mirror of
https://github.com/slsdetectorgroup/aare.git
synced 2025-06-11 06:47:14 +02:00
first draft of hdf5, reads master metadata, reads data dims, process of hyperslab
This commit is contained in:
@ -34,6 +34,31 @@ set( PYTHON_FILES
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aare/utils.py
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)
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# Conditionally add HDF5-related Python files
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# HDF5
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# if (AARE_HDF5)
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# find_package(h5py REQUIRED)
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# find_package(HDF5 1.10 COMPONENTS CXX REQUIRED)
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# add_definitions(
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# ${HDF5_DEFINITIONS}
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# )
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# list(APPEND PYTHON_FILES
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# aare/Hdf5File.py
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# )
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# if(HDF5_FOUND)
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# target_sources(_aare PRIVATE
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# ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5File.cpp
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# ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5MasterFile.cpp
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# )
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# target_link_libraries(_aare PUBLIC ${HDF5_LIBRARIES})
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# target_include_directories(_aare PUBLIC ${HDF5_INCLUDE_DIRS})
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# endif()
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# if(H5PY_FOUND)
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# set(H5PY_INCLUDE_DIRS ${H5PY_INCLUDE_DIR})
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# set(H5PY_LIBRARIES ${PYTHON_LIBRARIES})
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# endif()
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# Copy the python files to the build directory
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foreach(FILE ${PYTHON_FILES})
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configure_file(${FILE} ${CMAKE_BINARY_DIR}/${FILE} )
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66
python/aare/Hdf5File.py
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66
python/aare/Hdf5File.py
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@ -0,0 +1,66 @@
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from . import _aare
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import numpy as np
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#from .ScanParameters import ScanParameters
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class Hdf5File(_aare.Hdf5File):
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def __init__(self, fname, chunk_size = 1):
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super().__init__(fname)
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self._chunk_size = chunk_size
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def read(self) -> tuple:
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"""Read the entire file.
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Seeks to the beginning of the file before reading.
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Returns:
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tuple: header, data
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"""
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self.seek(0)
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return self.read_n(self.total_frames)
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# @property
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# def scan_parameters(self):
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# """Return the scan parameters.
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# Returns:
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# ScanParameters: Scan parameters.
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# """
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# return ScanParameters(self.master.scan_parameters)
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@property
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def master(self):
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"""Return the master file.
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Returns:
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Hdf5MasterFile: Master file.
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"""
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return super().master
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def __len__(self) -> int:
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"""Return the number of frames in the file.
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Returns:
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int: Number of frames in file.
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"""
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return super().frames_in_file
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def __enter__(self):
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return self
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def __exit__(self, exc_type, exc_value, traceback):
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pass
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def __iter__(self):
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return self
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def __next__(self):
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try:
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if self._chunk_size == 1:
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return self.read_frame()
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else:
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return self.read_n(self._chunk_size)
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except RuntimeError:
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# TODO! find a good way to check that we actually have the right exception
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raise StopIteration
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@ -11,4 +11,22 @@ from .CtbRawFile import CtbRawFile
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from .RawFile import RawFile
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from .ScanParameters import ScanParameters
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from .utils import random_pixels, random_pixel
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from .utils import random_pixels, random_pixel
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try:
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import h5py
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HDF5_FOUND = True
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except ImportError:
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HDF5_FOUND = False
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if HDF5_FOUND:
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from ._aare import Hdf5MasterFile
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from .Hdf5File import Hdf5File
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else:
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class Hdf5MasterFile:
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def __init__(self, *args, **kwargs):
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raise ImportError("h5py library not found. HDF5 Master File is not available.")
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class Hdf5File:
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def __init__(self, *args, **kwargs):
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raise ImportError("h5py library not found. HDF5 File is not available.")
