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_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_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_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_create_fancspace(self):
"""Check if the hemibrain space is created."""
layer_serverdir, layer_host = get_ngserver()
create_ngspace(ngspace='hemibrain')
ngspace = sys.modules['ngspace']
assert ngspace == 'hemibrain'
def test_upload_skeletonexception(self):
"""Check if exception occurs."""
neuronlist = (1, 2, 3)
layer_serverdir, layer_host = get_ngserver()
with pytest.raises(Exception):
skelsource, skelseglist, skelsegnamelist = to_ngskeletons(
neuronlist)
def test_create_fafbspace(self):
"""Check if the fafb ngspace is created."""
layer_serverdir, layer_host = get_ngserver()
create_ngspace(ngspace='FAFB')
ngspace = sys.modules['ngspace']
assert ngspace == 'FAFB'
def test_create_ngsegmentlayer(self):
"""Check if the segdataset seg_20190805 is created."""
layer_serverdir, layer_host = get_ngserver()
ngviewer = openviewer(None)
ngviewer2 = create_nglayer(ngviewer=ngviewer,
layer_kws={'type': 'segdataset', 'ngspace': 'FAFB', 'name': 'seg_20190805'})
assert ngviewer2 == ngviewer
def test_create_ngsynapticcleftslayer(self):
"""Check if the synaptic clefts layer is created."""
layer_serverdir, layer_host = get_ngserver()
ngviewer = openviewer(None)
ngviewer2 = create_nglayer(ngviewer=ngviewer,
layer_kws={'type': 'synapticclefts', 'ngspace': 'FAFB',
'name': 'clefts_Heinrich_etal'})
assert ngviewer2 == ngviewer
def test_create_ngbuhmannsynapselayer(self):
"""Check if the buhmann synapse layer is created."""
layer_serverdir, layer_host = get_ngserver()
ngviewer = openviewer(None)
ngviewer2 = create_nglayer(ngviewer=ngviewer,
layer_kws={'type': 'synapticlayer', 'ngspace': 'FAFB',
'name': 'synapses_buhmann2019'})
assert ngviewer2 == ngviewer
def test_create_ngexceptionlayoutlayer(self):
"""Check exception is layout is not set."""
layer_serverdir, layer_host = get_ngserver()
location_data = [{'x': 5, 'y': 10, 'z': 20}, {'x': 15, 'y': 25, 'z': 30}]
points = pd.DataFrame(location_data)
points['description'] = 'dummy data'
with pytest.raises(Exception):
create_nglayer(layout='xy-nd', layer_kws={'type': 'points', 'name': 'points1',
'source': points, 'scale': [8, 8, 8], 'color': 'yellow'})
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_synapsesexception(self):
"""Check if exception occurs."""
neuronlist = (1, 2, 3)
layer_serverdir, layer_host = get_ngserver()
presynlayer_kws = {
'type': 'synapses',
'ngspace': 'FAFB',
'source': neuronlist
}
with pytest.raises(Exception):
create_nglayer(layer_kws=presynlayer_kws)
def test_create_ngpointslayer(self):
"""Check if the points layer is created."""
layer_serverdir, layer_host = get_ngserver()
ngviewer = openviewer(None)
location_data = [{'x': 5, 'y': 10, 'z': 20}, {'x': 15, 'y': 25, 'z': 30}]
points = pd.DataFrame(location_data)
points['description'] = 'dummy data'
ngviewer2 = create_nglayer(layer_kws={'type': 'points', 'name': 'points1', 'ngspace': 'FAFB',
'source': points, 'scale': [8, 8, 8], 'color': 'yellow'})
assert ngviewer2 == ngviewer
def test_create_ngvolumelayer(self):
"""Check if the volume layer is created."""
layer_serverdir, layer_host = get_ngserver()
ngviewer = openviewer(None)
segid = 10
vertices = [(0, 0, 0), (0, 1, 0), (0, 2, 0)]
faces = [(0, 1, 2)]
testvolume = navis.Volume(vertices=vertices, faces=faces, name='test', id=segid)
ngviewer2 = create_nglayer(layer_kws={'type': 'volumes', 'source': testvolume, 'ngspace': 'FAFB',
'color': 'white', 'alpha': 0.3})
assert ngviewer2 == ngviewer
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_meshupload(self):
"""Check if the meshupload is done."""
segid = 10
vertices = [(0, 0, 0), (0, 1, 0), (0, 2, 0)]
faces = [(0, 1, 2)]
testvolume = navis.Volume(vertices=vertices,
faces=faces,
name='test',
id=segid)
volumedatasource, volumeidlist, volumenamelist = to_ngmesh(testvolume)
# segmentColors = dict(zip(volumeidlist, '#ffff00'))
layer_serverdir, layer_host = get_ngserver()
uploadmeshes(volumedatasource, volumeidlist, volumenamelist,
layer_serverdir, 'testvolume')
status = os.path.exists(
os.path.join(layer_serverdir, 'precomputed/testvolume/mesh',
str(segid)))
assert status
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