void SaveContainerFits::writeHeader(std::auto_ptr<CCfits::FITS> &fitsFile, CtSaving::HeaderMap &header)
{
DEB_MEMBER_FUNCT();
for(CtSaving::HeaderMap::iterator it = header.begin();it != header.end();++it)
{
std::string keyword = it->first;
std::transform(keyword.begin(), keyword.end(),
keyword.begin(), ::toupper);
fitsFile->pHDU().addKey(keyword,it->second, "Dynamic header information");
}
}
long SaveContainerHdf5::_writeFile(void* f,Data &aData,
CtSaving::HeaderMap &aHeader,
CtSaving::FileFormat aFormat) {
DEB_MEMBER_FUNCT();
_File* file = (_File*)f;
size_t buf_size = 0;
// get the proper data type
PredType data_type(PredType::NATIVE_UINT8);
switch (aData.type) {
case Data::UINT8:
break;
case Data::INT8:
data_type = PredType::NATIVE_INT8;
break;
case Data::UINT16:
data_type = PredType::NATIVE_UINT16;
break;
case Data::INT16:
data_type = PredType::NATIVE_INT16;
break;
case Data::UINT32:
data_type = PredType::NATIVE_UINT32;
break;
case Data::INT32:
data_type = PredType::NATIVE_INT32;
break;
case Data::UINT64:
data_type = PredType::NATIVE_UINT64;
break;
case Data::INT64:
data_type = PredType::NATIVE_INT64;
break;
case Data::FLOAT:
data_type = PredType::NATIVE_FLOAT;
break;
case Data::DOUBLE:
data_type = PredType::NATIVE_DOUBLE;
break;
case Data::UNDEF:
default:
THROW_CTL_ERROR(Error) << "Invalid image type";
}
try {
if (!file->m_format_written) {
// ISO 8601 Time format
time_t now;
time(&now);
char buf[sizeof("2011-10-08T07:07:09Z")];
#ifdef WIN32
struct tm gmtime_now;
gmtime_s(&gmtime_now, &now);
strftime(buf, sizeof(buf), "%FT%TZ", &gmtime_now);
#else
strftime(buf, sizeof(buf), "%FT%TZ", gmtime(&now));
#endif
string stime = string(buf);
write_h5_dataset(*file->m_entry,"start_time",stime);
// write header only once into "parameters" group
// but we should write some keys into measurement, like motor_pos counter_pos (spec)???
if (!aHeader.empty()) {
for (map<string, string>::const_iterator it = aHeader.begin(); it != aHeader.end(); it++) {
string key = it->first;
string value = it->second;
write_h5_dataset(*file->m_measurement_detector_parameters,
key.c_str(),value);
}
}
delete file->m_measurement_detector_parameters;
file->m_measurement_detector_parameters = NULL;
// create the image data structure in the file
hsize_t data_dims[3], max_dims[3];
data_dims[1] = aData.dimensions[1];
data_dims[2] = aData.dimensions[0];
data_dims[0] = m_nbframes;
max_dims[1] = aData.dimensions[1];
max_dims[2] = aData.dimensions[0];
max_dims[0] = H5S_UNLIMITED;
// Create property list for the dataset and setup chunk size
DSetCreatPropList plist;
hsize_t chunk_dims[RANK_THREE];
// test direct chunk write, so chunk dims is 1 image size
chunk_dims[0] = 1; chunk_dims[1] = data_dims[1]; chunk_dims[2] = data_dims[2];
plist.setChunk(RANK_THREE, chunk_dims);
#if defined(WITH_Z_COMPRESSION)
if (aFormat == CtSaving::HDF5GZ)
plist.setDeflate(m_compression_level);
#endif
#if defined(WITH_BS_COMPRESSION)
if (aFormat == CtSaving::HDF5BS) {
unsigned int opt_vals[2]= {0, BSHUF_H5_COMPRESS_LZ4};
plist.setFilter(BSHUF_H5FILTER, H5Z_FLAG_MANDATORY, 2, opt_vals);
}
#endif
// create new dspace
file->m_image_dataspace = new DataSpace(RANK_THREE, data_dims, NULL);
file->m_image_dataset =
new DataSet(file->m_measurement_detector->createDataSet("data",
data_type,
*file->m_image_dataspace,
plist));
string nxdata = "NXdata";
write_h5_attribute(*file->m_image_dataset, "NX_class", nxdata);
string image = "image";
write_h5_attribute(*file->m_image_dataset, "interpretation", image);
file->m_prev_images_written = 0;
file->m_format_written = true;
} else if (file->m_in_append && !m_is_multiset && !file->m_dataset_extended) {
hsize_t allocated_dims[3];
file->m_image_dataset = new DataSet(file->m_measurement_detector->
openDataSet("data"));