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@ -5,6 +5,11 @@
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#include "aare/RawMasterFile.hpp"
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#include "aare/RawSubFile.hpp"
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#ifdef HDF5_FOUND
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#include "aare/Hdf5File.hpp"
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#include "aare/Hdf5MasterFile.hpp"
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#endif
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#include "aare/defs.hpp"
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// #include "aare/fClusterFileV2.hpp"
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105
python/src/hdf5_file.hpp
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105
python/src/hdf5_file.hpp
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@ -0,0 +1,105 @@
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#include "aare/File.hpp"
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#include "aare/Frame.hpp"
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#include "aare/Hdf5File.hpp"
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#include "aare/Hdf5MasterFile.hpp"
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#include "aare/defs.hpp"
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// #include "aare/fClusterFileV2.hpp"
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#include <cstdint>
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#include <filesystem>
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#include <pybind11/iostream.h>
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#include <pybind11/numpy.h>
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#include <pybind11/pybind11.h>
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#include <pybind11/stl.h>
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#include <pybind11/stl/filesystem.h>
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#include <string>
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namespace py = pybind11;
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using namespace ::aare;
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void define_hdf5_file_io_bindings(py::module &m) {
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py::class_<Hdf5File>(m, "Hdf5File")
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.def(py::init<const std::filesystem::path &>())
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.def("read_frame",
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[](Hdf5File &self) {
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py::array image;
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std::vector<ssize_t> shape;
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shape.reserve(2);
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shape.push_back(self.rows());
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shape.push_back(self.cols());
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// return headers from all subfiles
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py::array_t<DetectorHeader> header(self.n_mod());
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const uint8_t item_size = self.bytes_per_pixel();
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if (item_size == 1) {
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image = py::array_t<uint8_t>(shape);
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} else if (item_size == 2) {
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image = py::array_t<uint16_t>(shape);
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} else if (item_size == 4) {
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image = py::array_t<uint32_t>(shape);
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}
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self.read_into(
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reinterpret_cast<std::byte *>(image.mutable_data()),
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header.mutable_data());
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return py::make_tuple(header, image);
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})
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.def(
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"read_n",
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[](Hdf5File &self, size_t n_frames) {
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// adjust for actual frames left in the file
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n_frames =
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std::min(n_frames, self.total_frames() - self.tell());
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if (n_frames == 0) {
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throw std::runtime_error("No frames left in file");
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}
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std::vector<size_t> shape{n_frames, self.rows(), self.cols()};
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// return headers from all subfiles
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py::array_t<DetectorHeader> header;
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if (self.n_mod() == 1) {
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header = py::array_t<DetectorHeader>(n_frames);
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} else {
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header =
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py::array_t<DetectorHeader>({self.n_mod(), n_frames});
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}
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// py::array_t<DetectorHeader> header({self.n_mod(), n_frames});
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py::array image;
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const uint8_t item_size = self.bytes_per_pixel();
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if (item_size == 1) {
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image = py::array_t<uint8_t>(shape);
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} else if (item_size == 2) {
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image = py::array_t<uint16_t>(shape);
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} else if (item_size == 4) {
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image = py::array_t<uint32_t>(shape);
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}
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self.read_into(
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reinterpret_cast<std::byte *>(image.mutable_data()),
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n_frames, header.mutable_data());
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return py::make_tuple(header, image);
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},
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R"(
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Read n frames from the file.
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)")
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.def("frame_number", &Hdf5File::frame_number)
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.def_property_readonly("bytes_per_frame", &Hdf5File::bytes_per_frame)
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.def_property_readonly("pixels_per_frame", &Hdf5File::pixels_per_frame)
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.def_property_readonly("bytes_per_pixel", &Hdf5File::bytes_per_pixel)
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.def("seek", &Hdf5File::seek, R"(
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Seek to a frame index in file.
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)")
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.def("tell", &Hdf5File::tell, R"(
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Return the current frame number.)")
