def __init__(self, reference_image, moving_image, segmentation,
points_file, reference_voxel_size, moving_voxel_size):
"""Constructor
:param reference_image: align to this image
:param moving_image: align this image
:param segmentation: the segmentation associated with the reference
image or None if no segmentation.
:param points_file: where to load and store points
:param reference_voxel_size: a 3-tuple giving the X, Y and Z voxel
size in nanometers.
:param moving_voxel_size: the voxel size for the moving image
"""
self.reference_image = reference_image
self.moving_image = moving_image
self.segmentation = segmentation
self.moving_images[id(self)] = moving_image
self.decimation = max(1, np.min(reference_image.shape) // 5)
n_elems = int(np.prod(self.reference_image.shape))
alignment_raw = multiprocessing.RawArray('f', n_elems)
self.alignment_raw[id(self)] = alignment_raw
self.reference_viewer = neuroglancer.Viewer()
self.moving_viewer = neuroglancer.Viewer()
self.points_file = points_file
self.warper = None
self.reference_voxel_size = reference_voxel_size
self.moving_voxel_size = moving_voxel_size
self.load_points()
self.init_state()
def add_volume(self, volume, layer_name=None, clear_layer=False):
if self.viewer is None:
self.viewer = neuroglancer.Viewer()
if layer_name is None:
layer_name = f'{self.layer_type}_{self.scales}'
source = neuroglancer.LocalVolume(
data=volume,
dimensions=neuroglancer.CoordinateSpace(names=['x', 'y', 'z'],
units='nm',
scales=self.scales),
voxel_offset=self.offset)
if self.layer_type == 'segmentation':
layer = neuroglancer.SegmentationLayer(source=source)
else:
layer = neuroglancer.ImageLayer(source=source)
with self.viewer.txn() as s:
if clear_layer:
s.layers.clear()
s.layers[layer_name] = layer
print(f'A new layer named {layer_name} is added to:')
print(self.viewer)
def __init__(self, filename):
self.filename = filename
self.point_annotation_layer_name = 'false-merges'
self.states = []
self.state_index = None
viewer = self.viewer = neuroglancer.Viewer()
self.other_state_segment_ids = dict()
viewer.actions.add('anno-next-state', lambda s: self.next_state())
viewer.actions.add('anno-prev-state', lambda s: self.prev_state())
viewer.actions.add('anno-save', lambda s: self.save())
viewer.actions.add('anno-show-all',
lambda s: self.set_combined_state())
viewer.actions.add(
'anno-add-segments-from-state',
lambda s: self.add_segments_from_state(s.viewer_state))
with viewer.config_state.txn() as s:
s.input_event_bindings.viewer['pageup'] = 'anno-prev-state'
s.input_event_bindings.viewer['pagedown'] = 'anno-next-state'
s.input_event_bindings.viewer['control+keys'] = 'anno-save'
s.input_event_bindings.viewer['control+keya'] = 'anno-show-all'
viewer.shared_state.add_changed_callback(self.on_state_changed)
self.cur_message = None
if not self.load():
self.set_state_index(None)
def _neuroglancer_link(self):
options = Options.instance()
store_path = Path(options.runs_base_dir).expanduser()
viewer = neuroglancer.Viewer()
with viewer.txn() as s:
train_layers = {}
for i, dataset in enumerate(self.train):
train_layers.update(
dataset._neuroglancer_layers(
exclude_layers=set(train_layers.keys())))
validate_layers = {}
if self.validate is not None:
for i, dataset in enumerate(self.validate):
validate_layers.update(
dataset._neuroglancer_layers(
exclude_layers=set(validate_layers.keys())))
for layer_name, (layer, kwargs) in itertools.chain(
train_layers.items(), validate_layers.items()):
s.layers.append(
name=layer_name,
layer=layer,
**kwargs,
)
s.layout = neuroglancer.row_layout([
neuroglancer.LayerGroupViewer(
