Python connect Exemples

Exemple #1

Fichier : zfcheck.py Projet : somhegyi-zz/catmaid_tools

    '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 = [], []

Exemple #2

Fichier : test_authentication.py Projet : somhegyi-zz/catmaid_tools

#!/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()

Exemple #3

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 = {}

Exemple #4

Fichier : catmaid_monitor.py Projet : somhegyi-zz/catmaid_tools

def connect_to_catmaid():
    return catmaid.connect(server=opts.server,
                           user=opts.username,
                           password=opts.password,
                           project=opts.authname)

Exemple #5

Fichier : gen_annotation_map.py Projet : AsaBarthMaron/catmaid_analysis

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 = {}