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.def_property_readonly("total_frames", &Hdf5File::total_frames)
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.def_property_readonly("rows", &Hdf5File::rows)
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.def_property_readonly("cols", &Hdf5File::cols)
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.def_property_readonly("bitdepth", &Hdf5File::bitdepth)
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.def_property_readonly("geometry", &Hdf5File::geometry)
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.def_property_readonly("n_mod", &Hdf5File::n_mod)
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.def_property_readonly("detector_type", &Hdf5File::detector_type)
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.def_property_readonly("master", &Hdf5File::master);
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}
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86
python/src/hdf5_master_file.hpp
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86
python/src/hdf5_master_file.hpp
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@ -0,0 +1,86 @@
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#include "aare/File.hpp"
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#include "aare/Frame.hpp"
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#include "aare/Hdf5File.hpp"
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#include "aare/Hdf5MasterFile.hpp"
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#include "aare/defs.hpp"
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// #include "aare/fClusterFileV2.hpp"
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#include <cstdint>
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#include <filesystem>
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#include <pybind11/iostream.h>
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#include <pybind11/numpy.h>
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#include <pybind11/pybind11.h>
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#include <pybind11/stl.h>
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#include <pybind11/stl/filesystem.h>
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#include <string>
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namespace py = pybind11;
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using namespace ::aare;
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void define_hdf5_master_file_bindings(py::module &m) {
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py::class_<Hdf5MasterFile>(m, "Hdf5MasterFile")
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.def(py::init<const std::filesystem::path &>())
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.def("data_fname", &Hdf5MasterFile::data_fname, R"(
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Parameters
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------------
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module_index : int
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module index (d0, d1 .. dN)
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file_index : int
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file index (f0, f1 .. fN)
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Returns
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----------
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os.PathLike
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The name of the data file.
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)")
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.def_property_readonly("version", &Hdf5MasterFile::version)
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.def_property_readonly("detector_type", &Hdf5MasterFile::detector_type)
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.def_property_readonly("timing_mode", &Hdf5MasterFile::timing_mode)
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.def_property_readonly("image_size_in_bytes",
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&Hdf5MasterFile::image_size_in_bytes)
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.def_property_readonly("frames_in_file",
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&Hdf5MasterFile::frames_in_file)
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.def_property_readonly("pixels_y", &Hdf5MasterFile::pixels_y)
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.def_property_readonly("pixels_x", &Hdf5MasterFile::pixels_x)
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.def_property_readonly("max_frames_per_file",
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&Hdf5MasterFile::max_frames_per_file)
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.def_property_readonly("bitdepth", &Hdf5MasterFile::bitdepth)
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.def_property_readonly("frame_padding", &Hdf5MasterFile::frame_padding)
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.def_property_readonly("frame_discard_policy",
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&Hdf5MasterFile::frame_discard_policy)
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.def_property_readonly("total_frames_expected",
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&Hdf5MasterFile::total_frames_expected)
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.def_property_readonly("geometry", &Hdf5MasterFile::geometry)
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.def_property_readonly("analog_samples",
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&Hdf5MasterFile::analog_samples, R"(
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Number of analog samples
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Returns
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----------
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int | None
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The number of analog samples in the file (or None if not enabled)
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)")
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.def_property_readonly("digital_samples",
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&Hdf5MasterFile::digital_samples, R"(
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Number of digital samples
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Returns
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----------
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int | None
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The number of digital samples in the file (or None if not enabled)
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)")
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.def_property_readonly("transceiver_samples",
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&Hdf5MasterFile::transceiver_samples)
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.def_property_readonly("number_of_rows",
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&Hdf5MasterFile::number_of_rows)
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.def_property_readonly("quad", &Hdf5MasterFile::quad)
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.def_property_readonly("scan_parameters",
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&Hdf5MasterFile::scan_parameters)
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.def_property_readonly("roi", &Hdf5MasterFile::roi);
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}
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@ -3,6 +3,10 @@
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#include "raw_file.hpp"
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#include "ctb_raw_file.hpp"
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#include "raw_master_file.hpp"
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#ifdef HDF5_FOUND
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#include "hdf5_file.hpp"
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#include "hdf5_master_file.hpp"
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#endif
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#include "var_cluster.hpp"
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#include "pixel_map.hpp"
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#include "pedestal.hpp"
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@ -20,6 +24,10 @@ PYBIND11_MODULE(_aare, m) {
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define_raw_file_io_bindings(m);
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define_ctb_raw_file_io_bindings(m);
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define_raw_master_file_bindings(m);
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#ifdef HDF5_FOUND
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define_hdf5_file_io_bindings(m);
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define_hdf5_master_file_bindings(m);
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#endif
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define_var_cluster_finder_bindings(m);
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define_pixel_map_bindings(m);
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define_pedestal_bindings<double>(m, "Pedestal");
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