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Change writer to do direct chunk write

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This commit is contained in:
babic_a
2020-06-02 17:27:00 +02:00
parent dbc07b6ad6
commit ec0f763b70
1 changed files with 27 additions and 31 deletions
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sf-writer/src/JFH5Writer.cpp
+27 -31
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@@ -3,12 +3,12 @@
#include <cstring>
#include <hdf5_hl.h>
//extern "C"
//{
extern "C"
{
// #include "H5DOpublic.h"
// #include <bitshuffle/bshuf_h5filter.h>
//}
#include "H5DOpublic.h"
}
using namespace std;
using namespace core_buffer;
@@ -33,9 +33,9 @@ JFH5Writer::JFH5Writer(const std::string& output_file,
H5::DataSpace image_dataspace(3, image_dataset_dims);
auto chunk_size = min(n_images_, BUFFER_BLOCK_SIZE);
// auto chunk_size = min(n_images_, BUFFER_BLOCK_SIZE);
hsize_t image_dataset_chunking[3] =
{chunk_size, n_modules * MODULE_Y_SIZE, MODULE_X_SIZE};
{1, n_modules * MODULE_Y_SIZE, MODULE_X_SIZE};
H5::DSetCreatPropList image_dataset_properties;
image_dataset_properties.setChunk(3, image_dataset_chunking);
@@ -148,30 +148,6 @@ void JFH5Writer::write(
throw runtime_error("Received unexpected block for stop_pulse_id.");
}
hsize_t b_i_dims[3] = {BUFFER_BLOCK_SIZE,
MODULE_Y_SIZE * n_modules_,
MODULE_X_SIZE};
H5::DataSpace b_i_space(3, b_i_dims);
hsize_t b_i_count[] = {n_images_to_copy,
MODULE_Y_SIZE * n_modules_,
MODULE_X_SIZE};
hsize_t b_i_start[] = {n_images_offset, 0, 0};
b_i_space.selectHyperslab(H5S_SELECT_SET, b_i_count, b_i_start);
hsize_t f_i_dims[3] = {n_images_,
MODULE_Y_SIZE * n_modules_,
MODULE_X_SIZE};
H5::DataSpace f_i_space(3, f_i_dims);
hsize_t f_i_count[] = {n_images_to_copy,
MODULE_Y_SIZE * n_modules_,
MODULE_X_SIZE};
hsize_t f_i_start[] = {current_write_index_, 0, 0};
f_i_space.selectHyperslab(H5S_SELECT_SET, f_i_count, f_i_start);
image_dataset_.write(
data, H5::PredType::NATIVE_UINT16, b_i_space, f_i_space);
// pulse_id
{
auto b_current_ptr = b_pulse_id_ + current_write_index_;
@@ -204,5 +180,25 @@ void JFH5Writer::write(
sizeof(uint8_t) * n_images_to_copy);
}
current_write_index_ += n_images_to_copy;
// images - direct chunk write one by one.
for (size_t i_pulse=n_images_offset;
i_pulse<BUFFER_BLOCK_SIZE;
i_pulse++) {
auto image_ptr = data + (i_pulse * n_modules_ * MODULE_N_BYTES);
hsize_t offset[] = {current_write_index_, 0, 0};
if(H5DOwrite_chunk(image_dataset_.getId(), H5P_DEFAULT, 0,
offset, MODULE_N_BYTES*n_modules_, data)) {
stringstream error_message;
error_message << "[JFH5Writer::write]";
error_message << "Error while writing image chunk to file.";
error_message << "Offset " << current_write_index_ << endl;
throw invalid_argument(error_message.str());
}
current_write_index_++;
}
}