def fetch_aligned_morphology(specimen_id=None, swc_file=None):
if specimen_id:
swc_file, m0 = fetch_cell(specimen_id)
morphology = swc.read_swc(swc_file)
t0 = np.eye(4)
t0[:, 3] = -np.dot(m0, [
morphology.root['x'], morphology.root['y'], morphology.root['z'], 1
])
r = xform.rotate3x(math.radians(-90))
else:
swc_file = swc_file
morphology = swc.read_swc(swc_file)
m0 = np.eye(4)
t0 = xform.translate3(-morphology.root['x'], -morphology.root['y'],
-morphology.root['z'])
r = xform.rotate3x(math.radians(90))
sz = xform.scale3(1, 1, 3)
sm = xform.scale3(.001, .001, .001)
m = np.dot(sm, np.dot(np.dot(r, np.dot(sz, t0)), m0))
morphology = make_transformed_morphology(morphology, m)
# rotate the apical
ra = align_apical_dendrite(morphology)
morphology = make_transformed_morphology(morphology, ra, .002)
return morphology
def __init__(self, morph_file, cell_id=None):
self.morph_file = morph_file
self.morph = swc.read_swc(morph_file)
self.soma_coord = np.array(
[self.morph.soma["x"], self.morph.soma["y"], self.morph.soma["z"]])
self.soma_rad = self.morph.soma['radius']
self.cell_id = cell_id
def get_reconstruction(self, specimen_id, file_name=None):
"""
Download and open a reconstruction for a single cell in the database.
Parameters
----------
specimen_id: int
The ID of a cell specimen to download.
file_name: string
File name to save/read the reconstruction SWC.
If file_name is None, the file_name will be pulled out of the
manifest. If caching is disabled, no file will be saved.
Default is None.
Returns
-------
Morphology
A class instance with methods for accessing morphology compartments.
"""
file_name = self.get_cache_path(file_name, self.RECONSTRUCTION_KEY, specimen_id)
if file_name is None:
raise Exception("Please enable caching (CellTypes.cache = True) or specify a save_file_name.")
if not os.path.exists(file_name):
self.api.save_reconstruction(specimen_id, file_name)
return swc.read_swc(file_name)
def _morph_layer_density(specimen_id, layer_list=None):
layer_list = layer_list or ["1", "2/3", "4", "5", "6a", "6b"]
df = layer_counts.query_lims_for_layers(specimen_id)
try:
soma_coords, pia_coords, wm_coords, layer_coords = layer_counts.get_coords(
df, layer_list)
except Exception:
return None
if None in [soma_coords, pia_coords, wm_coords, layer_coords]:
return None
ld = layer_counts.layer_depths(layer_coords, soma_coords, pia_coords,
wm_coords)
swc_filename, swc_path = lims_utils.get_swc_from_lims(specimen_id)
morph = swc.read_swc(swc_path)
soma_layer = soma_layer_from_morph(morph, layer_coords, soma_coords,
layer_list)
ax, dend, apic = layer_counts.compartment_counts_by_layer(
morph, layer_coords, soma_coords, layer_list)
all_dend = {k: dend[k] + apic[k] for k in dend}
return {
'soma_layer': soma_layer,
'ax': ax,
'dend': dend,
'apic': apic,
'all_dend': all_dend,
}
def check_swc_for_apical(morph_path):
morphology = swc.read_swc(morph_path)
no_apical = True
for n in morphology.compartment_list:
if n['type'] == 4:
no_apical = False
break
return no_apical
def validate_swc(swc_file):
"""
To be compatible with NEURON, SWC files must have the following properties:
1) a single root node with parent ID '-1'
2) sequentially increasing ID numbers
3) immediate children of the soma cannot branch
"""
soma_id = swc.Morphology.SOMA
morphology = swc.read_swc(swc_file)
# verify that there is a single root node
num_soma_nodes = sum([(int(c['type']) == soma_id)
for c in morphology.compartment_list])
if num_soma_nodes != 1:
raise Exception("SWC must have single soma compartment. Found: %d" %
num_soma_nodes)
# sanity check
root = morphology.root
if root is None:
raise Exception("Morphology has no root node")
# verify that children of the root have max one child
for root_child_id in root['children']:
root_child = morphology.compartment_index[root_child_id]
num_grand_children = len(root_child['children'])
if num_grand_children > 1:
raise Exception("Child of root (%s) has more than one child (%d)" %
(root_child_id, num_grand_children))
# get a list of all of the ids, make sure they are unique while we're at it
all_ids = set()
for compartment in morphology.compartment_list:
iid = int(compartment["id"])
if iid in all_ids:
raise Exception("Compartment ID %s is not unique." %
compartment["id"])
pid = int(compartment["parent"])
if iid < pid:
raise Exception(
"Compartment (%d) has a smaller ID that its parent (%d)" %
(iid, pid))
all_ids.add(iid)
# sort the ids and make sure there are no gaps
sorted_ids = sorted(all_ids)
for i in xrange(1, len(sorted_ids)):
if sorted_ids[i] - sorted_ids[i - 1] != 1:
raise Exception("Compartment IDs are not sequential")
return True
def get_reconstruction(self):
'''
Checks for a morphology .swc file associated with the biophysical model.
