def DVID_pull_cutout(args):
rmt = DVIDRemote({"protocol": "http", "host": args.host})
# 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.")
x_rng = [args.xmin, args.xmax]
y_rng = [args.ymin, args.ymax]
z_rng = [args.zmin, args.zmax]
# Verify that the cutout uploaded correctly.
attempts = 0
while attempts < 3:
try:
cutout_data = rmt.get_cutout(instance_setup, args.res, x_rng,
y_rng, z_rng)
break
except HTTPError as e:
if attempts < 3:
attempts += 1
print("Obtained HTTP error from server. Trial {}".format(
attempts))
else:
print("Failed 3 times: {}".format(e))
# Data will be in Z,Y,X format
# Change to X,Y,Z for pipeline
cutout_data = np.transpose(cutout_data, (2, 1, 0))
# Clean up.
with open(args.output, "w+b") as f:
np.save(f, cutout_data)
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",
})
volumeD = dvid.get_cutout(
dvid.get_channel("3ca15f84b1ee4fb780fef94c5771ffe6","dyer15_3_maskim"),0,
[1287,1387],[1200,1300],[390,490]
)
#Printing volumes:
print("Dvid volume: ")
print(volumeD)
#Graphing Dvid:
imgplot = plt.imshow(volumeD[3,:,:], cmap = "gray")
plt.show()
import intern
from intern.remote.dvid import DVIDRemote
import matplotlib.pyplot as plt
#DVID Data fetch:
dvid = DVIDRemote({
"protocol": "http",
"host": "localhost:8000",
})
chan = "UUID/ChannelName"
volumeD = dvid.get_cutout(dvid.get_channel(chan), 0, [0, 2560], [0, 2560],
[390, 392])
print(volumeD)
imgplot = plt.imshow(volumeD[0, :, :], cmap="gray")
plt.show()
})
volumeB = boss.get_cutout(
boss.get_channel("em", "pinky40", "v7"),
1,
[10000, 10500],
[10000, 10500],
[500, 550],
)
#DVID Data fetch:
dvid = DVIDRemote({
"protocol": "http",
"host": "localhost:8000",
})
volumeD = dvid.get_cutout(
dvid.get_channel("5cc94d532799484cb01788fcdb7cd9f0", "grayscale"), 0,
[2300, 4600], [2300, 4600], [1380, 1390])
#Printing volumes:
print("Dvid volume: ")
print(volumeD)
print("Boss volume: ")
print(volumeB)
#Graphing Boss:
imgplot = plt.imshow(volumeB[0, :, :], cmap="gray")
one = volumeB[0, :, :]
one_size = one.size
plt.show()
#Graphing Dvid:
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.dvid import DVIDRemote
from PIL import Image
import numpy as np
import os
import matplotlib.pyplot as plt
UUID = "30eb"
#Declare DVIDRemote
dvid = DVIDRemote({
"protocol": "http",
"host": "localhost:8000",
})
volumeD = dvid.get_cutout(
dvid.get_channel(UUID, "dyer15_3_maskim_DUmmy", "dyer15_3_maskim_DUmmy"),
0, [0, 2560], [0, 2560], [290, 292])
print(volumeD)
imgplot = plt.imshow(volumeD[0, :, :], cmap='gray')
plt.show()
#
# Prepare the data
img = Image.open("<somedir>/*.png")
data_tile = np.asarray(img)
print(data_tile.shape)
data_tile = np.expand_dims(data_tile, axis=0)
data_tile = data_tile.copy(order="C")
# Create the project
instance_setup_up = DataInstanceResource(
DATA_INSTANCE + "_the_second",
None,
"imagetile",
"Upload Test",
"Example channel.",
datatype="uint8",
)
chan_actual_up = dvid.create_project(instance_setup_up)
# Create the cutout
dvid.create_cutout(instance_setup_up, 0, [0, 454], [0, 480], [0, 1], data_tile)
print("Create cutout successful")
# Get the cutout
got_cutout = dvid.get_cutout(instance_setup_up, 0, [0, 454], [0, 480], [0, 1])
# Check for equality
if (got_cutout == data_tile).all():
print("Both tiles equate")
[10000, 10200],
[10000, 10200],
[501, 502],
)
#UPLOAD TO DVID REPOSITORY
dvid = DVIDRemote({
"protocol": "http",
"host": "localhost:8000",
})
chan_setup = dvid.ChannelResource('pinky40', 'BossData RemoteTest',
'Data uploaded from Boss to dvid')
proj = dvid.create_project(chan_setup)
UUID = chan_setup.split("/")
UUID = UUID[0]
xrang = [0, 32]
yrang = [0, 32]
zrang = [32, 64]
volume = dvid.create_cutout(proj, xrang, yrang, zrang, volumeB)
#Check DVID Data:
volumeD = dvid.get_cutout(dvid.get_channel(UUID, "pinky40", "Medulla"), 0,
[0, 200], [0, 200], [32, 33])
print(volumeD)
imgplot = plt.imshow(volumeD[:, :, 0], cmap="gray")
plt.show()
# Define the remote
dvid = DVIDRemote({
"protocol": "https",
"host": "emdata.janelia.org",
})
uuid = "822524777d3048b8bd520043f90c1d28"
name = "grayscale"
annos_name = "groundtruth"
print(dvid.get_extents(dvid.get_instance(uuid, name, datatype="uint8")))
# get cutout from actual dataset
volumeD = dvid.get_cutout(
dvid.get_instance(uuid, name, datatype="uint8"),
0,
[3000, 3150],
[3000, 3150],
[2000, 2010],
)
# get annotations from dataset
annosD = dvid.get_cutout(
dvid.get_instance(uuid, annos_name, datatype="uint64"),
0,
[3000, 3150],
[3000, 3150],
[2000, 2010],
)
# overlay the data
plt.imshow(volumeD[0, :, :], cmap="gray")