def setUpClass(cls):
"""
Override. Called by nosetests.
"""
# Choose names
cls.dvid_repo = "datasetA"
cls.data_name = "random_data"
cls.volume_location = "/repos/{dvid_repo}/volumes/{data_name}".format( **cls.__dict__ )
cls.data_uuid = get_testrepo_root_uuid()
cls.node_location = "/repos/{dvid_repo}/nodes/{data_uuid}".format( **cls.__dict__ )
# Generate some test data
#data = numpy.random.randint(0, 255, (128, 256, 512, 1)).astype( numpy.uint8 )
data = numpy.zeros((128, 256, 512, 1), dtype=numpy.uint8)
data.flat[:] = numpy.arange( numpy.prod((128, 256, 512, 1)) )
cls.original_data = data
cls.voxels_metadata = VoxelsMetadata.create_default_metadata(data.shape, data.dtype, "zyxc", 1.0, "")
# Write it to a new data instance
node_service = DVIDNodeService(TEST_DVID_SERVER, cls.data_uuid)
node_service.create_grayscale8(cls.data_name)
node_service.put_gray3D( cls.data_name, data[...,0], (0,0,0) )
def __init__(self, hostname, uuid, data_name, *args, **kwargs):
"""
Create a new VoxelsAccessor with all the same properties as the current instance,
except that it accesses a roi mask volume.
"""
# Create default mask metadata.
mask_metadata = {}
mask_metadata["Properties"] = { "Values" : [ { "DataType" : "uint8", "Label": "roi-mask" } ] }
# For now, we hardcode XYZ order
# The size/offset are left as None, because that doesn't apply to ROI data.
default_axis_info = { "Label": "", "Resolution": 1, "Units": "", "Size": 0, "Offset" : 0 }
mask_metadata["Axes"] = [copy.copy(default_axis_info),
copy.copy(default_axis_info),
copy.copy(default_axis_info)]
mask_metadata["Axes"][0]["Label"] = "X"
mask_metadata["Axes"][1]["Label"] = "Y"
mask_metadata["Axes"][2]["Label"] = "Z"
assert '_metadata' not in kwargs or kwargs['_metadata'] is None
kwargs['_metadata'] = VoxelsMetadata(mask_metadata)
assert '_access_type' not in kwargs or kwargs['_access_type'] is None
kwargs['_access_type'] = 'mask'
# Init base class with pre-formed metadata instead of querying for it.
super(RoiMaskAccessor, self).__init__( hostname, uuid, data_name, *args, **kwargs )
def run_export(self):
self.progressSignal(0)
url = self.NodeDataUrl.value
url_path = url.split('://')[1]
hostname, api, node, uuid, dataname = url_path.split('/')
assert api == 'api'
assert node == 'node'
axiskeys = self.Input.meta.getAxisKeys()
shape = self.Input.meta.shape
if self._transpose_axes:
axiskeys = reversed(axiskeys)
shape = tuple(reversed(shape))
axiskeys = "".join( axiskeys )
if self.OffsetCoord.ready():
offset_start = self.OffsetCoord.value
else:
offset_start = (0,) * len( self.Input.meta.shape )
self.progressSignal(5)
# Get the dataset details
try:
metadata = VoxelsAccessor.get_metadata(hostname, uuid, dataname)
except VoxelsAccessor.BadRequestError as ex:
# Dataset doesn't exist yet. Let's create it.
metadata = VoxelsMetadata.create_default_metadata( shape,
self.Input.meta.dtype,
axiskeys,
0.0,
"" )
VoxelsAccessor.create_new(hostname, uuid, dataname, metadata)
# Since this class is generally used to push large blocks of data,
# we'll be nice and set throttle=True
client = VoxelsAccessor( hostname, uuid, dataname, throttle=True )
def handle_block_result(roi, data):
# Send it to dvid
roi = numpy.asarray(roi)
roi += offset_start
start, stop = roi
if self._transpose_axes:
data = data.transpose()
start = tuple(reversed(start))
stop = tuple(reversed(stop))
client.post_ndarray( start, stop, data )
requester = BigRequestStreamer( self.Input, roiFromShape( self.Input.meta.shape ) )
requester.resultSignal.subscribe( handle_block_result )
requester.progressSignal.subscribe( self.progressSignal )
requester.execute()
self.progressSignal(100)
def _update_subvol_widget(self, node_uuid, dataname, typename):
"""
Update the subvolume widget with the min/max extents of the given node and dataname.
Note: The node and dataname do not necessarily have to match the currently
selected node and dataname.
