def test_create_region_ref(self):
file_path = 'test.h5'
data_utils.delete_existing_file(file_path)
data = np.random.rand(5, 7)
with h5py.File(file_path, mode='w') as h5_f:
h5_dset = h5_f.create_dataset('Source', data=data)
pos_inds = np.arange(0, h5_dset.shape[0], 2)
ref_inds = [((pos_start, 0), (pos_start, h5_dset.shape[1] - 1))
for pos_start in pos_inds]
ref_inds = np.array(ref_inds)
this_reg_ref = reg_ref.create_region_reference(h5_dset, ref_inds)
ref_slices = list()
for start, stop in ref_inds:
ref_slices.append(
[slice(start[0], stop[0] + 1),
slice(start[1], None)])
h5_reg = h5_dset[this_reg_ref]
h5_slice = np.vstack([
h5_dset[pos_slice, spec_slice]
for (pos_slice, spec_slice) in ref_slices
])
self.assertTrue(np.allclose(h5_reg, h5_slice))
os.remove(file_path)
def _write_results_chunk(self):
"""
Writes the provided SVD results to file
Parameters
----------
"""
comp_dim = Dimension('Principal Component', 'a. u.', len(self.__s))
h5_svd_group = create_results_group(self.h5_main, self.process_name,
h5_parent_group=self._h5_target_group)
self.h5_results_grp = h5_svd_group
self._write_source_dset_provenance()
write_simple_attrs(h5_svd_group, self.parms_dict)
write_simple_attrs(h5_svd_group, {'svd_method': 'sklearn-randomized'})
h5_u = write_main_dataset(h5_svd_group, np.float32(self.__u), 'U', 'Abundance', 'a.u.', None, comp_dim,
h5_pos_inds=self.h5_main.h5_pos_inds, h5_pos_vals=self.h5_main.h5_pos_vals,
dtype=np.float32, chunks=calc_chunks(self.__u.shape, np.float32(0).itemsize))
# print(get_attr(self.h5_main, 'quantity')[0])
h5_v = write_main_dataset(h5_svd_group, self.__v, 'V', get_attr(self.h5_main, 'quantity')[0],
'a.u.', comp_dim, None, h5_spec_inds=self.h5_main.h5_spec_inds,
h5_spec_vals=self.h5_main.h5_spec_vals,
chunks=calc_chunks(self.__v.shape, self.h5_main.dtype.itemsize))
# No point making this 1D dataset a main dataset
h5_s = h5_svd_group.create_dataset('S', data=np.float32(self.__s))
'''
Check h5_main for plot group references.
Copy them into V if they exist
'''
for key in self.h5_main.attrs.keys():
if '_Plot_Group' not in key:
continue
ref_inds = get_indices_for_region_ref(self.h5_main, self.h5_main.attrs[key], return_method='corners')
ref_inds = ref_inds.reshape([-1, 2, 2])
ref_inds[:, 1, 0] = h5_v.shape[0] - 1
svd_ref = create_region_reference(h5_v, ref_inds)
h5_v.attrs[key] = svd_ref
# Marking completion:
self._status_dset_name = 'completed_positions'
self._h5_status_dset = h5_svd_group.create_dataset(self._status_dset_name,
data=np.ones(self.h5_main.shape[0], dtype=np.uint8))
# keeping legacy option:
h5_svd_group.attrs['last_pixel'] = self.h5_main.shape[0]