def query_annotations(self, ts, layer, start=None, end=None, channels=None, limit=100, offset=0):
"""
Retrieves timeseries annotations for a particular range on array of channels.
"""
ch_list = self.requested_channels(ts, channels)
ts_start, ts_end = ts.limits()
if start is None:
start = ts_start
elif isinstance(start, datetime.datetime):
start = usecs_since_epoch(start)
if end is None:
end = ts_end
elif isinstance(end, datetime.datetime):
end = usecs_since_epoch(end)
params = {
'start': int(start),
'end': int(end),
'channelIds': ch_list,
'layerName': layer.name,
'limit': limit,
'offset': offset
}
path = self._uri('/{ts_id}/layers/{layer_id}/annotations',
ts_id = ts.id,layer_id = layer.id)
resp = self._get(path, params=params)
return [TimeSeriesAnnotation.from_dict(x, api=self.session) for x in resp['annotations']['results']]
def test_timeseries_annotations_can_get_more_than_default_limit(timeseries):
ch = TimeSeriesChannel(name="test_channel",
rate=256,
unit="uV",
start=0,
end=2e6)
timeseries.add_channels(ch)
layer = TimeSeriesAnnotationLayer(
name="limit_layer",
time_series_id=timeseries.id,
description="layer with many small annotations",
)
timeseries.add_layer(layer)
for i in range(200):
annotation = TimeSeriesAnnotation(
label="annotation_{}".format(i),
channel_ids=ch.id,
start=i * 1e4,
end=(i + 1) * 1e4,
)
layer.add_annotations(annotation)
# Should retrieve all annotations
assert len(layer.annotations()) == 200
# All of these annotations should be in the first 10-second window
annots = next(layer.iter_annotations())
assert len(annots) == 200
layer.delete()
def update_annotation(self, ts, layer, annot):
"""
Update annotation on the platform.
"""
path = self._uri('/{ts_id}/layers/{layer_id}/annotations/{annot_id}',
ts_id=self._get_id(ts),
layer_id=self._get_id(layer),
annot_id=self._get_id(annot))
resp = self._put(path, json=annot.as_dict())
return TimeSeriesAnnotation.from_dict(resp, api=self.session)
def get_annotation(self, ts, layer, annot):
"""
Returns a timeseries annotation
"""
path = self._uri('/{ts_id}/layers/{layer_id}/annotations/{annot_id}',
ts_id = self._get_id(ts),
layer_id = self._get_id(layer),
annot_id = self._get_id(annot))
resp = self._get(path)
return TimeSeriesAnnotation.from_dict(resp["annotation"], api=self.session)
def create_annotation(self, layer, annotation, **kwargs):
"""
Creates annotation for some timeseries package on the platform.
"""
if isinstance(annotation, TimeSeriesAnnotation):
data = annotation.as_dict()
elif all(x in kwargs for x in ["start", "end"]):
start_time = infer_epoch(kwargs["start"])
end_time = infer_epoch(kwargs["end"])
data = {
"name": "",
"label": annotation,
"start": int(start_time),
"end": int(end_time),
}
if kwargs["channel_ids"]:
channel_ids = kwargs["channel_ids"]
if isinstance(channel_ids, string_types):
channel_ids = [channel_ids]
data["channelIds"] = channel_ids
else:
ts = layer._api.core.get(layer.time_series_id)
data["channelIds"] = [x.id for x in ts.channels]
if "description" in annotation:
data["description"] = kwargs["description"]
else:
data["description"] = None
else:
raise Exception(
"Must provide TimeSeriesAnnotation object or 'annotation','start','end' at minimum"
)
data["time_series_id"] = layer.time_series_id
data["layer_id"] = layer.id
path = self._uri(
"/{ts_id}/layers/{layer_id}/annotations",
ts_id=layer.time_series_id,
layer_id=layer.id,
)
resp = self._post(path, json=data)
tmp = TimeSeriesAnnotation.from_dict(resp, api=self.session)
if isinstance(annotation, TimeSeriesAnnotation):
annotation.__dict__.update(tmp.__dict__)
return tmp
def create_annotation(self, layer, annotation, **kwargs):
"""
Creates annotation for some timeseries package on the platform.