layers=list(train_layers.keys())),
neuroglancer.LayerGroupViewer(
layers=list(validate_layers.keys())),
])
return f"http://neuroglancer-demo.appspot.com/#!{json.dumps(viewer.state.to_json())}"
def visualize(dataset, split, aff, ip, port):
"""
Opens a tab in your webbrowser showing the chosen dataset
"""
import neuroglancer
config = config_dict(dataset)
neuroglancer.set_static_content_source(
url='https://neuroglancer-demo.appspot.com')
neuroglancer.set_server_bind_address(bind_address=ip, bind_port=port)
viewer = neuroglancer.Viewer(voxel_size=[6, 6, 30])
if aff:
import augmentation
augmentation.maybe_create_affinities(split)
add_affinities(config.folder, split + '-affinities', viewer)
else:
add_file(config.folder, split + '-input', viewer)
add_file(config.folder, split + '-labels', viewer)
print('open your brower at:')
print(viewer.__str__().replace('172.17.0.2', '54.166.106.209')
) # Replace the second argument with your own server's ip address
webbrowser.open(viewer.__str__())
print("press any key to exit")
input()
def run_render(args):
keypoints = load_script(args.script)
viewer = neuroglancer.Viewer()
print('Open the specified URL to begin rendering')
print(viewer)
if args.browser:
webbrowser.open_new(viewer.get_viewer_url())
fps = args.fps
with viewer.config_state.txn() as s:
s.show_ui_controls = False
s.show_panel_borders = False
s.viewer_size = [args.width, args.height]
saver = neuroglancer.ScreenshotSaver(viewer, args.output_directory)
total_frames = sum(max(1, k['transition_duration'] * fps) for k in keypoints[:-1])
for i in range(len(keypoints) - 1):
a = keypoints[i]['state']
b = keypoints[i + 1]['state']
duration = keypoints[i]['transition_duration']
num_frames = max(1, int(duration * fps))
for frame_i in range(num_frames):
t = frame_i / num_frames
cur_state = neuroglancer.ViewerState.interpolate(a, b, t)
viewer.set_state(cur_state)
index, path = saver.capture()
print('[%07d/%07d] keypoint %.3f/%5d: %s' % (index, total_frames, i + t, len(keypoints), path))
def __init__(self):
viewer = self.viewer = neuroglancer.Viewer()
self.gt_vol = cloudvolume.CloudVolume(
'https://storage.googleapis.com/neuroglancer-public-data/flyem_fib-25/ground_truth',
mip=0,
bounded=True,
progress=False,
provenance={})
viewer.actions.add('start-fill', self._start_fill_action)
viewer.actions.add('stop-fill', self._stop_fill_action)
self.dimensions = neuroglancer.CoordinateSpace(
names=['x', 'y', 'z'],
units='nm',
scales=[8, 8, 8],
)
with viewer.config_state.txn() as s:
s.input_event_bindings.data_view['shift+mousedown0'] = 'start-fill'
s.input_event_bindings.data_view['keyt'] = 'stop-fill'
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(
source=
'precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth',
)
s.layers['ground_truth'].visible = False
self.flood_fill_event = None
def __call__(self, chunks: dict):
"""
Parameters:
chunks: multiple chunks
"""
ng.set_static_content_source(
url='https://neuromancer-seung-import.appspot.com')
ng.set_server_bind_address(bind_port=self.port)
viewer = ng.Viewer()
with viewer.txn() as s:
for chunk_name, chunk in chunks.items():
global_offset = chunk.global_offset
chunk = np.ascontiguousarray(chunk)
s.layers.append(
name=chunk_name,
layer=ng.LocalVolume(
data=chunk,
dimensions=neuroglancer.CordinateSpace(
scales=[1, *self.voxel_size[::-1]],
units=['', 'nm', 'nm', 'nm'],
names=['c^', 'x', 'y', 'z']),
# offset is in nm, not voxels
offset=list(o * v for o, v in zip(
global_offset[::-1][-3:], self.voxel_size[::-1]))))
print('Open this url in browser: ')
print(viewer)
input('Press Enter to exit neuroglancer.')
