void
Hdf5VolumeStore::retrieveAffinities(
ExplicitVolume<float>& xAffinities,
ExplicitVolume<float>& yAffinities,
ExplicitVolume<float>& zAffinities) {
readVolume(xAffinities, "xAffinities");
readVolume(yAffinities, "yAffinities");
readVolume(zAffinities, "zAffinities");
}
inline void
Volume<T>::read(HDF5Id file_id, u32 index)
{
HDF5Group volume_root_group;
HDF5Group::getRootGroup(file_id, kVolumeRootGroup, volume_root_group);
// get the size of the volume group name
u32 size = H5Lget_name_by_idx(volume_root_group.id(), ".",
H5_INDEX_CRT_ORDER,
H5_ITER_INC,
index,
NULL,
0,
H5P_DEFAULT);
// for some reason HDF5 shorts the name size by 1. Restore it to
// proper length here.
++size;
// get the name of the link at index
char buf[size];
H5Lget_name_by_idx(volume_root_group.id(), ".",
H5_INDEX_CRT_ORDER,
H5_ITER_INC,
index,
buf,
size,
H5P_DEFAULT);
String volume_name(buf);
// now read in this volume by name
readVolume(volume_root_group.id(), volume_name);
}
inline void
Volume<T>::read(HDF5Id file_id, String volume_name)
{
HDF5Group volume_root_group;
HDF5Group::getRootGroup(file_id, kVolumeRootGroup, volume_root_group);
readVolume(volume_root_group.id(), volume_name);
}
void
Hdf5VolumeStore::retrieveGroundTruth(ExplicitVolume<int>& labels) {
readVolume(labels, "groundtruth");
}
void
Hdf5VolumeStore::retrieveBoundaries(ExplicitVolume<float>& boundaries) {
readVolume(boundaries, "boundaries");
}
void
Hdf5VolumeStore::retrieveIntensities(ExplicitVolume<float>& intensities) {
readVolume(intensities, "intensities");
}
void
Hdf5VolumeStore::retrieveLabels(ExplicitVolume<int>& labels) {
_hdfFile.cd("/volumes");
readVolume(labels, "labels");
}
void
Hdf5VolumeStore::retrieveIntensities(ExplicitVolume<float>& intensities) {
_hdfFile.cd("/volumes");
readVolume(intensities, "intensities");
}
