How to use the ndlib.ndtype.ANNOTATION function in ndlib

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github neurodata / ndstore / test / makeunitdb.py View on Github external
def createTestDB ( project_name, channel_list=['unit_anno'], channel_type=ANNOTATION, channel_datatype=UINT32, public=PUBLIC_TRUE, ximagesize=10000, yimagesize=10000, zimagesize=1000, xvoxelres=4.0, yvoxelres=4.0, zvoxelres=3.0, scalingoption=ZSLICES, scalinglevels=5, readonly=READONLY_FALSE, propagate=NOT_PROPAGATED, window=[0,0], time=[0,0], default=False, nd_version=ND_VERSION, token_name='unittest', user='neurodata', dataset_name="unittest" ):
  """Create a unit test data base on the specified sit and name"""

  unituser = User.objects.get(username=user)

  ds = NDDataset(Dataset ( dataset_name=dataset_name, user=unituser, ximagesize=ximagesize, yimagesize=yimagesize, zimagesize=zimagesize,  xoffset=0, yoffset=0, zoffset=1, xvoxelres=xvoxelres, yvoxelres=yvoxelres, zvoxelres=zvoxelres, scalingoption=scalingoption, scalinglevels=scalinglevels, public=PUBLIC_TRUE, dataset_description="Unit test" ) )
  ds.create()

  # make the project entry
  pr = NDProject(Project(project_name=project_name, project_description='Unit test', user=unituser, dataset=ds._ds, nd_version=nd_version, host='localhost', kvengine=KV_ENGINE, kvserver=KV_SERVER, s3backend=0))
  pr.create()

  # create a token
  tk = NDToken(Token (token_name = token_name, user = unituser, token_description = 'Unit test token', project_id = pr.project_name, public = public))
  tk.create()
  
  # get the correct object for the kvengine
github neurodata / ndstore / test / test_annoid.py View on Github external
def setup_class(self):
    """Setup Parameters"""
    makeunitdb.createTestDB(p.token, p.channels, channel_type=ANNOTATION, channel_datatype=UINT32, public=True, ximagesize=1024, yimagesize=1024, zimagesize=10, xvoxelres=1.0, yvoxelres=1.0, zvoxelres=10.0, readonly=0)
github neurodata / ndstore / test / test_graphgen.py View on Github external
import numpy as np
import pytest
from contextlib import closing
import networkx as nx
import makeunitdb
from ndlib.ndtype import ANNOTATION, UINT32
from params import Params
from ramonmethods import H5AnnotationFile, setField, getField, queryField, makeAnno, createSpecificSynapse
from postmethods import putAnnotation, getAnnotation, getURL, postURL
from test_settings import *

p = Params()
p.token = 'unittest'
p.resolution = 0
p.channels = ['ANNO1']
p.channel_type = ANNOTATION
p.datatype = UINT32

@pytest.mark.skipif(True, reason='Test not necessary for dev mode')
class Test_GraphGen:

  def setup_class(self):
    """Create the unittest database"""
    makeunitdb.createTestDB(p.token, channel_list=p.channels, public=True, readonly=0, ximagesize=100, yimagesize=100, zimagesize=100)

    cutout1 = "0/2,5/1,3/1,3"
    cutout2 = "0/1,3/4,6/2,5"
    cutout3 = "0/4,6/2,5/5,7"
    cutout4 = "0/6,8/5,9/2,4"

    syn_segments1 = [7, 3]
    syn_segments2 = [7, 4]