def readStack(x, y, z, r):
xmin = 0
xmax = 1023
ymin = 0
ymax = 1023
zmin = 0
zmax = 99
if (Local_Neuroseg.IS_IN_CLOSE_RANGE(
x, xmin, xmax)) & (Local_Neuroseg.IS_IN_CLOSE_RANGE(
y, ymin, ymax)) & (Local_Neuroseg.IS_IN_CLOSE_RANGE(
z, zmin, zmax)):
box = np.zeros(6)
box[0] = math.floor(x - r)
box[1] = math.floor(y - r)
box[2] = math.floor(z - r)
box[3] = math.ceil(x + r)
box[4] = math.ceil(y + r)
box[5] = math.ceil(z + r)
boxSize = int(
(box[5] - box[2]) * (box[4] - box[1]) * (box[3] - box[0]))
connection = httplib.HTTPConnection("localhost:2048", timeout=5.0)
uuid = "hatu"
dvid_volume = voxels.VoxelsAccessor(connection, uuid, "grayscale")
stack = dvid_volume.get_ndarray(
(0, int(box[0]), int(box[1]), int(box[2])),
(1, int(box[3]), int(box[4]), int(box[5])))
stack = stack.reshape(boxSize)
return stack
else:
return np.zeros(0)
def test_get_partial_slicing(self):
# Retrieve from server
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
subvolume = dvid_vol[0:4, 9:10, 5:20, 50:150]
start, stop = (0, 9, 5, 50, 0), (4, 10, 20, 150, 3)
# Compare to file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def test_get_ellipsis_slicing(self):
# Retrieve from server
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
subvolume = dvid_vol[0:4, 9:10, ..., 1:2]
start, stop = (0, 9, 0, 0, 1), (4, 10, 100, 200, 2)
# Compare to file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def test_get_ndarray(self):
"""
Get some data from the server and check it.
"""
# Retrieve from server
start, stop = (0, 9, 5, 50, 0), (4, 10, 20, 150, 3)
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
subvolume = dvid_vol.get_ndarray(start, stop)
# Compare to file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def test_get_channel_slicing(self):
"""
Test that slicing in the channel dimension works.
This is a special case because the entire volume needs to be requested from DVID,
but only the requested subset of channels will be returned.
"""
# Retrieve from server
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
subvolume = dvid_vol[1:3, 9:10, 5:20, 50:150]
# Compare to file
start, stop = (1, 9, 5, 50, 0), (3, 10, 20, 150, 3)
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def test_get_full_volume_via_slicing(self):
# Retrieve from server
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
subvolume1 = dvid_vol[:]
start = (0, ) * len(self.original_data.shape)
stop = self.original_data.shape
# Compare to file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume1)
# Alternate sytax: Use Ellipsis
subvolume2 = dvid_vol[...]
# Results should match
assert (subvolume1 == subvolume2).all()
def test_post_reduced_dim_slicing(self):
# Cutout dims
start, stop = (0, 9, 5, 50, 0), (4, 10, 20, 150, 3)
shape = numpy.subtract(stop, start)
# Generate test data
subvolume = numpy.random.randint(0, 1000, shape).astype(numpy.uint32)
# Send to server
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
dvid_vol[0:4, 9, 5:20, 50:150, 0:3] = subvolume[:, 0, ...]
