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_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_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_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_create_nghandledimensionslayer(self): """Check if the dimensions are handled.""" dimensions = ng.CoordinateSpace(names=['x', 'y', 'z'], units='um', scales=[1, 1, 1]) dimensions2 = _handle_ngdimensions(layer_kws={'dimensions': dimensions}) assert dimensions2 == dimensions
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_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