From 42e357bf96ef4937b97fbf0f7784c94995692509 Mon Sep 17 00:00:00 2001
From: Aaron Cuevas Lopez <aacuelo@teleco.upv.es>
Date: Fri, 7 Jul 2017 02:17:33 +0200
Subject: [PATCH] Generalize hdf5 types
---
.../OpenEphysHDF5Lib/HDF5FileFormat.cpp | 219 +++++++++++-------
.../OpenEphysHDF5Lib/HDF5FileFormat.h | 51 ++--
2 files changed, 169 insertions(+), 101 deletions(-)
diff --git a/Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.cpp b/Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.cpp
index bed007fa9..fc3b8a080 100644
--- a/Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.cpp
+++ b/Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.cpp
@@ -111,13 +111,13 @@ void HDF5FileBase::close()
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);
}
-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;
Group gloc;
@@ -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};
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 chunks[3] = {chunkX, 0, 0};
@@ -350,7 +350,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si
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 chunks[3] = {chunkX, 0, 0};
@@ -360,7 +360,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si
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 chunks[3] = {chunkX, chunkY, 0};
@@ -370,7 +370,7 @@ HDF5RecordingData* HDF5FileBase::createDataSet(DataTypes type, int sizeX, int si
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;
DSetCreatPropList prop;
@@ -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)
- {
- case I8:
- return PredType::NATIVE_INT8;
- break;
- case I16:
- return PredType::NATIVE_INT16;
- break;
- case I32:
- return PredType::NATIVE_INT32;
- break;
- case I64:
- return PredType::NATIVE_INT64;
- break;
- case U8:
- return PredType::NATIVE_UINT8;
- break;
- case U16:
- return PredType::NATIVE_UINT16;
- break;
- case U32:
- return PredType::NATIVE_UINT32;
- break;
- case U64:
- return PredType::NATIVE_UINT64;
- break;
- case F32:
- return PredType::NATIVE_FLOAT;
- break;
- case F64:
- return PredType::NATIVE_DOUBLE;
- break;
- case STR:
- return StrType(PredType::C_S1,MAX_STR_SIZE);
- break;
- }
- return PredType::NATIVE_INT32;
+ H5::DataType baseType;
+
+ switch (type.type)
+ {
+ case BaseDataType::Type::T_I8:
+ baseType = PredType::NATIVE_INT8;
+ break;
+ case BaseDataType::Type::T_I16:
+ baseType = PredType::NATIVE_INT16;
+ break;
+ case BaseDataType::Type::T_I32:
+ baseType = PredType::NATIVE_INT32;
+ break;
+ case BaseDataType::Type::T_I64:
+ baseType = PredType::NATIVE_INT64;
+ break;
+ case BaseDataType::Type::T_U8:
+ baseType = PredType::NATIVE_UINT8;
+ break;
+ case BaseDataType::Type::T_U16:
+ baseType = PredType::NATIVE_UINT16;
+ break;
+ case BaseDataType::Type::T_U32:
+ baseType = PredType::NATIVE_UINT32;
+ break;
+ case BaseDataType::Type::T_U64:
+ baseType = PredType::NATIVE_UINT64;
+ break;
+ case BaseDataType::Type::T_F32:
+ baseType = PredType::NATIVE_FLOAT;
+ break;
+ case BaseDataType::Type::T_F64:
+ baseType = PredType::NATIVE_DOUBLE;
+ break;
+ case BaseDataType::Type::T_STR:
+ return StrType(PredType::C_S1, type.typeSize);
+ 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)
- {
- case I8:
- return PredType::STD_I8LE;
- break;
- case I16:
- return PredType::STD_I16LE;
- break;
- case I32:
- return PredType::STD_I32LE;
- break;
- case I64:
- return PredType::STD_I64LE;
- break;
- case U8:
- return PredType::STD_U8LE;
- break;
- case U16:
- return PredType::STD_U16LE;
- break;
- case U32:
- return PredType::STD_U32LE;
- break;
- case U64:
- return PredType::STD_U64LE;
- break;
- case F32:
- return PredType::IEEE_F32LE;
- break;
- case F64:
- return PredType::IEEE_F64LE;
- break;
- case STR:
- return StrType(PredType::C_S1,MAX_STR_SIZE);
- break;
- }