# Check file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def readStack(x, y, z, r, address, port, uuid):
xmin = 0
xmax = 99
ymin = 0
ymax = 99
zmin = 0
zmax = 99
if (Local_Neuroseg.IS_IN_CLOSE_RANGE(
x, xmin, xmax)) & (Local_Neuroseg.IS_IN_CLOSE_RANGE(
y, ymin, ymax)) & (Local_Neuroseg.IS_IN_CLOSE_RANGE(
z, zmin, zmax)):
box = np.zeros(6)
box[0] = math.floor(x - r)
box[1] = math.floor(y - r)
box[2] = math.floor(z - r)
box[3] = math.ceil(x + r) + 1
box[4] = math.ceil(y + r) + 1
box[5] = math.ceil(z + r) + 1
boxSize = int(
(box[5] - box[2]) * (box[4] - box[1]) * (box[3] - box[0]))
connection = httplib.HTTPConnection(address + ":" + port, timeout=5.0)
# uuid = "ae87"
dvid_volume = voxels.VoxelsAccessor(connection, uuid, "grayscale")
stack = dvid_volume.get_ndarray(
(0, int(box[0]), int(box[1]), int(box[2])),
(1, int(box[3]), int(box[4]), int(box[5])))
stack2 = np.zeros(boxSize)
t, a, b, c = stack.shape
index = 0
for i in range(c):
for j in range(b):
for k in range(a):
stack2[index] = stack[0][k][j][i]
k += 1
index += 1
j += 1
i += 1
return stack2.reshape(1, int(box[3] - box[0]), int(box[4] - box[1]),
int(box[5] - box[2]))
else:
return np.zeros(0)
def test_extra_query_args(self):
"""
Create a VoxelsAccessor that uses extra query args
They come after the '?' in the REST URI. For example:
http://localhost/api/node/mydata/_0_1_2/10_10_10/0_0_0?roi=whatever&attenuation=3
"""
# Retrieve from server
start, stop = (0, 9, 5, 50, 0), (4, 10, 20, 150, 3)
query_args = {'roi': 'some_ref', 'attenuation': 5}
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid,
self.data_name,
query_args=query_args)
subvolume = dvid_vol.get_ndarray(start, stop)
# Compare to file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def test_get_ndarray_throttled_2(self):
"""
Get some data from the server and check it.
Enable throttle via query_args
Note: This test doesn't really exercise our handling of 503 responses...
"""
# Retrieve from server
start, stop = (0, 9, 5, 50, 0), (4, 10, 20, 150, 3)
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid,
self.data_name,
query_args={'throttle': 'on'})
subvolume = dvid_vol.get_ndarray(start, stop)
# Compare to file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def test_post_ndarray(self):
"""
Modify a remote subvolume and verify that the server wrote it.
"""
# Cutout dims
start, stop = (0, 9, 5, 50, 0), (4, 10, 20, 150, 3)
shape = numpy.subtract(stop, start)
# Generate test data
subvolume = numpy.random.randint(0, 1000, shape).astype(numpy.uint32)
# Send to server
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
dvid_vol.post_ndarray(start, stop, subvolume)
# Check file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def test_zy_post_negative_coordinates(self):
"""
Just make sure nothing blows up if we post to negative coordinates.
(Right now, the mock server doesn't actually store this data, but it shouldn't crash.)
"""
# Cutout dims
start, stop = (0, -10, 5, -50, 0), (4, 10, 20, 150, 10)
shape = numpy.subtract(stop, start)
# Generate test data
subvolume = numpy.random.randint(0, 1000, shape).astype(numpy.uint32)
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
# Send to server
dvid_vol.post_ndarray(start, stop, subvolume)
# Now try to 'get' data from negative coords
dvid_vol.get_ndarray(start, stop)
def test_get_stepped_slicing(self):
"""
"""
# Retrieve from server
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
subvolume = dvid_vol[0:4:2, 1:10:3, 5:20:5, 50:150:10]
# Compare to file
full_start = (0, ) * len(self.original_data.shape)
full_stop = self.original_data.shape
full_stored_volume = self._get_subvolume_from_file(
self.test_filepath, self.data_uuid, self.data_name, full_start,
full_stop)
stored_stepped_volume = full_stored_volume[0:4:2, 1:10:3, 5:20:5,
50:150:10]
assert subvolume.shape == stored_stepped_volume.shape
assert subvolume.dtype == stored_stepped_volume.dtype
assert (subvolume == stored_stepped_volume).all()
def test_get_reduced_dim_slicing(self):
# Retrieve from server
dvid_vol = voxels.VoxelsAccessor(self.client_connection,
self.data_uuid, self.data_name)
subvolume = dvid_vol[
0:4, 9:10, 3, :,
1:2] # Note that the third dimension will be dropped...
