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_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_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_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_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_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_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
import sys import unittest from pyroglancer.layers import get_ngserver from pyroglancer.localserver import closedataserver from pyroglancer.localserver import startdataserver from pyroglancer.ngspaces import create_ngspace from pyroglancer.ngviewer import closeviewer from pyroglancer.ngviewer import openviewer # Add a common viewer, dataserver(specific port for travis) for each test module.. closeviewer() closedataserver() startdataserver(port=8005) # start dataserver.. openviewer(headless=True) # open ngviewer # def setup_module(module): # """Start all servers.""" # # Add a common viewer, dataserver for the whole serie of test.. # startdataserver() # start dataserver.. # openviewer(headless=True) # open ngviewer # # # def teardown_module(module): # """Stop all servers.""" # # Stop all viewers.. # closedataserver() # closeviewer()
def test_reuseoldviewer(self):
"""Check if old viewer is reused incase of new opening request."""
viewer1 = openviewer(None)
viewer2 = openviewer(viewer1)
assert viewer1 == viewer2
def test_newviewer(self):
"""Check if the viewer opens when no object is passed."""
viewer = openviewer(None)
assert isinstance(viewer, ng.viewer.Viewer)