"""
if isinstance(annotation, TimeSeriesAnnotation):
data = annotation.as_dict()
elif all(x in kwargs for x in ['start', 'end']):
start_time = infer_epoch(kwargs['start'])
end_time = infer_epoch(kwargs['end'])
data = {
'name': '',
'label': annotation,
'start': long(start_time),
'end': long(end_time),
}
if kwargs['channel_ids']:
channel_ids = kwargs['channel_ids']
if isinstance(channel_ids, basestring):
channel_ids = [channel_ids]
data['channelIds'] = channel_ids
else:
ts = layer._api.core.get(layer.time_series_id)
data['channelIds'] = [x.id for x in ts.channels]
if 'description' in annotation:
data['description'] = kwargs['description']
else:
data['description'] = None
else:
raise Exception(
"Must provide TimeSeriesAnnotation object or 'annotation','start','end' at minimum"
)
data['time_series_id'] = layer.time_series_id
data['layer_id'] = layer.id
path = self._uri('/{ts_id}/layers/{layer_id}/annotations',
ts_id=layer.time_series_id,
layer_id=layer.id)
resp = self._post(path, json=data)
tmp = TimeSeriesAnnotation.from_dict(resp, api=self.session)
if isinstance(annotation, TimeSeriesAnnotation):
annotation.__dict__.update(tmp.__dict__)
return tmp
def test_timeseries_annotations(client, timeseries):
assert timeseries.exists
print 'layers = ', timeseries.layers
#Create Layer
layer1 = TimeSeriesAnnotationLayer(name="test_layer", time_series_id = timeseries.id, description="test_description")
a = layer1.as_dict()
assert a['name'] == 'test_layer'
assert a['description'] == 'test_description'
# Add Layer
timeseries.add_layer(layer1)
assert layer1.exists
# Get Layer
layer1b = timeseries.get_layer('test_layer')
assert layer1b.exists
assert layer1b.name == "test_layer"
assert layer1.id == layer1b.id
assert layer1._api.timeseries is not None
# Add another layer
layer2 = timeseries.add_layer('test_layer2','test_description2')
assert layer2.exists
layer2copy = timeseries.add_layer('test_layer2')
assert layer2copy.id == layer2.id
# Get Layer
layer2b = timeseries.get_layer('test_layer2')
assert layer2b.exists
assert layer2b.name == "test_layer2"
assert layer2.id == layer2b.id
assert layer2._api.timeseries is not None
layers = timeseries.layers
assert len(layers)==2
assert layers[0].name == "test_layer"
assert layers[1].name == 'test_layer2'
#Create channels
ch = TimeSeriesChannel(
name='test_channel',
rate=256,
unit='uV',
start=1,
end=60*1e6)
#Create annotation over one channel
# create
timeseries.add_channels(ch)
assert ch.exists
assert ch.id in [x.id for x in timeseries.channels]
annot = TimeSeriesAnnotation(label = 'test_label', channel_ids = timeseries.channels[0].id,start = timeseries.channels[0].start,end=timeseries.channels[0].start+1*1e6)
#Add Annotation
layer1.add_annotations(annot)
assert annot.exists
# get annotations
annotb = layer1.annotations()
print "annotations = ", annotb
assert annotb[0].label == annot.label
#Create annotation over multiple channels
ch2 = TimeSeriesChannel(
name='test_channel',
rate=256,
unit='uV',
start=1,
end=60*1e6)
timeseries.add_channels(ch2)
channels = timeseries.channels
ch_ids = [x.id for x in channels]
assert ch2.exists
assert ch2.id in ch_ids
assert ch.id in ch_ids
for ch in channels:
assert ch.rate == 256
assert ch.exists
#add annotation over two channels
channel_ids = [timeseries.channels[x].id for x in range(len(timeseries.channels))]
annot2 = layer1.insert_annotation(annotation='test_label2', channel_ids = channel_ids,
start =timeseries.channels[0].start+1*1e6,
end = timeseries.channels[0].start+2*1e6)
assert annot2.exists
annot_gen = layer1.iter_annotations(1)
annot = annot_gen.next()
assert annot[0].label == 'test_label'
next_annot= annot_gen.next()
assert next_annot[0].label == 'test_label2'
### TEST DELETION
annot3 = TimeSeriesAnnotation(label= 'test_label3', channel_ids= channel_ids,start = timeseries.channels[0].start+1*1e6,end=timeseries.channels[0].start+2*1e6)
#layer1.add_annotations([annot2,annot3])
