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)