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(); }