This enables the right-click behavior, which can be used to
limit your data volume to the size of a different data volume.
"""
error_msg = None
try:
if typename == "roi":
node_service = DVIDNodeService(self._hostname, str(node_uuid))
roi_blocks_zyx = numpy.array(
node_service.get_roi(str(dataname)))
maxindex = tuple(DVID_BLOCK_WIDTH *
(1 + numpy.max(roi_blocks_zyx, axis=0)))
minindex = (0, 0, 0) # Rois are always 3D
axiskeys = "zyx"
# If the current selection is a dataset, then include a channel dimension
if self.get_selection().typename != "roi":
axiskeys = "zyxc"
minindex = minindex + (0, )
maxindex = maxindex + (
1,
) # FIXME: This assumes that the selected data has only 1 channel...
else:
# Query the server
raw_metadata = VoxelsAccessor.get_metadata(
self._hostname, node_uuid, dataname)
voxels_metadata = VoxelsMetadata(raw_metadata)
maxindex = voxels_metadata.shape
minindex = voxels_metadata.minindex
axiskeys = voxels_metadata.axiskeys
# If the current selection is a roi, then remove the channel dimension
if self.get_selection().typename == "roi":
axiskeys = "zyx"
minindex = minindex[:-1]
maxindex = maxindex[:-1]
except (DVIDException, ErrMsg) as ex:
error_msg = str(ex)
log_exception(logger)
else:
self._buttonbox.button(QDialogButtonBox.Ok).setEnabled(True)
if error_msg:
self._buttonbox.button(QDialogButtonBox.Ok).setEnabled(False)
QMessageBox.critical(self, "DVID Error", error_msg)
self._subvol_widget.initWithExtents("", (), (), ())
return
self._subvol_widget.initWithExtents(axiskeys, maxindex, minindex,
maxindex)
def get_metadata( hostname, uuid, data_name ):
"""
Query the voxels metadata for the given node/data_name.
"""
connection = DVIDConnection(hostname)
rest_query = "/node/{uuid}/{data_name}/metadata".format( uuid=uuid, data_name=data_name )
status, response_body, _err_msg = connection.make_request( rest_query, ConnectionMethod.GET )
try:
json_data = json.loads(response_body)
except ValueError:
raise RuntimeError("Response body could not be parsed as valid json:\n"
"GET " + rest_query + "\n" + response_body)
return VoxelsMetadata( json_data )
def _get_format_selection_error_msg(self, *args):
"""
If the currently selected format does not support the input image format,
return an error message stating why. Otherwise, return an empty string.
"""
if not self.Input.ready():
return "Input not ready"
output_format = self.OutputFormat.value
# These cases support all combinations
if output_format in ('hdf5', 'npy', 'blockwise hdf5'):
return ""
tagged_shape = self.Input.meta.getTaggedShape()
axes = OpStackWriter.get_nonsingleton_axes_for_tagged_shape( tagged_shape )
output_dtype = self.Input.meta.dtype
if output_format == 'dvid':
# dvid requires a channel axis, which must come last.
# Internally, we transpose it before sending it over the wire
if tagged_shape.keys()[-1] != 'c':
return "DVID requires the last axis to be channel."
# Make sure DVID supports this dtype/channel combo.
from libdvid.voxels import VoxelsMetadata
axiskeys = self.Input.meta.getAxisKeys()
# We reverse the axiskeys because the export operator (see below) uses transpose_axes=True
reverse_axiskeys = "".join(reversed( axiskeys ))
reverse_shape = tuple(reversed(self.Input.meta.shape))
metainfo = VoxelsMetadata.create_default_metadata( reverse_shape,
output_dtype,
reverse_axiskeys,
0.0,
'nanometers' )
try:
metainfo.determine_dvid_typename()
except Exception as ex:
return str(ex)
else:
return ""
return FormatValidity.check(self.Input.meta.getTaggedShape(),
self.Input.meta.dtype,
output_format)
def test_zz_quickstart_usage(self):
import json
import numpy
from libdvid import DVIDConnection, ConnectionMethod
from libdvid.voxels import VoxelsAccessor, VoxelsMetadata
# Open a connection to DVID
connection = DVIDConnection("127.0.0.1:8000")
# Get detailed dataset info: /api/repos/info (note: /api is prepended automatically)
status, body, _error_message = connection.make_request(
"/repos/info", ConnectionMethod.GET)
dataset_details = json.loads(body)
# print(json.dumps( dataset_details, indent=4 ))
# Create a new remote volume (assuming you already know the uuid of the node)
uuid = UUID
voxels_metadata = VoxelsMetadata.create_default_metadata(
(0, 0, 0, 1), numpy.uint8, 'zyxc', 1.0, "")
VoxelsAccessor.create_new("127.0.0.1:8000", uuid, "my_volume",
voxels_metadata)
# Use the VoxelsAccessor convenience class to manipulate a particular data volume
accessor = VoxelsAccessor("127.0.0.1:8000", uuid, "my_volume")