annot3 = timeseries.add_annotations(layer=layer1,annotations=annot3)
assert annot3.exists
annot3.delete()
assert not annot3.exists
annot4 = timeseries.insert_annotation(layer=layer1,annotation='test_label3',start= timeseries.channels[0].start+1*1e6,end=timeseries.channels[0].start+2*1e6)
assert annot4.exists
annot4.delete()
assert not annot4.exists
annot5 = timeseries.insert_annotation(layer='test_layer4',annotation='test_label3',start=timeseries.channels[0].start+1*1e6,end=timeseries.channels[0].start+2*1e6)
assert annot5.exists
annot5.delete()
assert not annot5.exists
layer1.add_annotations([annot2,annot3])
assert annot2.exists
assert annot3.exists
#test datetime input
annot4 = timeseries.insert_annotation(layer='test_layer4',annotation='test_label3',start= datetime.datetime.utcfromtimestamp((timeseries.channels[0].start+1*1e6)/1e6),end=datetime.datetime.utcfromtimestamp(timeseries.channels[0].start+2*1e6))
assert annot4.exists
annot4.delete()
assert not annot4.exists
layer = timeseries.get_layer('test_layer4')
assert layer.exists
layer.delete()
assert not layer.exists
# delete annotations
annot[0].delete()
assert not annot[0].exists
assert timeseries.exists
timeseries.delete_layer(layer1)
assert not layer1.exists
assert layer2.exists
layer2.delete()
assert not layer2.exists
def test_timeseries_annotations(client, timeseries):
assert timeseries.exists
print("layers = ", timeseries.layers)
# Create Layer
layer1 = TimeSeriesAnnotationLayer(name="test_layer",
time_series_id=timeseries.id,
description="test_description")
a = layer1.as_dict()
assert a["name"] == "test_layer"
assert a["description"] == "test_description"
# Add Layer
timeseries.add_layer(layer1)
assert layer1.exists
# Get Layer
layer1b = timeseries.get_layer("test_layer")
assert layer1b.exists
assert layer1b.name == "test_layer"
assert layer1.id == layer1b.id
assert layer1._api.timeseries is not None
# Add another layer
layer2 = timeseries.add_layer("test_layer2", "test_description2")
assert layer2.exists
layer2copy = timeseries.add_layer("test_layer2")
assert layer2copy.id == layer2.id
# Get Layer
layer2b = timeseries.get_layer("test_layer2")
assert layer2b.exists
assert layer2b.name == "test_layer2"
assert layer2.id == layer2b.id
assert layer2._api.timeseries is not None
layers = timeseries.layers
assert len(layers) == 2
assert set([layers[0].name,
layers[1].name]) == set(["test_layer", "test_layer2"])
# Create channels
ch = TimeSeriesChannel(name="test_channel",
rate=256,
unit="uV",
start=1,
end=60 * 1e6)
# Create annotation over one channel
# create
timeseries.add_channels(ch)
assert ch.exists
assert ch.id in [x.id for x in timeseries.channels]
annot = TimeSeriesAnnotation(
label="test_label",
channel_ids=timeseries.channels[0].id,
start=timeseries.channels[0].start,
end=timeseries.channels[0].start + 1 * 1e6,
)
# Add Annotation
layer1.add_annotations(annot)
assert annot.exists
# get annotations
annotb = layer1.annotations()
assert annotb[0].label == annot.label
annotc = client._api.timeseries.get_annotation(timeseries, layer1, annot)
assert annotc.label == annot.label
# Create annotation over multiple channels
ch2 = TimeSeriesChannel(name="test_channel",
rate=256,
unit="uV",
start=1,
end=60 * 1e6)
timeseries.add_channels(ch2)
channels = timeseries.channels
ch_ids = [x.id for x in channels]
assert ch2.exists
assert ch2.id in ch_ids
assert ch.id in ch_ids
for ch in channels:
assert ch.rate == 256
assert ch.exists
# add annotation over two channels
channel_ids = [
timeseries.channels[x].id for x in range(len(timeseries.channels))
]
annot2 = layer1.insert_annotation(
annotation="test_label2",
channel_ids=channel_ids,
start=timeseries.channels[0].start + 1 * 1e6,
end=timeseries.channels[0].start + 2 * 1e6,
)
assert annot2.exists
annot_gen = layer1.iter_annotations(1)
annot = next(annot_gen)
assert annot[0].label == "test_label"
next_annot = next(annot_gen)
