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_upload_skeletontreeneuron(self):
"""Check if skeleton upload works in a tree neuron."""
# 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
]
neuronlist = navis.core.NeuronList(neuronlist)
treeneuron = neuronlist[0]
layer_serverdir, layer_host = get_ngserver()
skelsource, skelseglist, skelsegnamelist = to_ngskeletons(treeneuron)
uploadskeletons(skelsource, skelseglist, skelsegnamelist,
layer_serverdir)
skeleton_path = os.path.join(layer_serverdir, 'precomputed/skeletons/',
str(treeneuron.id))
status = os.path.isfile(skeleton_path)
assert status
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
def test_create_ngtreeneuronlist(self):
"""Check if create layer 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]
neuronlist = navis.core.NeuronList(neuronlist)
ngviewer = openviewer(None)
ngviewer2 = create_nglayer(layer_kws={'type': 'skeletons', 'source': neuronlist, 'ngspace': 'FAFB',
'color': ['white', 'green', 'grey', 'yellow', 'magenta'],
'alpha': 0.9})
assert ngviewer2 == ngviewer
def test_upload_skeletoncatmaidneuron(self):
"""Check if skeleton upload works in a catmaid neuron."""
# 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])
catmaidneuron.soma = None # set this so you don't have to fetch from remote instance
layer_serverdir, layer_host = get_ngserver()
skelsource, skelseglist, skelsegnamelist = to_ngskeletons(
catmaidneuron)
uploadskeletons(skelsource, skelseglist, skelsegnamelist,
layer_serverdir)
skeleton_path = os.path.join(layer_serverdir, 'precomputed/skeletons/',
str(catmaidneuron.id))
status = os.path.isfile(skeleton_path)
assert status
def test_from_swc(swc_source):
n = navis.read_swc(swc_source)
assert isinstance(n, navis.TreeNeuron)
def test_from_swc_multi(swc_source_multi, parallel):
n = navis.read_swc(swc_source_multi, parallel=parallel)
assert isinstance(n, navis.NeuronList)
