def neuron_graph_from_annotations(annotation_list,
proj_opts,
anno_dict=None,
append_annotations=True):
# Build a neuron graph from a readable list of annotation strings
if anno_dict is None:
anno_dict = ci.get_annotation_dict(proj_opts)
anno_id_list = list()
for anno in annotation_list:
try:
anno_id_list.append(anno_dict[anno])
except KeyError:
print('Not a valid key: ' + anno + ' (skipping)')
skid_list = ci.get_ids_from_annotation(anno_id_list, proj_opts)
g = neuron_graph(skid_list, proj_opts)
if append_annotations:
g = append_annotation_list(g,
annotation_list,
proj_opts,
anno_dict=anno_dict)
return g
def main():
project_flag = sys.argv[1]
input_args = {
sys.argv[i]: sys.argv[i + 1]
for i in range(2, len(sys.argv), 2)
}
proj_opts = cpp.project_map(project_flag)
anno_dict = ci.get_annotation_dict(proj_opts)
arg_ids_to_expand = [
anno_dict[arg] for arg in input_args.keys() if input_args[arg] == '1'
]
arg_ids_noexpand = [
anno_dict[arg] for arg in input_args.keys() if input_args[arg] == '0'
]
if len(arg_ids_to_expand) > 0:
id_list_base = ci.get_ids_from_annotation(arg_ids_to_expand, proj_opts)
else:
id_list_base = []
if len(arg_ids_noexpand) > 0:
id_list_noexpand = ci.get_ids_from_annotation(arg_ids_noexpand,
proj_opts)
else:
id_list_noexpand = []
print(" Building id list...")
id_list = ci.increase_id_list(id_list_base, proj_opts, 1, 1)
for id in id_list_noexpand:
id_list.append(id)
id_list = list(set(id_list))
ci.write_skeletons_from_list(id_list, proj_opts)
def main():
project_flag = sys.argv[1]
input_args = [sys.argv[i] for i in range(2, len(sys.argv))]
proj_opts = cpp.project_map(project_flag)
anno_dict = ci.get_annotation_dict(proj_opts)
arg_ids = [anno_dict[arg] for arg in input_args]
f_anno = open('annotation_ids.txt', 'w')
for arg in input_args:
f_anno.write(arg)
id_list_base = ci.get_ids_from_annotation([anno_dict[arg]], proj_opts)
for skid in id_list_base:
f_anno.write(',' + str(skid))
f_anno.write('\n')
f_anno.close()
def append_annotation_list(g, annotation_list, proj_opts, anno_dict=None):
# Given a list of annotations (as a string), add a node property to each
# skeleton containing which annotations they have
if anno_dict is None:
anno_dict = ci.get_annotation_dict(proj_opts)
for anno in annotation_list:
try:
anno_id = [anno_dict[anno]]
for skid in ci.get_ids_from_annotation(anno_id, proj_opts):
if skid in g.nodes():
if 'annotations' in g.node[skid].keys():
if anno not in g.node[skid]['annotations']:
g.node[skid]['annotations'].append(anno)
else:
g.node[skid]['annotations'] = [anno]
except KeyError:
print('Not a valid key: ' + anno + ' (skipping)')
return g
def neurons_from_annotations(annotation_list, proj_opts, syns=None):
anno_dict = ci.get_annotation_dict(proj_opts)
id_list = ci.get_ids_from_annotation(
[anno_dict[anno] for anno in annotation_list], proj_opts)
(neurons, syns) = neurons_from_id_list(id_list, proj_opts, syns=syns)
return (neurons, syns)