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python works

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This commit is contained in:
maliakal_d 2024-12-04 15:02:57 +01:00
parent b23e697e26
commit 09de69c090
6 changed files with 28 additions and 80 deletions
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29
cmake/Findh5py.cmake
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@ -1,29 +0,0 @@
# Findh5py.cmake
#
# This module finds if h5py is installed and sets the H5PY_FOUND variable.
# It also sets the H5PY_INCLUDE_DIRS and H5PY_LIBRARIES variables.
find_package(PythonInterp REQUIRED)
find_package(PythonLibs REQUIRED)
execute_process(
COMMAND ${PYTHON_EXECUTABLE} -c "import h5py"
RESULT_VARIABLE H5PY_IMPORT_RESULT
OUTPUT_QUIET
ERROR_QUIET
)
if(H5PY_IMPORT_RESULT EQUAL 0)
set(H5PY_FOUND TRUE)
execute_process(
COMMAND ${PYTHON_EXECUTABLE} -c "import h5py; print(h5py.get_include())"
OUTPUT_VARIABLE H5PY_INCLUDE_DIR
OUTPUT_STRIP_TRAILING_WHITESPACE
)
set(H5PY_INCLUDE_DIRS ${H5PY_INCLUDE_DIR})
set(H5PY_LIBRARIES ${PYTHON_LIBRARIES})
else()
set(H5PY_FOUND FALSE)
endif()
mark_as_advanced(H5PY_INCLUDE_DIRS H5PY_LIBRARIES)

38
python/CMakeLists.txt
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@ -34,30 +34,22 @@ set( PYTHON_FILES
aare/utils.py
)
# Conditionally add HDF5-related Python files
# HDF5
# if (AARE_HDF5)
# find_package(h5py REQUIRED)
# find_package(HDF5 1.10 COMPONENTS CXX REQUIRED)
# add_definitions(
# ${HDF5_DEFINITIONS}
# )
# list(APPEND PYTHON_FILES
# aare/Hdf5File.py
# )
# if(HDF5_FOUND)
# target_sources(_aare PRIVATE
# ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5File.cpp
# ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5MasterFile.cpp
# )
# target_link_libraries(_aare PUBLIC ${HDF5_LIBRARIES})
# target_include_directories(_aare PUBLIC ${HDF5_INCLUDE_DIRS})
# endif()
# if(H5PY_FOUND)
# set(H5PY_INCLUDE_DIRS ${H5PY_INCLUDE_DIR})
# set(H5PY_LIBRARIES ${PYTHON_LIBRARIES})
# endif()
#HDF5
if (AARE_HDF5)
find_package(HDF5 1.10 COMPONENTS CXX REQUIRED)
add_definitions(
${HDF5_DEFINITIONS}
)
list(APPEND PYTHON_FILES
aare/Hdf5File.py
)
if(HDF5_FOUND)
add_definitions(-DHDF5_FOUND)
target_link_libraries(_aare PUBLIC ${HDF5_LIBRARIES})
target_include_directories(_aare PUBLIC ${HDF5_INCLUDE_DIRS})
endif()
endif()
# Copy the python files to the build directory
foreach(FILE ${PYTHON_FILES})

20
python/aare/__init__.py
View File

@ -2,31 +2,15 @@
from . import _aare
from ._aare import File, RawMasterFile, RawSubFile
from ._aare import File, RawMasterFile, RawSubFile, Hdf5MasterFile
from ._aare import Pedestal, ClusterFinder, VarClusterFinder
from ._aare import DetectorType
from ._aare import ClusterFile
from .CtbRawFile import CtbRawFile
from .RawFile import RawFile
from .Hdf5File import Hdf5File
from .ScanParameters import ScanParameters
from .utils import random_pixels, random_pixel
try:
import h5py
HDF5_FOUND = True
except ImportError:
HDF5_FOUND = False
if HDF5_FOUND:
from ._aare import Hdf5MasterFile
from .Hdf5File import Hdf5File
else:
class Hdf5MasterFile:
def __init__(self, *args, **kwargs):
raise ImportError("h5py library not found. HDF5 Master File is not available.")
class Hdf5File:
def __init__(self, *args, **kwargs):
raise ImportError("h5py library not found. HDF5 File is not available.")

1
python/src/hdf5_file.hpp
View File

@ -1,3 +1,4 @@
#include "H5Cpp.h"
#include "aare/File.hpp"
#include "aare/Frame.hpp"
#include "aare/Hdf5File.hpp"

8
python/src/hdf5_master_file.hpp
View File

@ -79,8 +79,8 @@ void define_hdf5_master_file_bindings(py::module &m) {
&Hdf5MasterFile::transceiver_samples)
.def_property_readonly("number_of_rows",
&Hdf5MasterFile::number_of_rows)
.def_property_readonly("quad", &Hdf5MasterFile::quad)
.def_property_readonly("scan_parameters",
&Hdf5MasterFile::scan_parameters)
.def_property_readonly("roi", &Hdf5MasterFile::roi);
.def_property_readonly("quad", &Hdf5MasterFile::quad);
//.def_property_readonly("scan_parameters",
// &Hdf5MasterFile::scan_parameters)
//.def_property_readonly("roi", &Hdf5MasterFile::roi);
}

12
src/Hdf5File.cpp
View File

@ -55,7 +55,7 @@ void Hdf5File::read_into(std::byte *image_buf, size_t n_frames,
}
};
size_t Hdf5File::n_mod() const { return 1; } // n_subfile_parts; }
size_t Hdf5File::n_mod() const { return 1; }
size_t Hdf5File::bytes_per_frame() {
return m_rows * m_cols * m_master.bitdepth() / 8;
@ -149,7 +149,7 @@ void Hdf5File::get_frame_into(size_t frame_index, std::byte *frame_buffer,
void Hdf5File::get_data_into(size_t frame_index, std::byte *frame_buffer) {
m_data_file->get_frame_into(frame_index, frame_buffer);
fmt::print("Read 2D data for frame {}\n", frame_index);
//fmt::print("Read 2D data for frame {}\n", frame_index);
}
void Hdf5File::get_header_into(size_t frame_index, DetectorHeader *header) {
@ -218,8 +218,8 @@ void Hdf5File::open_data_file() {
m_total_frames = m_data_file->dims[0];
m_rows = m_data_file->dims[1];
m_cols = m_data_file->dims[2];
fmt::print("Data Dataset dimensions: frames = {}, rows = {}, cols = {}\n",
m_total_frames, m_rows, m_cols);
//fmt::print("Data Dataset dimensions: frames = {}, rows = {}, cols = {}\n",
// m_total_frames, m_rows, m_cols);
} catch (const H5::Exception &e) {
m_data_file.reset();
fmt::print("Exception type: {}\n", typeid(e).name());
@ -236,8 +236,8 @@ void Hdf5File::open_header_files() {
try {
for (size_t i = 0; i != header_dataset_names.size(); ++i) {
m_header_files.push_back(std::make_unique<H5Handles>(m_master.master_fname().string(), metadata_group_name + header_dataset_names[i], 1));
fmt::print("{} Dataset dimensions: size = {}\n",
header_dataset_names[i], m_header_files[i]->dims[0]);
//fmt::print("{} Dataset dimensions: size = {}\n",
// header_dataset_names[i], m_header_files[i]->dims[0]);
}
} catch (const H5::Exception &e) {
m_header_files.clear();