- return PredType::STD_I32LE;
+ H5::DataType baseType;
+
+ switch (type.type)
+ {
+ case BaseDataType::Type::T_I8:
+ baseType = PredType::STD_I8LE;
+ break;
+ case BaseDataType::Type::T_I16:
+ baseType = PredType::STD_I16LE;
+ break;
+ case BaseDataType::Type::T_I32:
+ baseType = PredType::STD_I32LE;
+ break;
+ case BaseDataType::Type::T_I64:
+ baseType = PredType::STD_I64LE;
+ break;
+ case BaseDataType::Type::T_U8:
+ baseType = PredType::STD_U8LE;
+ break;
+ case BaseDataType::Type::T_U16:
+ baseType = PredType::STD_U16LE;
+ break;
+ case BaseDataType::Type::T_U32:
+ baseType = PredType::STD_U32LE;
+ break;
+ case BaseDataType::Type::T_U64:
+ baseType = PredType::STD_U64LE;
+ break;
+ case BaseDataType::Type::T_F32:
+ return PredType::IEEE_F32LE;
+ break;
+ case BaseDataType::Type::T_F64:
+ baseType = PredType::IEEE_F64LE;
+ break;
+ case BaseDataType::Type::T_STR:
+ return StrType(PredType::C_S1, type.typeSize);
+ 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)
{
DataSpace dSpace;
@@ -543,12 +590,12 @@ HDF5RecordingData::~HDF5RecordingData()
//Safety
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);
}
-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];
DataSpace fSpace;
@@ -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];
DataSpace fSpace;
diff --git a/Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.h b/Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.h
index 7f0796bd5..c5202f64b 100644
--- a/Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.h
+++ b/Source/Plugins/CommonLibs/OpenEphysHDF5Lib/HDF5FileFormat.h
@@ -33,7 +33,7 @@
#define CHUNK_XSIZE 2048
#endif
-#define MAX_STR_SIZE 256
+#define DEFAULT_STR_SIZE 256
namespace H5
{
@@ -59,18 +59,39 @@ public:
virtual String getFileName() = 0;
bool isOpen() const;
bool isReadyToOpen() const;
- typedef enum DataTypes { U8, U16, U32, U64, I8, I16, I32, I64, F32, F64, STR} DataTypes;
-
- static H5::DataType getNativeType(DataTypes type);
- static H5::DataType getH5Type(DataTypes type);
+ class COMMON_LIB BaseDataType {
+ public:
+ enum Type { T_U8, T_U16, T_U32, T_U64, T_I8, T_I16, T_I32, T_I64, T_F32, T_F64, T_STR };
+ 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:
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 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 createGroup(String path);
int createGroupIfDoesNotExist(String path);
@@ -78,10 +99,10 @@ protected:
HDF5RecordingData* getDataSet(String path);
//aliases for createDataSet
- 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);
- HDF5RecordingData* createDataSet(DataTypes type, int sizeX, int sizeY, int sizeZ, int chunkX, int chunkY, String path);
+ HDF5RecordingData* createDataSet(BaseDataType type, int sizeX, int chunkX, String path);
+ HDF5RecordingData* createDataSet(BaseDataType type, int sizeX, int sizeY, int chunkX, String path);
+ HDF5RecordingData* createDataSet(BaseDataType type, int sizeX, int sizeY, int sizeZ, int chunkX, String path);
+ HDF5RecordingData* createDataSet(BaseDataType type, int sizeX, int sizeY, int sizeZ, int chunkX, int chunkY, String path);
bool readyToOpen;
@@ -89,7 +110,7 @@ private:
int setAttributeStrArray(Array<const char*>& data, int maxSize, String path, String name);
//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);
ScopedPointer<H5::H5File> file;
bool opened;
@@ -103,10 +124,10 @@ public:
HDF5RecordingData(H5::DataSet* data);
~HDF5RecordingData();
- int writeDataBlock(int xDataSize, HDF5FileBase::DataTypes type, const void* data);
- int writeDataBlock(int xDataSize, int yDataSize, HDF5FileBase::DataTypes type, const void* data);
+ int writeDataBlock(int xDataSize, HDF5FileBase::BaseDataType 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);
--
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