start, stop = (0, 9, 3, 0, 1), (4, 10, 4, 200, 2)
# Check dimensionality/shape of returned volume
full_shape = numpy.array(stop) - start
reduced_shape = list(full_shape[:2]) + list(full_shape[3:])
assert subvolume.shape == tuple(reduced_shape)
# Before we compare to the file, re-insert the dropped axis
subvolume = subvolume[:, :, numpy.newaxis, ...]
# Compare to file
self._check_subvolume(self.test_filepath, self.data_uuid,
self.data_name, start, stop, subvolume)
def test_zz_quickstart_usage(self):
import json
import httplib
import numpy
from pydvid import voxels, general
# Open a connection to DVID
connection = httplib.HTTPConnection("localhost:8000", timeout=5.0)
# Get detailed dataset info: /api/datasets/info
dataset_details = general.get_repos_info(connection)
# print json.dumps( dataset_details, indent=4 )
# Create a new remote volume
uuid = 'abcde'
voxels_metadata = voxels.VoxelsMetadata.create_default_metadata(
(4, 0, 0, 0), numpy.uint8, 'cxyz', 1.0, "")
voxels.create_new(connection, uuid, "my_volume", voxels_metadata)
# Use the VoxelsAccessor convenience class to manipulate a particular data volume
dvid_volume = voxels.VoxelsAccessor(connection, uuid, "my_volume")
# print dvid_volume.axiskeys, dvid_volume.dtype, dvid_volume.minindex, dvid_volume.shape
# Add some data
updated_data = numpy.ones(
(4, 100, 100, 100),
dtype=numpy.uint8) # Must include all channels.
dvid_volume[:, 10:110, 20:120, 30:130] = updated_data
# OR:
dvid_volume.post_ndarray((0, 10, 20, 30), (4, 110, 120, 130),
updated_data)
# Read from it (First axis is channel.)
cutout_array = dvid_volume[:, 10:110, 20:120, 30:130]
# OR:
cutout_array = dvid_volume.get_ndarray((0, 10, 20, 30),
(4, 110, 120, 130))
assert isinstance(cutout_array, numpy.ndarray)
assert cutout_array.shape == (4, 100, 100, 100)
import numpy
from pydvid import voxels, general
connection = httplib.HTTPConnection("localhost:8001", timeout=5.0)
# Get detailed dataset info: /api/datasets/info
dataset_details = general.get_repos_info(connection)
# print json.dumps( dataset_details, indent=4 )
# Create a new remote volume
uuid = "25eb4d877a0d4f8391014fe1237ada8a"
voxels_metadata = voxels.VoxelsMetadata.create_default_metadata(
(4, 0, 0, 0), numpy.uint8, "cxyz", 1.0, "")
# voxels.create_new( connection, uuid, "my_volume", voxels_metadata )
# Use the VoxelsAccessor convenience class to manipulate a particular data volume
dvid_volume = voxels.VoxelsAccessor(connection, uuid, "my_volume")
print(dvid_volume.axiskeys, dvid_volume.dtype, dvid_volume.minindex,
dvid_volume.shape)
# Add some data
updated_data = numpy.ones((4, 100, 100, 100),
dtype=numpy.uint8) # Must include all channels.
# dvid_volume[:, 10:110, 20:120, 30:130] = updated_data
# OR:
dvid_volume.post_ndarray((0, 10, 20, 30), (4, 110, 120, 130), updated_data)
# Read from it (First axis is channel.)
cutout_array = dvid_volume[:, 10:110, 20:120, 30:130]
# OR:
cutout_array = dvid_volume.get_ndarray((0, 10, 20, 30), (4, 110, 120, 130))