If such a file is found, uses the AllenSDK swc helper functions to return a Morphology instance.
Returns
-------
Morphology
a morphology instance if a morphology file is found associated with the model. None otherwise.
'''
file_name = self.bp.ids['morphology'].values()[0]
if len(file_name) > 0:
file_name = os.path.join(os.getcwd(), self.model_dir, file_name)
return swc.read_swc(file_name)
else:
print "Could not find morphology file for model ", self.model_id, ", please check directory structure and try again."
return None
def validate_swc(swc_file):
"""
To be compatible with NEURON, SWC files must have the following properties:
1) a single root node with parent ID '-1'
2) sequentially increasing ID numbers
3) immediate children of the soma cannot branch
"""
soma_id = swc.Morphology.SOMA
morphology = swc.read_swc(swc_file)
# verify that there is a single root node
num_soma_nodes = sum([(int(c['type']) == soma_id)
for c in morphology.compartment_list])
if num_soma_nodes != 1:
raise Exception(
"SWC must have single soma compartment. Found: %d" % num_soma_nodes)
# sanity check
root = morphology.root
if root is None:
raise Exception("Morphology has no root node")
# verify that children of the root have max one child
for root_child_id in root['children']:
root_child = morphology.compartment_index[root_child_id]
num_grand_children = len(root_child['children'])
if num_grand_children > 1:
raise Exception("Child of root (%s) has more than one child (%d)" % (
root_child_id, num_grand_children))
# get a list of all of the ids, make sure they are unique while we're at it
all_ids = set()
for compartment in morphology.compartment_list:
iid = int(compartment["id"])
if iid in all_ids:
raise Exception("Compartment ID %s is not unique." %
compartment["id"])
pid = int(compartment["parent"])
if iid < pid:
raise Exception(
"Compartment (%d) has a smaller ID that its parent (%d)" % (iid, pid))
all_ids.add(iid)
# sort the ids and make sure there are no gaps
sorted_ids = sorted(all_ids)
for i in xrange(1, len(sorted_ids)):
if sorted_ids[i] - sorted_ids[i - 1] != 1:
raise Exception("Compartment IDs are not sequential")
return True
def write_morphology_vtk(vtk_file_name, cells, manifest):
points = []
pds = []
for cell in cells:
swc_path = manifest.get_path('MORPHOLOGY_%s' % cell['type'])
morphology = swc.read_swc(swc_path)
root = morphology.root
rootp = {'x': root['x'], 'y': root['y'], 'z': root['z']}
for compartment in morphology.compartment_list:
compartment['x'] = compartment['x'] - rootp['x'] + float(cell['x'])
compartment['y'] = compartment['y'] - rootp['y'] + float(cell['y'])
compartment['z'] = compartment['z'] - rootp['z'] + float(cell['z'])
pd = tube.generate_polydata(morphology.compartment_index,
morphology.root)
pds.append(pd)
pd = tube.merge_polydata(pds)
tube.save_polydata(pd, vtk_file_name)
def write_morphology_vtk(vtk_file_name, cells, manifest):
points = []
pds = []
for cell in cells:
swc_path = manifest.get_path('MORPHOLOGY_%s' % cell['type'])
morphology = swc.read_swc(swc_path)
root = morphology.root
rootp = { 'x': root['x'], 'y': root['y'], 'z': root['z'] }
for compartment in morphology.compartment_list:
compartment['x'] = compartment['x'] - rootp['x'] + float(cell['x'])
compartment['y'] = compartment['y'] - rootp['y'] + float(cell['y'])
compartment['z'] = compartment['z'] - rootp['z'] + float(cell['z'])
pd = tube.generate_polydata(morphology.compartment_index,
morphology.root)
pds.append(pd)
pd = tube.merge_polydata(pds)
tube.save_polydata(pd, vtk_file_name)
################################################################################
# Morphology
# Morphological neuron reconstructions are available for download as SWC files. The SWC file format is a white-space delimited text file with a standard set of headers. The file lists a set of 3D neuronal compartments, each of which has:
# Column Data Type Description
# id string compartment ID
# type integer compartment type
# x float 3D compartment position (x)
# y float 3D compartment position (y)
# z float 3D compartment position (z)
# radius float compartment radius
# parent string parent compartment ID
# Comment lines begin with a ‘#’. Reconstructions in the Allen Cell Types Database can contain the following compartment types:
################################################################################
file_name = 's-1-1.swc'
morphology = swc.read_swc(file_name)
# the compartment list has all of the nodes in the file
# print soma compartment data
if True:
import pprint
pprint.pprint(morphology.compartment_list)
fig, axes = plt.subplots(1, 2, sharey=True, sharex=True)
# Make a line drawing of x-y and y-z views
for n in morphology.compartment_list:
for c in morphology.children_of(n):
axes[0].plot([n['x'], c['x']], [n['y'], c['y']], color='black')
axes[1].plot([n['z'], c['z']], [n['y'], c['y']], color='black')
axes[0].set_ylabel('y')
# calculate features
cell_features = extract_cell_features(data_set,
sweep_numbers['Ramp'],
sweep_numbers['Short Square'],
sweep_numbers['Long Square'])
#===============================================================================
# example 3
#===============================================================================
import allensdk.core.swc as swc
# if you ran the examples above, you will have a reconstruction here
file_name = 'cell_types/specimen_485909730/reconstruction.swc'
morphology = swc.read_swc(file_name)
