# How to grab our data and put it into a .npy file

# To load data in code:

#

# import numpy as np

#

# membrane_images = np.load('nXp_data.npy')

#

import ndio

import ndio.remote.OCP as OCP

oo = OCP()

import ndio.remote.OCPMeta as NDLIMS

nn = NDLIMS()

import ndio.convert.tiff as ndtiff # For export to tiff later

import numpy as np

print "Done importing packages"

tokens = oo.get_public_tokens()

image_token = 'kasthuri11cc'

annotation_token = 'cv_kasthuri11_membrane_2014'

# Get channel ROI for token

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

# Get membrane ROI coordinates

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

# Sets membrane query in Python

membrane_query = {

}

print "Getting images"

membrane_images = oo.get_cutout(**membrane_query)

print "Printing to file"

np.save('nXp_data.npy', membrane_images)

print "Done."