'TODO branch',
'soma',
'myelinated',
'unmyelinated',
'root_myelinated',
'root_unmyelinated',
'ends',
'damage',
'axon',
'projection',
'backbone',
]
# connect to catmaid and get the source from the connection
# default to using environmental variables
c = catmaid.connect()
src = catmaid.get_source(c, ignore_none_skeletons=True)
# create logger
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
# creates two lists, one for error messages and one for url links
master_errors = []
master_urls = []
root_errors, root_urls = [], []
leaf_tag_errors, leaf_tag_urls = [], []
loop_errors, loop_urls = [], []
incorrect_tag_errors, incorrect_tag_urls = [], []
max_distance_errors, max_distance_urls = [], []
#!/usr/bin/env python
import sys
import catmaid
server = 'http://catmaid.hms.harvard.edu/catmaid3/'
if len(sys.argv) > 1:
server = sys.argv[1]
print "connecting to server: %s" % server
c = catmaid.connect(server)
print "api_token: %s" % c.api_token
projects = c.projects
print "projects: %s" % projects
for project in projects:
pid = project.get('pid', project.get('id', -1))
if pid == -1:
continue
print("Project[%s]: %s" % (pid, project['title']))
c.set_project(pid)
sids = c.skeleton_ids()
print("\t%i skeletons" % len(sids))
if len(sids):
sid = sids[0]
sk = c.skeleton(sid)
print("\tskeleton[%s] type=%s" % (sid, type(sk)))
wd = c.wiring_diagram()
import json
import os
import sys
import catmaid
if __name__ == "__main__":
if len(sys.argv) < 2:
outfile = '/home/simulation/tracing/sid_by_annotation.json'
else:
outfile = sys.argv[1]
c = catmaid.connect(
'http://catmaid2.hms.harvard.edu', # server
'wtobin', # username
'', # password
'wfly1') # project_id)
nids = c.neuron_ids()
nid_to_sid = c.nid_to_sid_map()
annotations = {}
for nid in nids:
try:
annotation = c.annotation_table(nid)
annotations[nid] = annotation
except Exception as e:
print("Failed to fetch annotations for: %s" % nid)
sid_by_annotation = {}
def connect_to_catmaid():
return catmaid.connect(server=opts.server,
user=opts.username,
password=opts.password,
project=opts.authname)
import json
import os
import sys
import catmaid
if len(sys.argv) < 2:
outfile = '/home/simulation/tracing/sid_by_annotation.json'
else:
outfile = sys.argv[1]
#c = catmaid.connect()
c = catmaid.connect('http://catmaid2.hms.harvard.edu', # server
'wtobin', # username
'', # password
'wfly1') # project_id)
nids = c.neuron_ids()
nid_to_sid = c.nid_to_sid_map()
annotations = {}
for nid in nids:
try:
annotation = c.annotation_table(nid)
annotations[nid] = annotation
except Exception as e:
print("Failed to fetch annotations for: %s" % nid)
sid_by_annotation = {}