliases for createDataSet //aliases for createDataSet
HDF5RecordingData* createDataSet(DataTypes type, int sizeX, int chunkX, String path); HDF5RecordingData* createDataSet(BaseDataType type, int sizeX, int chunkX, String path);
HDF5RecordingData* createDataSet(DataTypes type, int sizeX, int sizeY, int chunkX, String path); HDF5RecordingData* createDataSet(BaseDataType type, int sizeX, int sizeY, int chunkX, String path);
HDF5RecordingData* createDataSet(DataTypes type, int sizeX, int sizeY, int sizeZ, int chunkX, String path); HDF5RecordingData* createDataSet(BaseDataType type, int sizeX, int sizeY, int sizeZ, int chunkX, String path);
HDF5RecordingData* createDataSet(DataTypes type, int sizeX, int sizeY, int sizeZ, int chunkX, int chunkY, String path); HDF5RecordingData* createDataSet(BaseDataType type, int sizeX, int sizeY, int sizeZ, int chunkX, int chunkY, String path);
bool readyToOpen; bool readyToOpen;
...@@ -89,7 +110,7 @@ private: ...@@ -89,7 +110,7 @@ private:
int setAttributeStrArray(Array<const char*>& data, int maxSize, String path, String name); int setAttributeStrArray(Array<const char*>& data, int maxSize, String path, String name);
//create an extendable dataset //create an extendable dataset
HDF5RecordingData* createDataSet(DataTypes type, int dimension, int* size, int* chunking, String path); HDF5RecordingData* createDataSet(BaseDataType type, int dimension, int* size, int* chunking, String path);
int open(bool newfile, int nChans); int open(bool newfile, int nChans);
ScopedPointer<H5::H5File> file; ScopedPointer<H5::H5File> file;
bool opened; bool opened;
...@@ -103,10 +124,10 @@ public: ...@@ -103,10 +124,10 @@ public:
HDF5RecordingData(H5::DataSet* data); HDF5RecordingData(H5::DataSet* data);
~HDF5RecordingData(); ~HDF5RecordingData();
int writeDataBlock(int xDataSize, HDF5FileBase::DataTypes type, const void* data); int writeDataBlock(int xDataSize, HDF5FileBase::BaseDataType type, const void* data);
int writeDataBlock(int xDataSize, int yDataSize, HDF5FileBase::DataTypes type, const void* data); int writeDataBlock(int xDataSize, int yDataSize, HDF5FileBase::BaseDataType type, const void* data);
int writeDataRow(int yPos, int xDataSize, HDF5FileBase::DataTypes type, const void* data); int writeDataRow(int yPos, int xDataSize, HDF5FileBase::BaseDataType type, const void* data);
void getRowXPositions(Array<uint32>& rows); void getRowXPositions(Array<uint32>& rows);
......
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