diff --git a/src/cdtools/tools/data/data.py b/src/cdtools/tools/data/data.py index 19e7467..ed13542 100644 --- a/src/cdtools/tools/data/data.py +++ b/src/cdtools/tools/data/data.py @@ -485,9 +485,9 @@ def add_entry_info(cxi_file, metadata): # included in case the cxi spec becomes more permissive for key, value in metadata.items(): if isinstance(value,(str,bytes)): - cxi_file['entry_1'][key] = np.string_(value) + cxi_file['entry_1'][key] = np.bytes_(value) elif isinstance(value, datetime.datetime): - cxi_file['entry_1'][key] = np.string_(value.isoformat()) + cxi_file['entry_1'][key] = np.bytes_(value.isoformat()) elif isinstance(value, numbers.Number): cxi_file['entry_1'][key] = value elif isinstance(value, (np.ndarray,list,tuple)): @@ -525,9 +525,9 @@ def add_sample_info(cxi_file, metadata): if key == 'orientation': continue # this is a special case if isinstance(value,(str,bytes)): - s1[key] = np.string_(value) + s1[key] = np.bytes_(value) elif isinstance(value, datetime.datetime): - s1[key] = np.string_(value.isoformat()) + s1[key] = np.bytes_(value.isoformat()) elif isinstance(value, numbers.Number): s1[key] = value elif isinstance(value, (np.ndarray,list,tuple)): @@ -701,7 +701,7 @@ def add_data(cxi_file, data, axes=None, compression='gzip', axes_str = ':'.join(axes) else: axes_str = str(axes) - det1['data'].attrs['axes'] = np.string_(axes_str) + det1['data'].attrs['axes'] = np.bytes_(axes_str) def add_shot_to_shot_info(cxi_file, data, field_name): diff --git a/tests/conftest.py b/tests/conftest.py index 9eceb0c..ca3a2c7 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -77,28 +77,28 @@ def ptycho_cxi_1(): expected['entry metadata'] = {} e1e = expected['entry metadata'] e1e['start_time'] = datetime.datetime.now() - e1f['start_time'] = np.string_(e1e['start_time'].isoformat()) + e1f['start_time'] = np.bytes_(e1e['start_time'].isoformat()) e1e['end_time'] = datetime.datetime.now() - e1f['end_time'] = np.string_(e1e['end_time'].isoformat()) + e1f['end_time'] = np.bytes_(e1e['end_time'].isoformat()) e1e['experiment_identifier'] = 'Fake Experiment 1' - e1f['experiment_identifier'] = np.string_(e1e['experiment_identifier']) + e1f['experiment_identifier'] = np.bytes_(e1e['experiment_identifier']) e1e['experiment_description'] = 'A fully defined ptychography experiment to test the data loading' - e1f['experiment_description'] = np.string_(e1e['experiment_description']) + e1f['experiment_description'] = np.bytes_(e1e['experiment_description']) e1e['program_name'] = 'cdtools' - e1f['program_name'] = np.string_(e1e['program_name']) + e1f['program_name'] = np.bytes_(e1e['program_name']) e1e['title'] = 'The one experiment we did' - e1f['title'] = np.string_(e1e['title']) + e1f['title'] = np.bytes_(e1e['title']) # Set up the sample info s1f = e1f.create_group('sample_1') expected['sample info'] = {} s1e = expected['sample info'] s1e['name'] = 'Fake Sample' - s1f['name'] = np.string_(s1e['name']) + s1f['name'] = np.bytes_(s1e['name']) s1e['description'] = 'A sample that isn\'t real' - s1f['description'] = np.string_(s1e['description']) + s1f['description'] = np.bytes_(s1e['description']) s1e['unit_cell_group'] = 'P1' - s1f['unit_cell_group'] = np.string_(s1e['unit_cell_group']) + s1f['unit_cell_group'] = np.bytes_(s1e['unit_cell_group']) s1e['concentration'] = np.float32(np.random.rand()) s1f['concentration'] = s1e['concentration'] s1e['mass'] = np.float32(np.random.rand()) @@ -151,7 +151,7 @@ def ptycho_cxi_1(): d1f.create_dataset('data',data=data) data1f['data'] = h5py.SoftLink('/entry_1/instrument_1/detector_1/data') - d1f['data'].attrs['axes'] = np.string_('translation:y:x') + d1f['data'].attrs['axes'] = np.bytes_('translation:y:x') expected['axes'] = ['translation','y','x'] g1f = s1f.create_group('geometry_1') @@ -196,7 +196,7 @@ def ptycho_cxi_2(): expected['entry metadata'] = {} e1e = expected['entry metadata'] e1e['title'] = 'The one experiment we did' - e1f['title'] = np.string_(e1e['title']) + e1f['title'] = np.bytes_(e1e['title']) # Set up the sample info s1f = e1f.create_group('sample_1') @@ -277,9 +277,9 @@ def ptycho_cxi_3(): expected['entry metadata'] = {} e1e = expected['entry metadata'] e1e['start_time'] = datetime.datetime.now() - e1f['start_time'] = np.string_(e1e['start_time'].isoformat()) + e1f['start_time'] = np.bytes_(e1e['start_time'].isoformat()) e1e['end_time'] = datetime.datetime.now() - e1f['end_time'] = np.string_(e1e['end_time'].isoformat()) + e1f['end_time'] = np.bytes_(e1e['end_time'].isoformat()) # Set up the sample info expected['sample info'] = None @@ -314,7 +314,7 @@ def ptycho_cxi_3(): expected['data'] = data data1f.create_dataset('data',data=data) - data1f['data'].attrs['axes'] = np.string_('translation:y:x') + data1f['data'].attrs['axes'] = np.bytes_('translation:y:x') expected['axes'] = ['translation','y','x'] translations = np.arange(300).reshape((100,3)).astype(np.float32)