assert next_annot[0].label == "test_label2"
### TEST ANNOTATION COUNTS
layer1_expected_counts = [
{
"start": 0,
"end": 250000,
"value": 1.0
},
{
"start": 250000,
"end": 500000,
"value": 1.0
},
{
"start": 500000,
"end": 750000,
"value": 1.0
},
{
"start": 750000,
"end": 1000000,
"value": 1.0
},
{
"start": 1000000,
"end": 1250000,
"value": 2.0
},
{
"start": 1250000,
"end": 1500000,
"value": 1.0
},
{
"start": 1500000,
"end": 1750000,
"value": 1.0
},
{
"start": 1750000,
"end": 2000000,
"value": 1.0
},
{
"start": 2000000,
"end": 2000001,
"value": 1.0
},
]
def _sort_counts(counts):
return sorted(counts, key=lambda c: c["start"])
assert (_sort_counts(
timeseries.annotation_counts(
start=timeseries.channels[0].start * 1e6,
end=timeseries.channels[0].start + 2 * 1e6,
layers=[layer1],
period="0.25s",
)[str(layer1.id)]) == layer1_expected_counts)
assert (_sort_counts(
layer1.annotation_counts(
start=timeseries.channels[0].start * 1e6,
end=timeseries.channels[0].start + 2 * 1e6,
period="0.25s",
)[str(layer1.id)]) == layer1_expected_counts)
### TEST DELETION
annot3 = TimeSeriesAnnotation(
label="test_label3",
channel_ids=channel_ids,
start=timeseries.channels[0].start + 1 * 1e6,
end=timeseries.channels[0].start + 2 * 1e6,
)
layer1.add_annotations([annot2, annot3])
annot3 = timeseries.add_annotations(layer=layer1, annotations=annot3)
assert annot3.exists
annot3.delete()
assert not annot3.exists
annot4 = timeseries.insert_annotation(
layer=layer1,
annotation="test_label3",
start=timeseries.channels[0].start + 1 * 1e6,
end=timeseries.channels[0].start + 2 * 1e6,
)
assert annot4.exists
annot4.delete()
assert not annot4.exists
annot5 = timeseries.insert_annotation(
layer="test_layer4",
annotation="test_label3",
start=timeseries.channels[0].start + 1 * 1e6,
end=timeseries.channels[0].start + 2 * 1e6,
)
assert annot5.exists
annot5.delete()
assert not annot5.exists
layer1.add_annotations([annot2, annot3])
assert annot2.exists
assert annot3.exists
# test datetime input
annot4 = timeseries.insert_annotation(
layer="test_layer4",
annotation="test_label3",
start=datetime.datetime.utcfromtimestamp(
(timeseries.channels[0].start + 1 * 1e6) / 1e6),
end=datetime.datetime.utcfromtimestamp(timeseries.channels[0].start +
2 * 1e6),
)
assert annot4.exists
annot4.delete()
assert not annot4.exists
layer = timeseries.get_layer("test_layer4")
assert layer.exists
layer.delete()
assert not layer.exists
# delete annotations
annot[0].delete()
assert not annot[0].exists
assert timeseries.exists
timeseries.delete_layer(layer1)
assert not layer1.exists
assert layer2.exists
layer2.delete()
assert not layer2.exists
def test_timeseries_annotations(client, timeseries):
assert timeseries.exists
print('layers = ', timeseries.layers)
#Create Layer
layer1 = TimeSeriesAnnotationLayer(name="test_layer",
time_series_id=timeseries.id,
description="test_description")
a = layer1.as_dict()
assert a['name'] == 'test_layer'
assert a['description'] == 'test_description'
# Add Layer
timeseries.add_layer(layer1)
assert layer1.exists
# Get Layer
layer1b = timeseries.get_layer('test_layer')
assert layer1b.exists
assert layer1b.name == "test_layer"
assert layer1.id == layer1b.id
assert layer1._api.timeseries is not None
# Add another layer
layer2 = timeseries.add_layer('test_layer2', 'test_description2')
assert layer2.exists
layer2copy = timeseries.add_layer('test_layer2')
assert layer2copy.id == layer2.id
# Get Layer
layer2b = timeseries.get_layer('test_layer2')
assert layer2b.exists
assert layer2b.name == "test_layer2"
assert layer2.id == layer2b.id
assert layer2._api.timeseries is not None
layers = timeseries.layers
assert len(layers) == 2
assert layers[0].name == "test_layer"
assert layers[1].name == 'test_layer2'
#Create channels
ch = TimeSeriesChannel(name='test_channel',
rate=256,
unit='uV',
start=1,
end=60 * 1e6)
#Create annotation over one channel
# create
timeseries.add_channels(ch)
