def DVID_push_cutout(args):
rmt = DVIDRemote({"protocol": "http", "host": args.host})
# data is desired range
data = np.load(args.input)
numpyType = np.uint8
if args.datatype == "uint32":
numpyType = np.uint32
elif args.datatype == "uint64":
numpyType = np.uint64
if data.dtype != args.datatype:
data = data.astype(numpyType)
sources = []
if args.source:
sources.append(args.source)
# Create or get a channel to write to
instance_setup = DataInstanceResource(
UUID=args.uuid,
name=args.data_instance,
type=args.type,
alias=args.alias,
datatype=args.datatype,
)
print("Data Instance setup.")
chan_actual_up = rmt.create_project(instance_setup)
x_rng = [args.xmin, args.xmax]
y_rng = [args.ymin, args.ymax]
z_rng = [args.zmin, args.zmax]
print("Data model setup. UUID: {}".format(chan_actual_up))
# Pipeline Data will be in X,Y,Z format
# Change to Z,Y,X for upload
data = np.transpose(data, (2, 1, 0))
data = data.copy(order="C")
# Verify that the cutout uploaded correctly.
attempts = 0
while attempts < 3:
try:
rmt.create_cutout(instance_setup, args.res, x_rng, y_rng, z_rng,
data)
break
except HTTPError as e:
if attempts < 3:
attempts += 1
print("These are the dimensions: ")
print(data.shape)
print("This is the data type:")
print(data.dtype)
print("Specified data type was:")
print(args.dtype)
print("Specified image type")
print(args.itype)
print("Obtained HTTP error from server. Trial {}".format(
attempts))
print("The error: {}".format(e))
else:
raise Exception("Failed 3 times: {}".format(e))
from subprocess import call
import intern
from intern.remote.dvid import DVIDRemote
# #Starts Dockers
# call(["docker-compose", "up"])
#DVID Data fetch:
dvid = DVIDRemote({
"protocol": "http",
"host": "localhost:8000",
})
#Creating Project, and chanel to store boxed data in
proj = dvid.create_project('Xbrain_Proj1', 'Data upload test')
chan_setup = dvid.ChannelResource(proj, "MaskedImg1")
#Uploads Data
call([
"docker-compose", "exec", "dvid", "dvid", "node", proj, "MaskedImg1",
"load", "0" + "," + "0" + "," + "390", "dataLoad/*.tif"
])
print("The dvid instance has your requested data sample.")
from intern.remote.dvid import DVIDRemote
from intern.resource.dvid import DataInstanceResource
import numpy as np
dvid = DVIDRemote({"protocol": "http", "host": "localhost:8001",})
# Prepare the data
data_cube = np.load("/My/dummy/dir/validation_grayscale.npy").astype(np.uint8)
data_cube = data_cube[0:512, 0:512, 0:512]
data_cube = data_cube.copy(order="C")
print(data_cube.dtype)
print(data_cube.shape)
# Create the project
instance_setup_up = DataInstanceResource(
alias="local_dvid_test",
type="uint8blk",
name="validation",
UUID=None,
datatype="uint8",
)
chan_actual_up = dvid.create_project(instance_setup_up)
# Create the cutout
dvid.create_cutout(instance_setup_up, 0, [0, 512], [0, 512], [0, 512], data_cube)
print("Create cutout successful")
# Get the cutout
got_cutout = dvid.get_cutout(instance_setup_up, 0, [0, 512], [0, 512], [0, 1])
print(got_cutout.shape)
print("Arrays match: {}".format(np.array_equal(got_cutout, data_cube[0:1, :, :])))
import intern
from intern.remote.boss import BossRemote
from intern.resource.boss.resource import ChannelResource
from intern.remote.dvid import DVIDRemote
import matplotlib.pyplot as plt
import numpy as np
#DVID Data fetch:
dvid = DVIDRemote({
"protocol": "http",
"host": "localhost:8000",
})
chan_setup = dvid.ChannelResource('Xbrain_Proj_Dummy', 'dyer15_3_maskim_DUmmy',
'masked_images', 'Data upload test', '')
proj = dvid.create_project(chan_setup)
print(proj)
# dvid.delete_project("8ef")
})
DATA_INSTANCE = "ex_EM"
ALIAS = "Test_alias"
########### Test Project API ###########
## Create DataInstanceResource and force the creation of a RepositoryResource
instance_setup_em = DataInstanceResource(DATA_INSTANCE,
None,
"uint8blk",
ALIAS,
"Example channel.",
datatype="uint8")
# Get the channel and create a project
instance_actual_repo = dvid.create_project(instance_setup_em)
print("Repo UUID:" + instance_actual_repo)
# Create an instance within given repo(UUID)
instance_setup_anno = DataInstanceResource(
DATA_INSTANCE + "_the_second",
instance_actual_repo,
"uint8blk",
ALIAS,
"Example channel.",
datatype="uint8",
)
instance_actual_anno_uuid = dvid.create_project(instance_setup_anno)
print("Data Instance UUID: {}".format(instance_actual_anno_uuid))