[file_hdf5] read data hdf5 files

diff --git a/src/io/file_hdf5.c b/src/io/file_hdf5.c
new file mode 100644 (file)
index 0000000..332b48a
--- /dev/null
+++ b/src/io/file_hdf5.c
@@ -0,0 +1,123 @@
+/*
+  Copyright (C) 2018 Paul Brossier <piem@aubio.org>
+
+  This file is part of aubio.
+
+  aubio is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+
+  aubio is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with aubio.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
+
+#include "aubio_priv.h"
+
+#ifdef HAVE_HDF5
+
+#include "fmat.h"
+#include "ai/tensor.h"
+#include "file_hdf5.h"
+
+#include <hdf5.h>
+#include <hdf5_hl.h>
+
+struct _aubio_file_hdf5_t {
+  const char_t *path;
+  hid_t fid;
+  hid_t datatype;
+};
+
+aubio_file_hdf5_t *new_aubio_file_hdf5(const char_t *path)
+{
+  aubio_file_hdf5_t *f = AUBIO_NEW(aubio_file_hdf5_t);
+
+  f->fid = H5Fopen(path, H5F_ACC_RDONLY, H5P_DEFAULT);
+  if (f->fid <= 0) goto failure;
+
+  f->path = path;
+  return f;
+
+failure:
+  del_aubio_file_hdf5(f);
+  return NULL;
+}
+
+uint_t aubio_file_hdf5_load_dataset_into_tensor (aubio_file_hdf5_t *f,
+    const char_t *key, aubio_tensor_t *tensor) {
+  uint_t i;
+  AUBIO_ASSERT(f && key && tensor);
+  // check file is open
+  if (!f->fid)
+    return AUBIO_FAIL;
+  // find key in file
+  hid_t data_id = H5Dopen(f->fid, key, H5P_DEFAULT);
+  if (data_id <= 0) {
+    AUBIO_ERR("file_hdf5: failed getting key %s in %s\n", key, f->path);
+    return AUBIO_FAIL;
+  }
+  // get dimensions
+  hsize_t shape[10];
+  hid_t space = H5Dget_space(data_id);
+  int ndim = H5Sget_simple_extent_dims(space, shape, NULL);
+  if (ndim <= 0) {
+    AUBIO_ERR("file_hdf5: failed to get dims of %s in %s\n", key, f->path);
+    return AUBIO_FAIL;
+  }
+
+  // check output tensor dimension matches
+  AUBIO_ASSERT(ndim == (sint_t)tensor->ndim);
+  for (i = 0; i < (uint_t)ndim; i++) {
+    //AUBIO_DBG("file_hdf5: found dim %d : %d %d (%s in %s)\n", i, dims[i],
+    //    tensor->shape[i], key, f->path);
+    AUBIO_ASSERT(shape[i] == tensor->shape[i]);
+  }
+
+  if (ndim != (sint_t)tensor->ndim) return AUBIO_FAIL;
+  for (i = 0; i < (uint_t)ndim; i++) {
+    if (shape[i] != tensor->shape[i]) return AUBIO_FAIL;
+  }
+
+  // read data from hdf5 file into tensor buffer
+  smpl_t *buffer = tensor->buffer;
+  herr_t err = H5LTread_dataset_float(f->fid, key, buffer);
+
+  if (err < 0) {
+    return AUBIO_FAIL;
+  }
+
+  H5Dclose(data_id);
+  return AUBIO_OK;
+}
+
+uint_t aubio_file_hdf5_load_dataset_into_matrix(aubio_file_hdf5_t *f,
+    const char_t *key, fmat_t *mat) {
+  aubio_tensor_t t;
+  if (aubio_fmat_as_tensor (mat, &t)) return AUBIO_FAIL;
+  return aubio_file_hdf5_load_dataset_into_tensor(f, key, &t);
+}
+
+
+uint_t aubio_file_hdf5_load_dataset_into_vector(aubio_file_hdf5_t *f,
+    const char_t *key, fvec_t *vec) {
+  aubio_tensor_t t;
+  if (aubio_fvec_as_tensor (vec, &t)) return AUBIO_FAIL;
+  return aubio_file_hdf5_load_dataset_into_tensor(f, key, &t);
+}
+
+void del_aubio_file_hdf5(aubio_file_hdf5_t *f)
+{
+  AUBIO_ASSERT(f);
+  if (f->fid > 0)
+    H5Fclose(f->fid);
+  AUBIO_FREE(f);
+}
+
+#endif /* HAVE_HDF5 */

diff --git a/src/io/file_hdf5.h b/src/io/file_hdf5.h
new file mode 100644 (file)
index 0000000..333700a
--- /dev/null
+++ b/src/io/file_hdf5.h
@@ -0,0 +1,39 @@
+/*
+  Copyright (C) 2018 Paul Brossier <piem@aubio.org>
+
+  This file is part of aubio.
+
+  aubio is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+
+  aubio is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with aubio.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
+
+#ifndef AUBIO_FILE_HDF5_H
+#define AUBIO_FILE_HDF5_H
+
+typedef struct _aubio_file_hdf5_t aubio_file_hdf5_t;
+
+aubio_file_hdf5_t *new_aubio_file_hdf5(const char_t *path);
+
+void del_aubio_file_hdf5(aubio_file_hdf5_t *f);
+
+uint_t aubio_file_hdf5_load_dataset_into_tensor (aubio_file_hdf5_t *f,
+    const char_t *key, aubio_tensor_t *tensor);
+
+uint_t aubio_file_hdf5_load_dataset_into_matrix(aubio_file_hdf5_t *f,
+    const char_t *key, fmat_t *mat);
+
+uint_t aubio_file_hdf5_load_dataset_into_vector (aubio_file_hdf5_t *f,
+    const char_t *key, fvec_t *vec);
+
+#endif /* AUBIO_FILE_HDF5_H */