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import numpy as np
import neuroglancer
ap = argparse.ArgumentParser()
ap.add_argument(
'-a',
'--bind-address',
help='Bind address for Python web server. Use 127.0.0.1 (the default) to restrict access '
'to browers running on the local machine, use 0.0.0.0 to permit access from remote browsers.')
ap.add_argument(
'--static-content-url', help='Obtain the Neuroglancer client code from the specified URL.')
args = ap.parse_args()
if args.bind_address:
neuroglancer.set_server_bind_address(args.bind_address)
if args.static_content_url:
neuroglancer.set_static_content_source(url=args.static_content_url)
viewer = neuroglancer.Viewer()
a = np.zeros((3, 100, 100, 100), dtype=np.uint8)
ix, iy, iz = np.meshgrid(* [np.linspace(0, 1, n) for n in a.shape[1:]], indexing='ij')
a[0, :, :, :] = np.abs(np.sin(4 * (ix + iy))) * 255
a[1, :, :, :] = np.abs(np.sin(4 * (iy + iz))) * 255
a[2, :, :, :] = np.abs(np.sin(4 * (ix + iz))) * 255
with viewer.txn() as s:
s.layers['image'] = neuroglancer.ImageLayer(
source='precomputed://gs://neuroglancer-public-data/flyem_fib-25/image',
)
s.layers['ground_truth'] = neuroglancer.SegmentationLayer(
import argparse
import numpy as np
import neuroglancer
ap = argparse.ArgumentParser()
ap.add_argument(
'-a',
'--bind-address',
help='Bind address for Python web server. Use 127.0.0.1 (the default) to restrict access '
'to browers running on the local machine, use 0.0.0.0 to permit access from remote browsers.')
ap.add_argument(
'--static-content-url', help='Obtain the Neuroglancer client code from the specified URL.')
args = ap.parse_args()
if args.bind_address:
neuroglancer.set_server_bind_address(args.bind_address)
if args.static_content_url:
neuroglancer.set_static_content_source(url=args.static_content_url)
a = np.zeros((3, 100, 100, 100), dtype=np.uint8)
ix, iy, iz = np.meshgrid(* [np.linspace(0, 1, n) for n in a.shape[1:]], indexing='ij')
a[0, :, :, :] = np.abs(np.sin(4 * (ix + iy))) * 255
a[1, :, :, :] = np.abs(np.sin(4 * (iy + iz))) * 255
a[2, :, :, :] = np.abs(np.sin(4 * (ix + iz))) * 255
b = np.cast[np.uint32](np.floor(np.sqrt((ix - 0.5)**2 + (iy - 0.5)**2 + (iz - 0.5)**2) * 10))
b = np.pad(b, 1, 'constant')
viewer = neuroglancer.Viewer()
dimensions = neuroglancer.CoordinateSpace(
names=['x', 'y', 'z'],
units='nm',
help='Number of top synaptic partners to display.')
ap.add_argument(
'--order',
choices=['min', 'sum'],
default='min',
help='Method by which to combine synaptic partner counts from multiple segments.')
ap.add_argument(
'-a',
'--bind-address',
help='Bind address for Python web server. Use 127.0.0.1 (the default) to restrict access '
'to browers running on the local machine, use 0.0.0.0 to permit access from remote browsers.')
ap.add_argument(
'--static-content-url', help='Obtain the Neuroglancer client code from the specified URL.')
args = ap.parse_args()
if args.bind_address:
neuroglancer.set_server_bind_address(args.bind_address)
if args.static_content_url:
neuroglancer.set_static_content_source(url=args.static_content_url)
demo = Demo(
synapse_path=args.synapses,
num_top_partners=args.num_partners,
top_method=args.order,
)
print(demo.viewer)
import time
time.sleep(5000)
while True:
time.sleep(1000)
np.minimum(dist_transform, 5) / 5.0 * 254)
self.inf_volume.invalidate()
if __name__ == '__main__':
ap = argparse.ArgumentParser()
ap.add_argument(
'-a',
'--bind-address',
help='Bind address for Python web server. Use 127.0.0.1 (the default) to restrict access '
'to browers running on the local machine, use 0.0.0.0 to permit access from remote browsers.')
ap.add_argument(
'--static-content-url', help='Obtain the Neuroglancer client code from the specified URL.')
args = ap.parse_args()
if args.bind_address:
neuroglancer.set_server_bind_address(args.bind_address)
if args.static_content_url:
neuroglancer.set_static_content_source(url=args.static_content_url)
inf = InteractiveInference()
print(inf.viewer)
while True:
time.sleep(1000)
ap.add_argument('--bodies', required=True, help='Path to list of bodies to proofread')
ap.add_argument(
'-a',
'--bind-address',
help='Bind address for Python web server. Use 127.0.0.1 (the default) to restrict access '
'to browers running on the local machine, use 0.0.0.0 to permit access from remote browsers.'
)
ap.add_argument(
'--static-content-url', help='Obtain the Neuroglancer client code from the specified URL.')
ap.add_argument('--labels', nargs='+', help='Labels to use')
ap.add_argument('--prefetch', type=int, default=10, help='Number of bodies to prefetch')
args = ap.parse_args()
if args.bind_address:
neuroglancer.set_server_bind_address(args.bind_address)
if args.static_content_url:
neuroglancer.set_static_content_source(url=args.static_content_url)
bodies = []
with open(args.bodies, 'r') as f:
csv_reader = csv.DictReader(f)
for row in csv_reader:
bodies.append(
Body(
segment_id=int(row['id']),
num_voxels=int(row['num_voxels']),
bbox_start=np.array(
[
int(row['bbox.start.x']),
int(row['bbox.start.y']),
def _stop_fill_action(self, action_state):
self._stop_flood_fill()
if __name__ == '__main__':
ap = argparse.ArgumentParser()
ap.add_argument(
'-a',
'--bind-address',
help='Bind address for Python web server. Use 127.0.0.1 (the default) to restrict access '
'to browers running on the local machine, use 0.0.0.0 to permit access from remote browsers.')
ap.add_argument(
'--static-content-url', help='Obtain the Neuroglancer client code from the specified URL.')
args = ap.parse_args()
if args.bind_address:
neuroglancer.set_server_bind_address(args.bind_address)
if args.static_content_url:
neuroglancer.set_static_content_source(url=args.static_content_url)
inf = InteractiveInference()
print(inf.viewer)
while True:
time.sleep(1000)
def run_interactive(args, graph):
# Make splitter a global variable so that it is accessible from the
# interactive `python -i` shell.
global splitter
if args.bind_address:
neuroglancer.set_server_bind_address(args.bind_address)
if args.static_content_url:
neuroglancer.set_static_content_source(url=args.static_content_url)
splitter = InteractiveSplitter(
graph,
agglo_id=args.agglo_id,
image_url=args.image_url,
segmentation_url=args.segmentation_url,
state_path=args.state)
print(splitter.viewer)