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