def setUp(self):
self.oo = neurodata()
self.ramon_segment = self.oo.get_ramon('kasthuri2015_ramon_v4',
'neurons',
3,
3,
include_cutout=True)
self.default_ramon_segment = ndio.ramon.RAMONSynapse()
def put_ramon_volume(self, token, channel, annofile, ramonobj, x_start,
y_start, z_start, resolution=1, conncomp=0,
remote='neurodata'):
vol, ramons = self.create_ramon_volume(token, channel, annofile,
ramonobj, conncomp=conncomp,
remote='neurodata')
if remote is 'neurodata':
import ndio.remote.neurodata as neurodata
nd = neurodata()
else:
raise ValueError("remote option not implemented.")
# upload paint
print('uploading paint...')
nd.post_cutout(token, channel,
x_start, y_start, z_start,
vol, resolution=1)
# upload ramon
print('uploading RAMON...')
print('Sorry, I can\'t upload RAMONObjects yet...' \
'waiting for new functionality.')
def setUp(self):
self.nd = neurodata()
self.nd_force_chunk = neurodata(chunk_threshold=0)
def setUp(self):
self.nd = neurodata()
self.nd_force_chunk = neurodata(chunk_threshold=0)
def setUp(self):
self.nd = neurodata()
def setUp(self):
self.nd = neurodata()
self.t = "kasthuri2015_ramon_v4"
self.c = "neurons"
self.ramon_id = 1
"""
... and collect all of the region names in a dictionary with the "id" field as keys.
"""
regionDict = getChildrenNames(root)
#print(leafList)
#for key in regionDict.keys():
# print('{0}, "{1}"'.format(key, regionDict[key]))
#print(regionDict)
#sys.exit()
"""
Next we RAMONify the data
"""
token = "ara3_to_AutA"
channel = "annotation_draft"
nd = neurodata(hostname='synaptomes.neurodata.io/nd/')
for regionId in regionDict.keys():
regionName = regionDict[regionId]
kvpairs = {'name': regionName}
ramonObj = ndramon.RAMONGeneric(id=regionId, resolution=0, kvpairs=kvpairs)
try:
nd.post_ramon(token, channel, ramonObj)
print "Successfully posted ramon obj {0} for {1}".format(
regionId, regionName)
except:
print "Failed to post ramon obj {0} for {1}".format(
regionId, regionName)
def setUp(self):
self.n = neurodata()
self.t = 'kasthuri2015_ramon_v4'
self.c = 'neurons'
def setUp(self):
self.oo = neurodata()
self.ramon_segment = self.oo.get_ramon("kasthuri2015_ramon_v4", "neurons", 3, 3, include_cutout=True)
self.default_ramon_segment = ndio.ramon.RAMONSynapse()
def setUp(self):
self.nd = neurodata(check_tokens=True)
def setUp(self):
self.nd = neurodata()
self.ramon_id = 1
def setUp(self):
self.nd = neurodata(check_tokens=True)
def setUp(self):
self.nd = neurodata()
self.ramon_id = 1
def setUp(self):
self.nd = neurodata()
self.t = 'kasthuri2015_ramon_v4'
self.c = 'neurons'
self.ramon_id = 1
from PyTablePrinter import tableprinter
import ndio.remote.neurodata as neurodata
nd = neurodata()
public_datasets_and_tokens = nd.get_public_datasets_and_tokens()
public_datasets_and_tokens = [
{'name': k, 'channels': cs} for k, cs in public_datasets_and_tokens.items()
]
def channel_summary(item):
return len(item['channels'])
table_printer = tableprinter.TablePrinter(public_datasets_and_tokens, col_order=[
# lookup Col Title # Function to generate data
('name', 'Name', None),
(None, 'Number of Channels', channel_summary)
])
print(table_printer.to_markdown())
import os
import argparse
from PIL import Image
import numpy as np
import ndio
from ndio.remote import neurodata
# setup ndio (note that because of the /ocp redirect, we force /nd)
nd = neurodata(hostname='synaptomes.neurodata.io/nd/')
def create_annotation_channel(token, channel):
try:
ret = nd.create_channel(name=channel, token=token, channel_type='annotation', dtype='uint32', readonly=False)
if ret == True:
print "Created channel for {}".format(channel)
else:
print "Error creating channel {}".format(channel)
except ndio.remote.RemoteDataUploadError, e:
print e
def ingest_annotation_slice(filename, token, channel, zindex):
imdata = Image.open(filename, 'r')
imarr = np.asarray(imdata, dtype=np.uint32)
imarr = np.transpose(imarr)
imstack = imarr[:,:,np.newaxis]
try:
ret = nd.post_cutout(token=token, channel=channel, x_start=0, y_start=0, z_start=zindex, data=imstack, resolution=0)
if ret == True:
print "Posted slice {} for channel {}".format(zindex, channel)
else:
def setUp(self):
self.oo = neurodata()
def setUp(self):
self.oo = neurodata()
import ndio
import scipy.io as io
import os
import ndio.remote.neurodata as neurodata
nd = neurodata()
# LIST OF PROJECT NAMES
#'Ex2R18C1', 'Ex2R18C2', 'Ex3R43C1', 'Ex3R43C2', 'Ex3R43C3', 'Ex6R15C1', 'Ex6R15C2', 'Ex10R55','Ex12R75', 'Ex12R76', 'Ex13R51',
volumeList = [
'Ex2R18C1', 'Ex2R18C2', 'Ex3R43C1', 'Ex3R43C2', 'Ex3R43C3', 'Ex6R15C1',
'Ex6R15C2', 'Ex10R55', 'Ex12R75', 'Ex12R76', 'Ex13R51'
]
#
#baseStr = "/data/anish/Synaptome/kristina15/rawVolumes/";
baseStr = "/Users/anish/Documents/Connectome/Synaptome-Duke/"
folderStrBoolean = os.path.isdir(baseStr)
if (folderStrBoolean == False):
os.mkdir(baseStr)
print "Folder Created"
for token in volumeList:
print token
channels = nd.get_channels(token)
x_stop, y_stop, z_stop = nd.get_image_size(token, resolution=0)
print x_stop, y_stop, z_stop
# See if directory exists
def setUp(self):
self.nd = neurodata()