# print(dvid_volume.axiskeys, dvid_volume.dtype, dvid_volume.minindex, dvid_volume.shape)
# Add some data (must be block-aligned)
# Must include all channels.
updated_data = numpy.ones((256, 192, 128, 1), dtype=numpy.uint8)
accessor[256:512, 32:224, 0:128, 0] = updated_data
# OR:
#accessor.post_ndarray( (0,10,20,30), (1,110,120,130), updated_data )
# Read from it (First axis is channel.)
cutout_array = accessor[300:330, 40:120, 10:110, 0]
# OR:
cutout_array = accessor.get_ndarray((300, 40, 10, 0),
(330, 120, 110, 1))
assert isinstance(cutout_array, numpy.ndarray)
assert cutout_array.shape == (30, 80, 100, 1)
def test_zz_quickstart_usage(self):
import json
import numpy
from libdvid import DVIDConnection, ConnectionMethod
from libdvid.voxels import VoxelsAccessor, VoxelsMetadata
# Open a connection to DVID
connection = DVIDConnection( "localhost:8000" )
# Get detailed dataset info: /api/repos/info (note: /api is prepended automatically)
status, body, error_message = connection.make_request( "/repos/info", ConnectionMethod.GET)
dataset_details = json.loads(body)
# print json.dumps( dataset_details, indent=4 )
# Create a new remote volume (assuming you already know the uuid of the node)
uuid = UUID
voxels_metadata = VoxelsMetadata.create_default_metadata( (1,0,0,0), numpy.uint8, 'cxyz', 1.0, "" )
VoxelsAccessor.create_new( "localhost:8000", uuid, "my_volume", voxels_metadata )
# Use the VoxelsAccessor convenience class to manipulate a particular data volume
accessor = VoxelsAccessor( "localhost:8000", uuid, "my_volume" )
# print dvid_volume.axiskeys, dvid_volume.dtype, dvid_volume.minindex, dvid_volume.shape
# Add some data (must be block-aligned)
# Must include all channels.
# Must be FORTRAN array, using FORTRAN indexing order conventions
# (Use order='F', and make sure you're indexing it as cxyz)
updated_data = numpy.ones( (1,128,192,256), dtype=numpy.uint8, order='F' )
updated_data = numpy.asfortranarray(updated_data)
accessor[:, 0:128, 32:224, 256:512] = updated_data
# OR:
#accessor.post_ndarray( (0,10,20,30), (1,110,120,130), updated_data )
# Read from it (First axis is channel.)
cutout_array = accessor[:, 10:110, 40:120, 300:330]
# OR:
cutout_array = accessor.get_ndarray( (0,10,40,300), (1,110,120,330) )
assert isinstance(cutout_array, numpy.ndarray)
assert cutout_array.shape == (1,100,80,30)
def setUpClass(cls):
"""
Override. Called by nosetests.