file->m_image_dataspace = new DataSpace(file->m_image_dataset->getSpace());
file->m_image_dataspace->getSimpleExtentDims(allocated_dims);
hsize_t data_dims[3];
data_dims[1] = aData.dimensions[1];
data_dims[2] = aData.dimensions[0];
data_dims[0] = allocated_dims[0] + m_nbframes;
if (data_dims[1] != allocated_dims[1] && data_dims[2] != allocated_dims[2]) {
THROW_CTL_ERROR(Error) << "You are trying to extend the dataset with mismatching image dimensions";
}
file->m_image_dataset->extend(data_dims);
file->m_image_dataspace->close();
delete file->m_image_dataset;
file->m_image_dataspace = new DataSpace(file->m_image_dataset->getSpace());
file->m_prev_images_written = allocated_dims[0];
file->m_dataset_extended = true;
}
// write the image data
hsize_t image_nb = aData.frameNumber % m_nbframes;
// we test direct chunk write
hsize_t offset[RANK_THREE] = {image_nb, 0U, 0U};
uint32_t filter_mask = 0;
hid_t dataset = file->m_image_dataset->getId();
herr_t status;
void * buf_data;
hid_t dxpl;
dxpl = H5Pcreate(H5P_DATASET_XFER);
if ((aFormat == CtSaving::HDF5GZ) || (aFormat == CtSaving::HDF5BS))
{
ZBufferType* buffers = _takeBuffer(aData.frameNumber);
// with single chunk, only one buffer allocated
buf_size = buffers->front()->used_size;
buf_data = buffers->front()->buffer;
//DEB_ALWAYS() << "Image #"<< aData.frameNumber << " buf_size = "<< buf_size;
status = H5DOwrite_chunk(dataset, dxpl , filter_mask, offset, buf_size, buf_data);
if (status<0) {
THROW_CTL_ERROR(Error) << "H5DOwrite_chunk() failed";
}
delete buffers->front();
delete buffers;
}
else
{
buf_data = aData.data();
buf_size = aData.size();
//DEB_ALWAYS() << "Image #"<< aData.frameNumber << " buf_size = "<< buf_size;
status = H5DOwrite_chunk(dataset, dxpl , filter_mask, offset, buf_size, buf_data);
if (status<0) {
THROW_CTL_ERROR(Error) << "H5DOwrite_chunk() failed";
}
} // else
// catch failure caused by the DataSet operations
}catch (DataSetIException& error) {
THROW_CTL_ERROR(Error) << "DataSet not created successfully " << error.getCDetailMsg();
error.printError();
}
// catch failure caused by the DataSpace operations
catch (DataSpaceIException& error) {
THROW_CTL_ERROR(Error) << "DataSpace not created successfully " << error.getCDetailMsg();
}
// catch failure caused by any other HDF5 error
catch (H5::Exception &e) {
THROW_CTL_ERROR(Error) << e.getCDetailMsg();
}
// catch anything not hdf5 related
catch (Exception &e) {
THROW_CTL_ERROR(Error) << e.getErrMsg();
}
DEB_RETURN();
return buf_size;
}
void SaveContainerHdf5::_writeFile(Data &aData, CtSaving::HeaderMap &aHeader, CtSaving::FileFormat aFormat) {
DEB_MEMBER_FUNCT();
if (aFormat == CtSaving::HDF5) {
// get the proper data type
PredType data_type(PredType::NATIVE_UINT8);
switch (aData.type) {
case Data::UINT8:
break;
case Data::INT8:
data_type = PredType::NATIVE_INT8;
break;
case Data::UINT16:
data_type = PredType::NATIVE_UINT16;
break;
case Data::INT16:
data_type = PredType::NATIVE_INT16;
break;
case Data::UINT32:
data_type = PredType::NATIVE_UINT32;
break;
case Data::INT32:
data_type = PredType::NATIVE_INT32;
break;
case Data::UINT64:
data_type = PredType::NATIVE_UINT64;
break;
case Data::INT64:
data_type = PredType::NATIVE_INT64;
break;
case Data::FLOAT:
data_type = PredType::NATIVE_FLOAT;
break;
case Data::DOUBLE:
data_type = PredType::NATIVE_DOUBLE;
break;
case Data::UNDEF:
default:
THROW_CTL_ERROR(Error) << "Invalid image type";
}
try {
if (!m_format_written) {
// ISO 8601 Time format
time_t now;
time(&now);
char buf[sizeof("2011-10-08T07:07:09Z")];
strftime(buf, sizeof(buf), "%FT%TZ", gmtime(&now));
string stime = string(buf);
write_h5_dataset(*m_entry,"start_time",stime);
// write header only once into "parameters" group
// but we should write some keys into measurement, like motor_pos counter_pos (spec)???
