def _get_data(self):
"""
Loads data and metadata for the C. elegans connectome.
"""
# Get subfolder with .obj files
subdirs = get_subdirs(self.data_folder)
if not subdirs:
raise ValueError(
"The data folder should include a subfolder which stores the neurons .obj files"
)
try:
self.objs_fld = [f for f in subdirs if "objs_smoothed" in f][0]
except:
raise FileNotFoundError(
"Could not find subdirectory with .obj files")
# Get filepath to each .obj
self.neurons_files = [
f for f in listdir(self.objs_fld) if f.lower().endswith(".obj")
]
# Get synapses and skeleton files
try:
skeletons_file = [
f for f in listdir(self.data_folder)
if f.endswith("skeletons.json")
][0]
except:
raise FileNotFoundError(
"Could not find file with neurons skeleton data")
try:
synapses_file = [
f for f in listdir(self.data_folder)
if f.endswith("synapses.csv")
][0]
except:
raise FileNotFoundError("Could not find file with synapses data")
# load data
self.skeletons_data = load_json(skeletons_file)
self.synapses_data = pd.read_csv(synapses_file, sep=";")
# Get neurons metadata
try:
metadata_file = [
f for f in listdir(self.data_folder)
if "neuron_metadata.csv" in f
][0]
except:
raise FileNotFoundError(
f"Could not find neurons metadata file {metadata_file}")
self.neurons_metadata = pd.read_csv(metadata_file)
self.neurons_names = list(self.neurons_metadata.neuron.values)
def _load_cached_neuron(self, neuron_name):
"""
Load a cached neuron's VTK actors
:param neuron_name: str with neuron name
"""
if not neuron_name or neuron_name is None:
return None
if self.render_neurites:
allowed_components = ['soma', 'axon', 'dendrites']
skipped_components = []
else:
allowed_components = ['soma']
skipped_components = ['axon', 'dendrites']
neuron_files = [
f for f in listdir(self.morphology_cache) if neuron_name in f
]
if not neuron_files: return None
else:
neuron_actors = {}
for f in neuron_files:
component = os.path.split(f)[-1].split(".")[0].split("_")[-1]
if component not in allowed_components and component not in skipped_components:
raise ValueError(
"Weird file name, unsure what to do: {}".format(f))
elif component not in allowed_components and component in skipped_components:
continue
neuron_actors[component] = load(f)
return neuron_actors
def _load_cached_neuron(self, neuron_name, params):
"""
Load a cached neuron's VTK actors
:param neuron_name: str with neuron name
"""
if not neuron_name or neuron_name is None:
return None
# Load the yaml file with metadata about previously rendered neurons
if not neuron_name in self.cache_metadata.keys(
): # the neuron was cached before the metadata was in place
return None
# Check if the params match those of the cached neuron
cached_params = self.cache_metadata[neuron_name]
diff_params = [v1 for v1,v2 in zip(cached_params.values(), params.values())\
if v1 != v2]
if diff_params:
return None
# All is good with the params, load cached actors
if self.render_neurites:
if self.render_dendrites and self.render_axons:
allowed_components = ['soma', 'axon', 'dendrites']
skipped_components = []
elif not self.render_dendrites and not self.render_axons:
allowed_components = ['soma']
skipped_components = ['axon', 'dendrites']
elif not self.render_dendrites:
allowed_components = ['soma', 'axon']
skipped_components = ['dendrites']
else:
allowed_components = ['soma', 'dendrites']
skipped_components = ['axon']
else:
allowed_components = ['soma']
skipped_components = ['axon', 'dendrites']
neuron_files = [
f for f in listdir(self.morphology_cache) if neuron_name in f
]
if not neuron_files: return None
else:
neuron_actors = {}
for f in neuron_files:
component = os.path.split(f)[-1].split(".")[0].split("_")[-1]
if component not in allowed_components and component not in skipped_components:
raise ValueError(
"Weird file name, unsure what to do: {}".format(f))
elif component not in allowed_components and component in skipped_components:
continue
neuron_actors[component] = load(f)
return neuron_actors
def load_cached_gene(cache, metric, grid_size):
"""
Loads a gene's data from cache
"""
files = [
f for f in listdir(cache) if metric in f and not f.endswith(".mhd")
]
if not files:
return None
if len(files) > 1:
raise NotImplementedError("Deal with more than one file found")
else:
return read_raw(files[0], grid_size)
def add_neuron(self, neuron, shadow_axis=None, shadow_offset=-20, **kwargs): if isinstance(neuron, list): neurons = neuron else: if isinstance(neuron, str): if os.path.isdir(neuron): neurons = listdir(neuron) else: neurons = [neuron] actors = [] for neuron in neurons: if isinstance(neuron, str): neuron = self.parse_neuron_swc(neuron, **kwargs) elif isinstance(neuron, Morphology): neuron = self.parse_neurons_swc_allen(neuron, **kwargs) actor = self.scene.add_vtkactor(neuron) # scals = actor.points()[:, 1] # alphas = np.linspace(0.82, .83, 250) # actor.pointColors(scals, alpha=alphas, cmap="Greens_r") # actor.points()[:, 0] += np.random.normal(0, 2000) # actor.points()[:, 2] += np.random.normal(0, 2000) if shadow_axis == 'x': actor.addShadow(x = shadow_offset) elif shadow_axis == 'y': actor.addShadow(y = shadow_offset) elif shadow_axis == 'z': actor.addShadow(z = shadow_offset) actors.append(neuron) return actors
def test_io():
fld = os.getcwd()
if not isinstance(listdir(fld), list):
raise ValueError(f"listdir returned: {listdir(fld)}")
if not isinstance(get_subdirs(fld), list):
raise ValueError(f"get_subdirs returned: {get_subdirs(fld)}")
def test_streamlines():
scene = Scene()
streamlines_files = listdir("Examples/example_files/streamlines")[:2]
scene.add_streamlines(streamlines_files, color="green")
