def get_nested_dict_from_shot(filepath):
row = runmanager.get_shot_globals(filepath)
with h5py.File(filepath, 'r') as h5_file:
if 'results' in h5_file:
for groupname in h5_file['results']:
resultsgroup = h5_file['results'][groupname]
row[groupname] = get_attributes(resultsgroup)
if 'images' in h5_file:
for orientation in h5_file['images'].keys():
if isinstance(h5_file['images'][orientation], h5py.Group):
row[orientation] = get_attributes(
h5_file['images'][orientation])
for label in h5_file['images'][orientation]:
row[orientation][label] = {}
group = h5_file['images'][orientation][label]
for image in group:
row[orientation][label][image] = {}
for key, val in get_attributes(
group[image]).items():
if not isinstance(val, h5py.Reference):
row[orientation][label][image][key] = val
row['filepath'] = _ensure_str(filepath)
row['agnostic_path'] = labscript_utils.shared_drive.path_to_agnostic(
filepath)
seq_id = _ensure_str(h5_file.attrs['sequence_id'])
row['sequence'] = asdatetime(seq_id.split('_')[0])
try:
row['sequence_index'] = h5_file.attrs['sequence_index']
except KeyError:
row['sequence_index'] = None
if 'script' in h5_file:
row['labscript'] = _ensure_str(h5_file['script'].attrs['name'])
try:
row['run time'] = asdatetime(_ensure_str(
h5_file.attrs['run time']))
except KeyError:
row['run time'] = float('nan')
try:
row['run number'] = h5_file.attrs['run number']
except KeyError:
row['run number'] = float('nan')
try:
row['run repeat'] = h5_file.attrs['run repeat']
except KeyError:
row['run repeat'] = 0
try:
row['n_runs'] = h5_file.attrs['n_runs']
except KeyError:
row['n_runs'] = float('nan')
return row
def get_image_attributes(self, orientation):
with h5py.File(self.h5_path, 'r') as h5_file:
if not 'images' in h5_file:
raise Exception('File does not contain any images')
if not orientation in h5_file['images']:
raise Exception('File does not contain any images with orientation \'%s\''%orientation)
return get_attributes(h5_file['images'][orientation])
def get_attrs(self, group):
"""Returns all attributes of the specified group as a dictionary.
Args:
group (str): Group for which attributes are desired.
Raises:
Exception: If the `group` does not exist.
Returns:
dict: Dictionary of attributes.
"""
with h5py.File(self.h5_path, 'r') as h5_file:
if not group in h5_file:
raise Exception('The group \'%s\' does not exist' % group)
return get_attributes(h5_file[group])
def get_image_attributes(self, orientation):
"""Return the attributes of a saved orientation image group.
Args:
orientation (str): Orientation label to get attributes of.
Raises:
Exception: If images or orientation group do not exist.
Returns:
dict: Dictionary of attributes and their values.
"""
with h5py.File(self.h5_path, 'r') as h5_file:
if not 'images' in h5_file:
raise Exception('File does not contain any images')
if not orientation in h5_file['images']:
raise Exception(
'File does not contain any images with orientation \'%s\''
% orientation)
return get_attributes(h5_file['images'][orientation])
def get_attrs(self, group):
"""Returns all attributes of the specified group as a dictionary."""
with h5py.File(self.h5_path) as h5_file:
if not group in h5_file:
raise Exception('The group \'%s\' does not exist' % group)
return get_attributes(h5_file[group])
def get_attrs(self, group, h5_file=None):
"""Returns all attributes of the specified group as a dictionary."""
if not group in h5_file:
raise Exception('The group \'%s\' does not exist' % group)
return get_attributes(h5_file[group])