"""
# Choose names
cls.dvid_repo = "datasetA"
cls.data_name = "indices_data"
cls.volume_location = "/repos/{dvid_repo}/volumes/{data_name}".format( **cls.__dict__ )
cls.data_uuid = get_testrepo_root_uuid()
cls.node_location = "/repos/{dvid_repo}/nodes/{data_uuid}".format( **cls.__dict__ )
# Generate some test data
data = numpy.random.randint(0, 255, (1, 128, 256, 512))
data = numpy.asfortranarray(data, numpy.uint8)
cls.original_data = data
cls.voxels_metadata = VoxelsMetadata.create_default_metadata(data.shape, data.dtype, "cxyz", 1.0, "")
# Write it to a new data instance
node_service = DVIDNodeService(TEST_DVID_SERVER, cls.data_uuid)
node_service.create_grayscale8(cls.data_name)
node_service.put_gray3D( cls.data_name, data[0,...], (0,0,0) )
def _update_display(self):
super(DvidDataSelectionBrowser, self)._update_display()
hostname, dset_uuid, dataname, node_uuid = self.get_selection()
enable_contents = self._repos_info is not None and dataname != "" and node_uuid != ""
self._roi_groupbox.setEnabled(enable_contents)
if not dataname or not node_uuid:
self._roi_widget.initWithExtents("", (), (), ())
return
error_msg = None
try:
# Query the server
raw_metadata = VoxelsAccessor.get_metadata(hostname, node_uuid,
dataname)
voxels_metadata = VoxelsMetadata(raw_metadata)
except DVIDException as ex:
error_msg = ex.message
except ErrMsg as ex:
error_msg = str(ErrMsg)
except VoxelsAccessor.BadRequestError as ex:
# DVID will return an error if the selected dataset
# isn't a 'voxels' dataset and thus has no voxels metadata
self._buttonbox.button(QDialogButtonBox.Ok).setEnabled(False)
return
else:
self._buttonbox.button(QDialogButtonBox.Ok).setEnabled(True)
if error_msg:
QMessageBox.critical(self, "DVID Error", error_msg)
self._roi_widget.initWithExtents("", (), (), ())
return
self._roi_widget.initWithExtents(voxels_metadata.axiskeys,
voxels_metadata.shape,
voxels_metadata.minindex,
voxels_metadata.shape)
def test_zz_quickstart_usage(self):
import json
import numpy
from libdvid import DVIDConnection, ConnectionMethod
from libdvid.voxels import VoxelsAccessor, VoxelsMetadata
# Open a connection to DVID
connection = DVIDConnection( "127.0.0.1:8000" )
# Get detailed dataset info: /api/repos/info (note: /api is prepended automatically)
status, body, _error_message = connection.make_request( "/repos/info", ConnectionMethod.GET)
dataset_details = json.loads(body)
# print(json.dumps( dataset_details, indent=4 ))
# Create a new remote volume (assuming you already know the uuid of the node)
uuid = UUID
voxels_metadata = VoxelsMetadata.create_default_metadata( (0,0,0,1), numpy.uint8, 'zyxc', 1.0, "" )
VoxelsAccessor.create_new( "127.0.0.1:8000", uuid, "my_volume", voxels_metadata )
# Use the VoxelsAccessor convenience class to manipulate a particular data volume
accessor = VoxelsAccessor( "127.0.0.1:8000", uuid, "my_volume" )
# print(dvid_volume.axiskeys, dvid_volume.dtype, dvid_volume.minindex, dvid_volume.shape)
# Add some data (must be block-aligned)
# Must include all channels.
updated_data = numpy.ones( (256,192,128,1), dtype=numpy.uint8)
accessor[256:512, 32:224, 0:128, 0] = updated_data
# OR:
#accessor.post_ndarray( (0,10,20,30), (1,110,120,130), updated_data )
# Read from it (First axis is channel.)
cutout_array = accessor[300:330, 40:120, 10:110, 0]
# OR:
cutout_array = accessor.get_ndarray( (300,40,10,0), (330,120,110,1) )
assert isinstance(cutout_array, numpy.ndarray)
assert cutout_array.shape == (30,80,100,1)
def main():
# Read cmd-line args
parser = argparse.ArgumentParser()
parser.add_argument("--hostname", default="localhost:8000")
parser.add_argument("--uuid", required=False, help="The node to upload to. If not provided, a new repo will be created (see --new-repo-alias).")
parser.add_argument("--data-name", required=False, help="The name of the data instance to modify. If it doesn't exist, it will be created first.")
parser.add_argument("--new-repo-alias", required=False, help="If no uuid is provided, a new repo is created, with this name.")
parser.add_argument("input_file", help="For example: /tmp/myfile.h5/dataset")
args = parser.parse_args()
if '.h5' not in args.input_file:
sys.stderr.write("File name does not indicate hdf5.\n")
sys.exit(1)
filepath, dset_name = args.input_file.split('.h5')
filepath += '.h5'
if not dset_name:
sys.stderr.write("You must provide a dataset name, e.g. myfile.h5/mydataset\n")
sys.exit(1)
if not os.path.exists(filepath):
sys.stderr.write("File doesn't exist: {}\n".format(filepath))
sys.exit(1)
# If no uuid given, create a new repo on the server
uuid = args.uuid
if uuid is None:
alias = args.new_repo_alias or "testrepo"
server = DVIDServerService(args.hostname)
uuid = server.create_new_repo(alias, "This is a test repo loaded with data from ".format(args.input_file))
uuid = str(uuid)
# Read the input data from the file
print("Reading {}{}".format( filepath, dset_name ))
with h5py.File(filepath) as f_in:
data = f_in[dset_name][:]
# We assume data is 3D or 4D, in C-order
# We adjust it to 4D, fortran-order
if data.ndim == 3:
data = data[...,None]
data = data.transpose()
assert data.flags['F_CONTIGUOUS'], "Data is not contiguous!"
