# change data orientation to be top=ventral, right=lateral
imgseq = block.segments[0].imagesequences[0]
imgseq = flip_image(imgseq, axis=-2)
imgseq = rotate_image(imgseq, rotation=-90)
block.segments[0].imagesequences[0] = imgseq
# Transform into analogsignals
block.segments[0].analogsignals = []
block = ImageSequence2AnalogSignal(block)
block.segments[0].analogsignals[0] = time_slice(
block.segments[0].analogsignals[0], args.t_start, args.t_stop)
if args.annotations is not None:
block.segments[0].analogsignals[0].annotations.\
update(parse_string2dict(args.annotations))
block.segments[0].analogsignals[0].annotations.update(
orientation_top=args.orientation_top)
block.segments[0].analogsignals[0].annotations.update(
orientation_right=args.orientation_right)
# ToDo: add metadata
block.name = args.data_name
block.segments[0].name = 'Segment 1'
block.segments[0].description = 'Loaded from mat file. '\
.format(neo.__version__)
if block.segments[0].analogsignals[0].description is None:
block.segments[0].analogsignals[0].description = ''
block.segments[0].analogsignals[0].description += 'MF simulation output '
except Exception as e:
print(e)
block = load_neo(args.data, try_signal_grouping=True)
asigs = block.segments[0].analogsignals
if len(asigs) > 1:
print(f'Merging {len(asigs)} AnalogSignals into one.')
asig = merge_analogsingals(asigs)
else:
asig = asigs[0]
asig = time_slice(asig, args.t_start, args.t_stop)
# add metadata
kwargs = parse_string2dict(args.kwargs)
channels = asig.array_annotations[kwargs['ELECTRODE_ANNOTATION_NAME']]
coords = np.array([
kwargs['NAME2COORDS'][str(channel)] for channel in channels.astype(int)
])
asig.array_annotations.update(x_coords=coords[:, 0])
asig.array_annotations.update(y_coords=coords[:, 1])
# locations = []
# for channel in channels:
# locations.append([loc for loc in kwargs['ELECTRODE_LOCATION'].keys()
# if channel in kwargs['ELECTRODE_LOCATION'][loc]][0])
# asig.array_annotations.update(electrode_location=locations)
block = load_neo(args.data)
# If there is no Neo IO for the data type available,
# the data must be loaded conventioally and added to a newly constructed
# Neo block. For building a Neo objects, have a look into the documentation
# https://neo.readthedocs.io/
# In case the dataset is imagaging data and therefore stored as an
# ImageSequence object, it needs to be transformed into an AnalogSignal
# object. To do this use the function ImageSequence2AnalogSignal in utils.py
asig = block.segments[0].analogsignals[0]
asig = time_slice(asig, args.t_start, args.t_stop)
# Add metadata from ANNOTIATION dict
asig.annotations.update(parse_string2dict(args.annotations))
asig.annotations.update(spatial_scale=args.spatial_scale * pq.mm)
asog.annotations.update(orientation_top=args.orientation_top)
asog.annotations.update(orientation_right=args.orientation_right)
# Add metadata from ARRAY_ANNOTIATION dict
asig.array_annotations.update(parse_string2dict(args.array_annotations))
# Do custom metadata processing from KWARGS dict (optional)
# kwargs = parse_string2dict(args.kwargs)
# ... do something
# Add description to the Neo object
block.name = args.data_name
block.segments[0].name = 'Segment 1'
block.segments[0].description = 'Loaded with neo.io version {}'\