def test_annotate_annotate_points(self):
"""Check if individual annotation works."""
layer_serverdir, layer_host = get_ngserver()
layer_kws = {}
layer_kws['ngspace'] = 'FAFB'
dimensions = _handle_ngdimensions(layer_kws)
location_data = [{
'x': 5,
'y': 10,
'z': 20
}, {
'x': 15,
'y': 25,
'z': 30
}]
points = pd.DataFrame(location_data)
points['description'] = 'dummy data'
ngviewer = openviewer(None)
layer_scale = (1, 1, 1)
annot_colors = '#ff0000'
status = annotate_points(ngviewer, dimensions, annot_colors, points,
'points', layer_scale)
assert status
def test_put_postsynapsefile(self):
"""Check if the synapse file is stored."""
layer_serverdir, layer_host = get_ngserver()
layer_kws = {}
layer_kws['ngspace'] = 'FAFB'
dimensions = _handle_ngdimensions(layer_kws)
synapse_path = create_synapseinfo(dimensions, layer_serverdir)
location_data = [{
'x': 5,
'y': 10,
'z': 20
}, {
'x': 15,
'y': 25,
'z': 30
}]
presynapses = pd.DataFrame(location_data)
skeletonid = 456
type = 'postsynapses'
put_synapsefile(synapse_path, type, presynapses, skeletonid)
synapsefilepath = synapse_path + '/precomputed/' + \
type + '/' + type + '_cell/' + str(skeletonid)
status = os.path.isfile(synapsefilepath)
assert status
def test_put_pointfile(self):
"""Check if the point file is stored."""
layer_serverdir, layer_host = get_ngserver()
layer_kws = {}
layer_kws['ngspace'] = 'FAFB'
dimensions = _handle_ngdimensions(layer_kws)
layer_name = 'points'
points_path = create_pointinfo(dimensions, layer_serverdir, layer_name)
location_data = [{
'x': 5,
'y': 10,
'z': 20
}, {
'x': 15,
'y': 25,
'z': 30
}]
points = pd.DataFrame(location_data)
points['description'] = 'dummy data'
upload_points(points, points_path, 'points', [1, 1, 1])
pointfilepath = points_path + '/precomputed/' + layer_name + '/spatial0/0_0_0'
status = os.path.isfile(pointfilepath)
assert status
def test_annotate_synapsescatmaidneuron(self):
"""Check if individual annotation works."""
# load some example neurons..
swc_path = os.path.join(BASE_DIR, 'data/swc')
# print('swc_path: ', swc_path)
swc_files = glob.glob(os.path.join(swc_path, '*.swc'))
# print('swc_file: ', swc_files)
neuronlist = []
neuronlist += [
navis.read_swc(f,
units='8 nm',
connector_labels={
'presynapse': 7,
'postsynapse': 8
},
id=int(os.path.splitext(os.path.basename(f))[0]))
for f in swc_files
]
catmaidneuron = pymaid.core.CatmaidNeuron(neuronlist[0])
ngviewer = openviewer(None)
layer_kws = {}
layer_kws['ngspace'] = 'FAFB'
dimensions = _handle_ngdimensions(layer_kws)
status = annotate_synapses(ngviewer, dimensions, catmaidneuron)
assert status
def test_create_nghandledimensionslayer(self):
"""Check if the dimensions are handled."""
dimensions = ng.CoordinateSpace(names=['x', 'y', 'z'], units='um', scales=[1, 1, 1])
dimensions2 = _handle_ngdimensions(layer_kws={'dimensions': dimensions})
assert dimensions2 == dimensions
def test_create_pointinfo(self):
"""Check if the point info is stored."""
layer_serverdir, layer_host = get_ngserver()
layer_kws = {}
layer_kws['ngspace'] = 'FAFB'
dimensions = _handle_ngdimensions(layer_kws)
create_pointinfo(dimensions, layer_serverdir, 'points')
status = os.path.isfile(
os.path.join(layer_serverdir, 'precomputed/points', 'info'))
assert status
def test_annotate_synapsesexception(self):
"""Check if exception occurs."""
neuronlist = (1, 2, 3)
layer_serverdir, layer_host = get_ngserver()
ngviewer = openviewer(None)
layer_kws = {}
layer_kws['ngspace'] = 'FAFB'
dimensions = _handle_ngdimensions(layer_kws)
with pytest.raises(Exception):
annotate_synapses(ngviewer, dimensions, neuronlist)
def test_upload_synapsescatmaidneuron(self):
"""Check if synapse upload works in a tree neuronlist."""
# load some example neurons..
swc_path = os.path.join(BASE_DIR, 'data/swc')
# print('swc_path: ', swc_path)
swc_files = glob.glob(os.path.join(swc_path, '*.swc'))
# print('swc_file: ', swc_files)
neuronlist = []
neuronlist += [
navis.read_swc(f,
units='8 nm',
connector_labels={
'presynapse': 7,
'postsynapse': 8
},
id=int(os.path.splitext(os.path.basename(f))[0]))
for f in swc_files
]
catmaidneuron = pymaid.core.CatmaidNeuron(neuronlist[0])
layer_serverdir, layer_host = get_ngserver()
layer_kws = {}
layer_kws['ngspace'] = 'FAFB'
dimensions = _handle_ngdimensions(layer_kws)
synapse_path = create_synapseinfo(dimensions, layer_serverdir)
presynlayer_kws = {
'type': 'synapses',
'ngspace': 'FAFB',
'source': catmaidneuron
}
create_nglayer(layer_kws=presynlayer_kws)
type = 'presynapses'
synapsefilepath = synapse_path + '/precomputed/' +\
type + '/' + type + '_cell/' + str(catmaidneuron.id)
status = os.path.isfile(synapsefilepath)
assert status