assert data.ndim == 4, "Data must be 3D with axes zyx or 4D with axes zyxc (C-order)"
assert data.shape[0] == 1, "Data must have exactly 1 channel, not {}".format( data.shape[0] )
# Choose a default data instance name if necessary
if data.dtype == numpy.uint8:
data_name = args.data_name or "grayscale"
elif data.dtype == numpy.uint64:
data_name = args.data_name or "segmentation"
else:
sys.stderr.write("Unsupported dtype: {}\n".format(data.dtype))
sys.exit(1)
# Create the new data instance if it doesn't exist already
try:
metadata = VoxelsAccessor.get_metadata(args.hostname, uuid, data_name)
print("Data instance '{}' already exists. Will update.".format( data_name ))
except DVIDException:
print("Creating new data instance: {}".format( data_name ))
metadata = VoxelsMetadata.create_default_metadata(data.shape, data.dtype, 'cxyz', 1.0, 'nanometers')
VoxelsAccessor.create_new(args.hostname, uuid, data_name, metadata)
# Finally, push the data to the server
print("Pushing data to {}".format( '{}/api/node/{}/{}'.format( args.hostname, uuid, data_name ) ))
accessor = VoxelsAccessor(args.hostname, uuid, data_name)
accessor.post_ndarray((0,0,0,0), data.shape, data)
print("DONE.")
def main():
# Read cmd-line args
parser = argparse.ArgumentParser()
parser.add_argument("--hostname", default="localhost:8000")
parser.add_argument(
"--uuid",
required=False,
help=
"The node to upload to. If not provided, a new repo will be created (see --new-repo-alias)."
)
parser.add_argument(
"--data-name",
required=False,
help=
"The name of the data instance to modify. If it doesn't exist, it will be created first."
)
parser.add_argument(
"--new-repo-alias",
required=False,
help="If no uuid is provided, a new repo is created, with this name.")
parser.add_argument("input_file",
help="For example: /tmp/myfile.h5/dataset")
args = parser.parse_args()
if '.h5' not in args.input_file:
sys.stderr.write("File name does not indicate hdf5.\n")
sys.exit(1)
filepath, dset_name = args.input_file.split('.h5')
filepath += '.h5'
if not dset_name:
sys.stderr.write(
"You must provide a dataset name, e.g. myfile.h5/mydataset\n")
sys.exit(1)
if not os.path.exists(filepath):
sys.stderr.write("File doesn't exist: {}\n".format(filepath))
sys.exit(1)
# If no uuid given, create a new repo on the server
uuid = args.uuid
if uuid is None:
alias = args.new_repo_alias or "testrepo"
server = DVIDServerService(args.hostname)
uuid = server.create_new_repo(
alias, "This is a test repo loaded with data from ".format(
args.input_file))
uuid = str(uuid)
# Read the input data from the file
print("Reading {}{}".format(filepath, dset_name))
with h5py.File(filepath) as f_in:
data = f_in[dset_name][:]
# We assume data is 3D or 4D, in C-order
# We adjust it to 4D, fortran-order
if data.ndim == 3:
data = data[..., None]
data = data.transpose()
assert data.flags['F_CONTIGUOUS'], "Data is not contiguous!"
assert data.ndim == 4, "Data must be 3D with axes zyx or 4D with axes zyxc (C-order)"
assert data.shape[
0] == 1, "Data must have exactly 1 channel, not {}".format(
data.shape[0])
# Choose a default data instance name if necessary
if data.dtype == numpy.uint8:
data_name = args.data_name or "grayscale"
elif data.dtype == numpy.uint64:
data_name = args.data_name or "segmentation"
else:
sys.stderr.write("Unsupported dtype: {}\n".format(data.dtype))
sys.exit(1)
# Create the new data instance if it doesn't exist already
try:
metadata = VoxelsAccessor.get_metadata(args.hostname, uuid, data_name)
print("Data instance '{}' already exists. Will update.".format(
data_name))
except DVIDException:
print("Creating new data instance: {}".format(data_name))
metadata = VoxelsMetadata.create_default_metadata(
data.shape, data.dtype, 'cxyz', 1.0, 'nanometers')
VoxelsAccessor.create_new(args.hostname, uuid, data_name, metadata)
# Finally, push the data to the server
print("Pushing data to {}".format('{}/api/node/{}/{}'.format(
args.hostname, uuid, data_name)))
accessor = VoxelsAccessor(args.hostname, uuid, data_name)
accessor.post_ndarray((0, 0, 0, 0), data.shape, data)
print("DONE.")
