### ndio membrane segmentation imports

import ndio

import ndio.remote.OCP as OCP

import ndio.remote.OCPMeta as NDLIMS

import numpy as np

### Create OCP / OCPMeta objects

oo = OCP()

nn = NDLIMS()

###

print "Done importing packages"

image_token = 'kasthuri11cc'

annotation_token = 'kasthuri2015_ramon_v'

segmentation_token = 'ac3ac4'

# Get channel ROI for token

channel_ROI = nn.get_metadata(segmentation_token)['channels']

# Get membrane ROI coordinates

membrane_group_ROI = channel_ROI['ac4_neuron_truth']['rois']['ac4']

# Sets membrane query in Python

membrane_query = {

}

print "Getting images"

# Sets cutout arguments for ground truth membrane annotation

membrane_anno = oo.get_cutout(**membrane_query)

print "Printing to file"

np.save('nXp_ground.npy', membrane_anno)

print "Done."