[IO] Add H5 reader file_frame_slice support

include/lima/io/h5/reader.hpp

@@ -43,8 +43,7 @@ namespace io::h5
         using params_t = loading_params;
         using file_exists_policy_t = read_file_exists_policy;
 
-        reader(std::filesystem::path const& filename, params_t const& params = {}) :
-            m_nb_frames(params.nb_frames_per_file)
+        reader(std::filesystem::path const& filename, params_t const& params = {}) : m_frame_slice(params.frame_slice)
         {
             bool is_nexus = (params.file_type == file_type_enum::nexus);
             const char* type_str = is_nexus ? "Nexus" : "HDF5";
@@ -77,11 +76,13 @@ namespace io::h5
                 LIMA_THROW_EXCEPTION(lima::hdf5_error("Error querying H5 dataset dimensions")
                                      << boost::errinfo_h5_path(dataset_path));
 
-            if (m_nb_frames == 0)
-                m_nb_frames = dims[0];
-            else if (dims[0] < m_nb_frames)
-                LIMA_THROW_EXCEPTION(lima::hdf5_error("Mismatch in number of frames in dataset")
-                                     << boost::errinfo_h5_path(dataset_path));
+            m_frame_slice.count = m_frame_slice.calc_count(dims[0]);
+
+            if (params.nb_frames_per_file != 0) {
+                if (params.nb_frames_per_file > m_frame_slice.count)
+                    LIMA_THROW_EXCEPTION(lima::invalid_argument("Reader frame_slice.count / frames_per_file mismatch"));
+                m_frame_slice.count = std::min(params.nb_frames_per_file, m_frame_slice.count);
+            }
 
             m_frame_dims = dimensions_t(dims[2], dims[1]);
 
@@ -115,7 +116,7 @@ namespace io::h5
         template <typename View>
         void read_view(View const& v, hsize_t frame_idx = 0)
         {
-            if (frame_idx >= m_nb_frames)
+            if (frame_idx >= m_frame_slice.count)
                 LIMA_THROW_EXCEPTION(lima::hdf5_error("Frame number out of bound")
                                      << boost::errinfo_frame_idx(frame_idx));
             else if (v.dimensions() != m_frame_dims)
@@ -125,7 +126,8 @@ namespace io::h5
             dataspace file_space = m_dset.space();
             if (m_nb_dims == 3) {
                 hsize_t mem_offset[] = {0, 0, 0};
-                hsize_t file_offset[] = {frame_idx, 0, 0};
+                hsize_t file_idx = frame_idx * m_frame_slice.stride + m_frame_slice.start;
+                hsize_t file_offset[] = {file_idx, 0, 0};
                 hsize_t count[] = {1, 1, 1};
                 hsize_t block[] = {1, hsize_t(m_frame_dims.y), hsize_t(m_frame_dims.x)};
                 mem_space.select_hyperslab(H5S_SELECT_SET, mem_offset, nullptr, count, block);
@@ -140,10 +142,10 @@ namespace io::h5
       protected:
         dataset m_dset; //!< The dataset
 
-        dimensions_t m_frame_dims; //!< The dimensions of data frame
-        hsize_t m_nb_dims;         //!< The number of dimensions of the dataset
-        hsize_t m_nb_frames;       //!< The number of frames in the dataset
-        pixel_enum m_pixel;        //!< The pixel type
+        dimensions_t m_frame_dims;      //!< The dimensions of data frame
+        hsize_t m_nb_dims;              //!< The number of dimensions of the dataset
+        file_frame_slice m_frame_slice; //!< The frame slice in the dataset
+        pixel_enum m_pixel;             //!< The pixel type
     };
 
 } //namespace io::h5

include/lima/io/params.describe.hpp

@@ -68,7 +68,23 @@ namespace io
 
     LIMA_IO_DESCRIBE_FILENAME(filename_loading_params)
 
-    BOOST_DESCRIBE_STRUCT(loading_params, (filename_loading_params), (start_number, nb_frames_per_file))
+    BOOST_DESCRIBE_STRUCT(file_frame_slice, (), (start, count, stride))
+
+    // clang-format off
+    BOOST_ANNOTATE_MEMBER(file_frame_slice, start,
+        (desc, "start"),
+        (doc, "First frame of the slice"))
+
+    BOOST_ANNOTATE_MEMBER(file_frame_slice, count,
+        (desc, "count"),
+        (doc, "Number of frames in the slice [0 = container-limited]"))
+
+    BOOST_ANNOTATE_MEMBER(file_frame_slice, stride,
+        (desc, "stride"),
+        (doc, "Frame index step the slice"))
+    // clang-format on
+
+    BOOST_DESCRIBE_STRUCT(loading_params, (filename_loading_params), (start_number, nb_frames_per_file, frame_slice))
 
     // clang-format off
     BOOST_ANNOTATE_MEMBER(loading_params, start_number,
@@ -78,6 +94,10 @@ namespace io
     BOOST_ANNOTATE_MEMBER(loading_params, nb_frames_per_file,
         (desc, "nb frames per file"),
         (doc, "Number of frames per file [0 = autodetect]"))
+
+    BOOST_ANNOTATE_MEMBER(loading_params, frame_slice,
+        (desc, "frame slice"),
+        (doc, "Slice selecting the frames to load"))
     // clang-format on
 
 } //namespace io

include/lima/io/params.hpp

@@ -9,6 +9,8 @@
 #include <filesystem>
 #include <string>
 
+#include <lima/exceptions.hpp>
+
 #include <lima/io/const.hpp>
 #include <lima/io/enums.hpp>
 
@@ -70,10 +72,53 @@ namespace io
     };
     using filename_loading_params = filename_params_base<DefaultLoadingValues>;
 
+    struct file_frame_slice
+    {
+        int start = 0;
+        int count = 0; //!< End of slice given by container
+        int stride = 1;
+
+        void check() const
+        {
+            if ((start < 0) || (count < 0) || (stride < 1))
+                LIMA_THROW_EXCEPTION(lima::invalid_argument("Invalid file frame slice"));
+        }
+
+        int calc_count(int nb_frames) const
+        {
+            check();
+            if (start >= nb_frames)
+                LIMA_THROW_EXCEPTION(lima::invalid_argument("Invalid file frame slice start/nb_frames"));
+            auto slice_frames = (nb_frames - start - 1) / stride + 1;
+            if (count == 0)
+                return slice_frames;
+            else if (count <= slice_frames)
+                return count;
+            else
+                LIMA_THROW_EXCEPTION(lima::invalid_argument("Invalid file frame slice count/nb_frames"));
+        }
+
+        void apply_sub_slice(file_frame_slice const& o)
+        {
+            check();
+            o.check();
+
+            start += o.start * stride;
+            stride *= o.stride;
+            if (o.count == 0)
+                return;
+            if ((count == 0) || (count >= o.count))
+                count = o.count;
+            else
+                LIMA_THROW_EXCEPTION(lima::invalid_argument("Sub-slice larger than original one"));
+        }
+    };
+
     struct loading_params : filename_loading_params
     {
         int start_number = 0;
         int nb_frames_per_file = 0; //!< Automatic detection
+        file_frame_slice frame_slice;
     };
 
 } //namespace io