python works

cmake/Findh5py.cmake

@@ -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)

python/CMakeLists.txt

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

python/aare/__init__.py

@@ -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.")

python/src/hdf5_file.hpp

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

python/src/hdf5_master_file.hpp

@@ -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("quad", &Hdf5MasterFile::quad);
-        .def_property_readonly("scan_parameters",
+        //.def_property_readonly("scan_parameters",
-                               &Hdf5MasterFile::scan_parameters)
+        //                       &Hdf5MasterFile::scan_parameters)
-        .def_property_readonly("roi", &Hdf5MasterFile::roi);
+        //.def_property_readonly("roi", &Hdf5MasterFile::roi);
 }

src/Hdf5File.cpp

@@ -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",
+        //fmt::print("Data Dataset dimensions: frames = {}, rows = {}, cols = {}\n",
-                   m_total_frames, m_rows, m_cols);
+                  // 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",
+            //fmt::print("{} Dataset dimensions: size = {}\n",
-                   header_dataset_names[i], m_header_files[i]->dims[0]);
+             //      header_dataset_names[i], m_header_files[i]->dims[0]);
         }
     } catch (const H5::Exception &e) {
         m_header_files.clear();