assert ch.exists
assert ch.id in [x.id for x in timeseries.channels]
annot = TimeSeriesAnnotation(label='test_label',
channel_ids=timeseries.channels[0].id,
start=timeseries.channels[0].start,
end=timeseries.channels[0].start + 1 * 1e6)
#Add Annotation
layer1.add_annotations(annot)
assert annot.exists
# get annotations
annotb = layer1.annotations()
assert annotb[0].label == annot.label
annotc = client._api.timeseries.get_annotation(timeseries, layer1, annot)
assert annotc.label == annot.label
#Create annotation over multiple channels
ch2 = TimeSeriesChannel(name='test_channel',
rate=256,
unit='uV',
start=1,
end=60 * 1e6)
timeseries.add_channels(ch2)
channels = timeseries.channels
ch_ids = [x.id for x in channels]
assert ch2.exists
assert ch2.id in ch_ids
assert ch.id in ch_ids
for ch in channels:
assert ch.rate == 256
assert ch.exists
#add annotation over two channels
channel_ids = [
timeseries.channels[x].id for x in range(len(timeseries.channels))
]
annot2 = layer1.insert_annotation(
annotation='test_label2',
channel_ids=channel_ids,
start=timeseries.channels[0].start + 1 * 1e6,
end=timeseries.channels[0].start + 2 * 1e6)
assert annot2.exists
annot_gen = layer1.iter_annotations(1)
annot = next(annot_gen)
assert annot[0].label == 'test_label'
next_annot = next(annot_gen)
assert next_annot[0].label == 'test_label2'
### TEST ANNOTATION COUNTS
layer1_expected_counts = [{
'start': 0,
'end': 250000,
'value': 1.0
}, {
'start': 250000,
'end': 500000,
'value': 1.0
}, {
'start': 500000,
'end': 750000,
'value': 1.0
}, {
'start': 750000,
'end': 1000000,
'value': 1.0
}, {
'start': 1000000,
'end': 1250000,
'value': 2.0
}, {
'start': 1250000,
'end': 1500000,
'value': 1.0
}, {
'start': 1500000,
'end': 1750000,
'value': 1.0
}, {
'start': 1750000,
'end': 2000000,
'value': 1.0
}, {
'start': 2000000,
'end': 2000001,
'value': 1.0
}]
def _sort_counts(counts):
return sorted(counts, key=lambda c: c['start'])
assert _sort_counts(
timeseries.annotation_counts(
start=timeseries.channels[0].start * 1e6,
end=timeseries.channels[0].start + 2 * 1e6,
layers=[layer1],
period="0.25s")[str(layer1.id)]) == layer1_expected_counts
assert _sort_counts(
layer1.annotation_counts(start=timeseries.channels[0].start * 1e6,
end=timeseries.channels[0].start + 2 * 1e6,
period="0.25s")[str(
layer1.id)]) == layer1_expected_counts
### TEST DELETION
annot3 = TimeSeriesAnnotation(label='test_label3',
channel_ids=channel_ids,
start=timeseries.channels[0].start + 1 * 1e6,
end=timeseries.channels[0].start + 2 * 1e6)
layer1.add_annotations([annot2, annot3])
annot3 = timeseries.add_annotations(layer=layer1, annotations=annot3)
assert annot3.exists
annot3.delete()
assert not annot3.exists
annot4 = timeseries.insert_annotation(
layer=layer1,
annotation='test_label3',
start=timeseries.channels[0].start + 1 * 1e6,
end=timeseries.channels[0].start + 2 * 1e6)
assert annot4.exists
annot4.delete()
assert not annot4.exists
annot5 = timeseries.insert_annotation(
layer='test_layer4',
annotation='test_label3',
start=timeseries.channels[0].start + 1 * 1e6,
end=timeseries.channels[0].start + 2 * 1e6)
assert annot5.exists
annot5.delete()
assert not annot5.exists
layer1.add_annotations([annot2, annot3])
assert annot2.exists
assert annot3.exists
# test datetime input
annot4 = timeseries.insert_annotation(
layer='test_layer4',
annotation='test_label3',
start=datetime.datetime.utcfromtimestamp(
(timeseries.channels[0].start + 1 * 1e6) / 1e6),
end=datetime.datetime.utcfromtimestamp(timeseries.channels[0].start +
2 * 1e6))
assert annot4.exists
annot4.delete()
assert not annot4.exists
layer = timeseries.get_layer('test_layer4')
assert layer.exists
layer.delete()
assert not layer.exists
# delete annotations
annot[0].delete()
assert not annot[0].exists
assert timeseries.exists
timeseries.delete_layer(layer1)
assert not layer1.exists
assert layer2.exists
layer2.delete()
assert not layer2.exists