if (!aHeader.empty()) {
for (map<string, string>::const_iterator it = aHeader.begin(); it != aHeader.end(); it++) {
string key = it->first;
string value = it->second;
write_h5_dataset(*m_measurement_detector_parameters,key.c_str(),value);
}
}
delete m_measurement_detector_parameters;m_measurement_detector_parameters = NULL;
// create the image data structure in the file
hsize_t data_dims[3], max_dims[3];
data_dims[1] = aData.dimensions[1];
data_dims[2] = aData.dimensions[0];
data_dims[0] = m_nbframes;
max_dims[1] = aData.dimensions[1];
max_dims[2] = aData.dimensions[0];
max_dims[0] = H5S_UNLIMITED;
// Create property list for the dataset and setup chunk size
DSetCreatPropList plist;
hsize_t chunk_dims[3];
// calculate a optimized chunking
calculate_chunck(data_dims, chunk_dims, aData.depth());
plist.setChunk(RANK_THREE, chunk_dims);
m_image_dataspace = new DataSpace(RANK_THREE, data_dims, max_dims); // create new dspace
m_image_dataset = new DataSet(m_measurement_detector->createDataSet("data", data_type, *m_image_dataspace, plist));
string nxdata = "NXdata";
write_h5_attribute(*m_image_dataset, "NX_class", nxdata);
string image = "image";
write_h5_attribute(*m_image_dataset, "interpretation", image);
m_prev_images_written = 0;
m_format_written = true;
} else if (m_in_append && !m_is_multiset && !m_dataset_extended) {
hsize_t allocated_dims[3];
m_image_dataset = new DataSet(m_measurement_detector->openDataSet("data"));
m_image_dataspace = new DataSpace(m_image_dataset->getSpace());
m_image_dataspace->getSimpleExtentDims(allocated_dims);
hsize_t data_dims[3];
data_dims[1] = aData.dimensions[1];
data_dims[2] = aData.dimensions[0];
data_dims[0] = allocated_dims[0] + m_nbframes;
if (data_dims[1] != allocated_dims[1] && data_dims[2] != allocated_dims[2]) {
THROW_CTL_ERROR(Error) << "You are trying to extend the dataset with mismatching image dimensions";
}
m_image_dataset->extend(data_dims);
m_image_dataspace->close();
delete m_image_dataset;
m_image_dataspace = new DataSpace(m_image_dataset->getSpace());
m_prev_images_written = allocated_dims[0];
m_dataset_extended = true;
}
// write the image data
hsize_t slab_dim[3];
slab_dim[2] = aData.dimensions[0];
slab_dim[1] = aData.dimensions[1];
slab_dim[0] = 1;
DataSpace slabspace = DataSpace(RANK_THREE, slab_dim);
int image_nb = aData.frameNumber % m_nbframes;
hsize_t start[] = { m_prev_images_written + image_nb, 0, 0 };
hsize_t count[] = { 1, aData.dimensions[1], aData.dimensions[0] };
m_image_dataspace->selectHyperslab(H5S_SELECT_SET, count, start);
m_image_dataset->write((u_int8_t*) aData.data(), data_type, slabspace, *m_image_dataspace);
// catch failure caused by the DataSet operations
} catch (DataSetIException& error) {
THROW_CTL_ERROR(Error) << "DataSet not created successfully " << error.getCDetailMsg();
error.printError();
}
// catch failure caused by the DataSpace operations
catch (DataSpaceIException& error) {
THROW_CTL_ERROR(Error) << "DataSpace not created successfully " << error.getCDetailMsg();
}
// catch failure caused by any other HDF5 error
catch (H5::Exception &e) {
THROW_CTL_ERROR(Error) << e.getCDetailMsg();
}
// catch anything not hdf5 related
catch (Exception &e) {
THROW_CTL_ERROR(Error) << e.getErrMsg();
}
}
DEB_RETURN();
}