# subsample the morphology 3x. root, soma, junctions, and the first child of the root are preserved.
sparse_morphology = morphology.sparsify(3)
# compartments in the order that they were specified in the file
compartment_list = sparse_morphology.compartment_list
# a dictionary of compartments indexed by compartment id
compartments_by_id = sparse_morphology.compartment_index
# the root soma compartment
soma = morphology.soma
# all compartments are dictionaries of compartment properties
# compartments also keep track of ids of their children
def parse_neuron_swc(self, filepath, neuron_number):
"""
Given an swc file, render the neuron
:param filepath: str with path to swc file
:param neuron_number: numnber of neuron being rendered
"""
# details on swc files: http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html
_sample = namedtuple("sample", "sampleN structureID x y z r parent"
) # sampleN structureID x y z r parent
# in json {'allenId': 1021, 'parentNumber': 5, 'radius': 0.5, 'sampleNumber': 6,
# 'structureIdentifier': 2, 'x': 6848.52419500001, 'y': 2631.9816355, 'z': 3364.3552898125}
if not os.path.isfile(filepath) or not ".swc" in filepath.lower():
raise ValueError("unrecognized file path: {}".format(filepath))
try:
morphology = allen_swc.read_swc(filepath)
return self.parse_neurons_swc_allen(morphology, neuron_number)
except:
pass # the .swc file fas not generate with by allen
f = open(filepath)
content = f.readlines()
f.close()
# crate empty dicts for soma axon and dendrites
data = {
'soma':
dict(allenId=[],
parentNumber=[],
radius=[],
sampleNumber=[],
x=[],
y=[],
z=[]),
'axon':
dict(allenId=[],
parentNumber=[],
radius=[],
sampleNumber=[],
x=[],
y=[],
z=[]),
'dendrite':
dict(allenId=[],
parentNumber=[],
radius=[],
sampleNumber=[],
x=[],
y=[],
z=[])
}
# start looping around samples
for sample in content:
if sample[0] == '#':
continue # skip comments
s = _sample(
*
[float(samp.replace("\n", "")) for samp in sample.split("\t")])
# what structure is this
if s.structureID in [1., -1.]: key = "soma"
elif s.structureID in [2.]: key = 'axon'
elif s.structureID in [3., 4.]: key = 'dendrite'
else:
raise ValueError(
"unrecognised sample in SWC file: {}".format(s))
# append data to dictionary
data[key]['parentNumber'].append(int(s.parent))
data[key]['radius'].append(s.r)
data[key]['x'].append(s.x)
data[key]['y'].append(s.y)
data[key]['z'].append(s.z)
data[key]['sampleNumber'].append(int(s.sampleN))
data[key]['allenId'].append(-1) # TODO get allen ID from coords
return data
for r in radii :
header.append( str(r) )
cwriter.writerow( header )
for idx, cell in enumerate(cells) :
#if cell['id'] != 397351623:
# continue
print '%d: %d' % (idx,cell['id'])
fname = os.path.join( 'swc', '%d_morphology.swc' % cell['id'] )
if download_file :
ct.save_reconstruction( cell['id'], fname )
morphology = swc.read_swc(fname)
compartment_list = morphology.compartment_list
root = compartment_list[0]
if root['type'] != 1 :
print 'first node is not soma'
continue
sholl = np.zeros( radii.shape )
for n in morphology.compartment_list :
node_soma_diff = np.array([root['x'],root['y'],root['z']]) - np.array([n['x'],n['y'], n['z']])
node_soma_diff_norm = np.linalg.norm( node_soma_diff )
node_soma_diff_norm_square = node_soma_diff_norm ** 2
#print node_soma_diff
for r in radii:
header.append(str(r))
cwriter.writerow(header)
for idx, cell in enumerate(cells):
#if cell['id'] != 397351623:
# continue
print '%d: %d' % (idx, cell['id'])
fname = os.path.join('swc', '%d_morphology.swc' % cell['id'])
if download_file:
ct.save_reconstruction(cell['id'], fname)
morphology = swc.read_swc(fname)
compartment_list = morphology.compartment_list
root = compartment_list[0]
if root['type'] != 1:
print 'first node is not soma'
continue
sholl = np.zeros(radii.shape)
for n in morphology.compartment_list:
node_soma_diff = np.array([root['x'], root['y'], root['z']
]) - np.array([n['x'], n['y'], n['z']])
node_soma_diff_norm = np.linalg.norm(node_soma_diff)
node_soma_diff_norm_square = node_soma_diff_norm**2