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deal with the string_ related issues

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This commit is contained in:
allevitan
2024-10-13 13:08:17 -04:00
parent 7fba211b5d
commit 25224d4d44
2 changed files with 19 additions and 19 deletions
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src/cdtools/tools/data/data.py
+5 -5
View File
@@ -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):
tests/conftest.py
+14 -14
View File
@@ -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)