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Support Empty Array Annotations in NixIO #806

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merged 2 commits into from
Nov 6, 2020
Merged

Support Empty Array Annotations in NixIO #806

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9db5911
Support empty array annotations
Kleinjohann Apr 15, 2020
141fc3d
Add test with empty array annotation
Kleinjohann Apr 15, 2020
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12 changes: 6 additions & 6 deletions neo/io/nixio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -854,7 +854,7 @@ def _write_analogsignal(self, anasig, nixblock, nixgroup):
if anasig.array_annotations:
for k, v in anasig.array_annotations.items():
p = self._write_property(metadata, k, v)
p.definition = ARRAYANNOTATION
p.type = ARRAYANNOTATION

self._signal_map[nix_name] = nixdas

Expand Down Expand Up @@ -992,7 +992,7 @@ def _write_irregularlysampledsignal(self, irsig, nixblock, nixgroup):
if irsig.array_annotations:
for k, v in irsig.array_annotations.items():
p = self._write_property(metadata, k, v)
p.definition = ARRAYANNOTATION
p.type = ARRAYANNOTATION

self._signal_map[nix_name] = nixdas

Expand Down Expand Up @@ -1047,7 +1047,7 @@ def _write_event(self, event, nixblock, nixgroup):
if event.array_annotations:
for k, v in event.array_annotations.items():
p = self._write_property(metadata, k, v)
p.definition = ARRAYANNOTATION
p.type = ARRAYANNOTATION

nixgroup.multi_tags.append(nixmt)

Expand Down Expand Up @@ -1115,7 +1115,7 @@ def _write_epoch(self, epoch, nixblock, nixgroup):
if epoch.array_annotations:
for k, v in epoch.array_annotations.items():
p = self._write_property(metadata, k, v)
p.definition = ARRAYANNOTATION
p.type = ARRAYANNOTATION

nixgroup.multi_tags.append(nixmt)

Expand Down Expand Up @@ -1177,7 +1177,7 @@ def _write_spiketrain(self, spiketrain, nixblock, nixgroup):
if spiketrain.array_annotations:
for k, v in spiketrain.array_annotations.items():
p = self._write_property(metadata, k, v)
p.definition = ARRAYANNOTATION
p.type = ARRAYANNOTATION

if nixgroup:
nixgroup.multi_tags.append(nixmt)
Expand Down Expand Up @@ -1390,7 +1390,7 @@ def _nix_attr_to_neo(nix_obj):
if prop.definition in (DATEANNOTATION, TIMEANNOTATION,
DATETIMEANNOTATION):
values = dt_from_nix(values, prop.definition)
if prop.definition == ARRAYANNOTATION:
if prop.type == ARRAYANNOTATION:
if 'array_annotations' in neo_attrs:
neo_attrs['array_annotations'][prop.name] = values
else:
Expand Down
30 changes: 24 additions & 6 deletions neo/test/iotest/test_nixio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -418,7 +418,7 @@ def create_full_nix_file(cls, filename):
asig_md.create_property(arr_ann_name,
arr_ann_val.magnitude.flatten())
asig_md.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
asig_md.props[arr_ann_name].definition = 'ARRAYANNOTATION'
asig_md.props[arr_ann_name].type = 'ARRAYANNOTATION'

for idx in range(10):
da_asig = blk.create_data_array(
Expand Down Expand Up @@ -452,7 +452,7 @@ def create_full_nix_file(cls, filename):
imgseq_md.create_property(arr_ann_name,
arr_ann_val.magnitude.flatten())
imgseq_md.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
imgseq_md.props[arr_ann_name].definition = 'ARRAYANNOTATION'
imgseq_md.props[arr_ann_name].type = 'ARRAYANNOTATION'

for idx in range(10):
da_imgseq = blk.create_data_array(
Expand Down Expand Up @@ -485,7 +485,7 @@ def create_full_nix_file(cls, filename):
isig_md.create_property(arr_ann_name,
arr_ann_val.magnitude.flatten())
isig_md.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
isig_md.props[arr_ann_name].definition = 'ARRAYANNOTATION'
isig_md.props[arr_ann_name].type = 'ARRAYANNOTATION'
for idx in range(7):
da_isig = blk.create_data_array(
"{}.{}".format(isig_name, idx),
Expand Down Expand Up @@ -527,7 +527,7 @@ def create_full_nix_file(cls, filename):
mtag_st_md.create_property(arr_ann_name,
arr_ann_val.magnitude.flatten())
mtag_st_md.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
mtag_st_md.props[arr_ann_name].definition = 'ARRAYANNOTATION'
mtag_st_md.props[arr_ann_name].type = 'ARRAYANNOTATION'

waveforms = cls.rquant((10, 8, 5), 1)
wfname = "{}.waveforms".format(mtag_st.name)
Expand Down Expand Up @@ -579,7 +579,7 @@ def create_full_nix_file(cls, filename):
mtag_ep.metadata.create_property(arr_ann_name,
arr_ann_val.magnitude.flatten())
mtag_ep.metadata.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
mtag_ep.metadata.props[arr_ann_name].definition = 'ARRAYANNOTATION'
mtag_ep.metadata.props[arr_ann_name].type = 'ARRAYANNOTATION'

label_dim = mtag_ep.positions.append_set_dimension()
label_dim.labels = cls.rsentence(5).split(" ")
Expand Down Expand Up @@ -612,7 +612,7 @@ def create_full_nix_file(cls, filename):
mtag_ev.metadata.create_property(arr_ann_name,
arr_ann_val.magnitude.flatten())
mtag_ev.metadata.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
mtag_ev.metadata.props[arr_ann_name].definition = 'ARRAYANNOTATION'
mtag_ev.metadata.props[arr_ann_name].type = 'ARRAYANNOTATION'

label_dim = mtag_ev.positions.append_set_dimension()
label_dim.labels = cls.rsentence(5).split(" ")
Expand Down Expand Up @@ -1486,6 +1486,24 @@ def test_annotations_special_cases(self):

# TODO: multi dimensional value (GH Issue #501)

def test_empty_array_annotations(self):
wblock = Block("block with spiketrain")
wseg = Segment()
wseg.spiketrains = [SpikeTrain(times=[] * pq.s, t_stop=1 * pq.s,
array_annotations={'empty': []})]
wblock.segments = [wseg]
self.writer.write_block(wblock)
try:
rblock = self.writer.read_block(neoname="block with spiketrain")
except Exception as exc:
self.fail('The following exception was raised when'
+ ' reading the block with an empty array annotation:\n'
+ str(exc))
rst = rblock.segments[0].spiketrains[0]
self.assertEqual(len(rst.array_annotations), 1)
self.assertIn('empty', rst.array_annotations.keys())
self.assertEqual(len(rst.array_annotations['empty']), 0)

def test_write_proxyobjects(self):

def generate_complete_block():
Expand Down