def show_link(root, prefix, local_mode):
viewer = neuroglancer.Viewer()
# out_root = '/home/hanyu/ng/HL007/precom_theta_full/region_3400_4360_0_2048_2048_512_v3/stage_1'
stage_list = [
i.strip(prefix) for i in glob.glob(os.path.join(root, 'precomputed*'))
]
seg_sources = [header + i for i in stage_list]
# sk_source = header + '/HL007/precom_theta_full/region_3400_4360_0_2048_2048_512_v3/stage_1/skeletons_mip_0'
# print(seg_sources)
with viewer.txn() as s:
# s.layers['image'] = neuroglancer.ImageLayer(
# source='precomputed://'+im_source
# )
for i, seg in enumerate(seg_sources[:5]):
# print(i, seg)
s.layers['seg_%d' % i] = neuroglancer.SegmentationLayer(
source='precomputed://%s' % seg)
# s.layers['sk'] = neuroglancer.SegmentationLayer(
# skeletons='precomputed://%s' % sk_source,
# )
link = url_state.to_url(viewer.state)
if local_mode:
link = re.sub(r'https://neuroglancer-demo.appspot.com',
r'http://localhost:8080', link)
else:
link = re.sub(r'https://', r'http://', link)
pprint(link)
def __init__(self, script_path, transition_duration, fullscreen_width,
fullscreen_height, frames_per_second):
self.script_path = script_path
self.viewer = neuroglancer.Viewer()
self.frames_per_second = frames_per_second
self.default_transition_duration = transition_duration
self.fullscreen_width = fullscreen_width
self.fullscreen_height = fullscreen_height
self.keypoint_index = 0
if os.path.exists(script_path):
self.keypoints = load_script(script_path,
self.default_transition_duration)
else:
self.keypoints = []
self.transition_duration = transition_duration
self.viewer.shared_state.add_changed_callback(
self._viewer_state_changed)
self.quit_event = threading.Event()
self.is_dirty = True
self.is_fullscreen = False
keybindings = [
('keyk', 'add-keypoint'),
('bracketleft', 'prev-keypoint'),
('bracketright', 'next-keypoint'),
('backspace', 'delete-keypoint'),
('shift+bracketleft', 'decrease-duration'),
('shift+bracketright', 'increase-duration'),
('home', 'first-keypoint'),
('end', 'last-keypoint'),
('keyq', 'quit'),
('enter', 'toggle-play'),
('keyf', 'toggle-fullscreen'),
('keyj', 'revert-script'),
('comma', 'prev-frame'),
('period', 'next-frame'),
]
with self.viewer.config_state.txn() as s:
for k, a in keybindings:
s.input_event_bindings.viewer[k] = a
s.input_event_bindings.slice_view[k] = a
s.input_event_bindings.perspective_view[k] = a
self._keybinding_message = ' '.join('%s=%s' % x for x in keybindings)
self.viewer.actions.add('add-keypoint', self._add_keypoint)
self.viewer.actions.add('prev-keypoint', self._prev_keypoint)
self.viewer.actions.add('next-keypoint', self._next_keypoint)
self.viewer.actions.add('delete-keypoint', self._delete_keypoint)
self.viewer.actions.add('increase-duration', self._increase_duration)
self.viewer.actions.add('decrease-duration', self._decrease_duration)
self.viewer.actions.add('first-keypoint', self._first_keypoint)
self.viewer.actions.add('last-keypoint', self._last_keypoint)
self.viewer.actions.add('quit', self._quit)
self.viewer.actions.add('toggle-play', self._toggle_play)
self.viewer.actions.add('toggle-fullscreen', self._toggle_fullscreen)
self.viewer.actions.add('revert-script', self._revert_script)
self.viewer.actions.add('next-frame', self._next_frame)
self.viewer.actions.add('prev-frame', self._prev_frame)
self.playback_manager = None
self._set_keypoint_index(1)
def __init__(self, url, points, voxel_size):
self.url = url
self.points = points
self.voxel_size = voxel_size
self.viewer = neuroglancer.Viewer()
self.brightness = 20.0
self.init_actions()
self.refresh()
def __init__(self, raw, embedding, mst, classifier):
self.raw = raw
self.embedding = embedding
self.classifier = classifier
self.mst = mst
self.points = []
self.mst_graph = nx.Graph()
self.mst_graph.add_weighted_edges_from(mst)
self.threshold = 0.5
self.raw_dimensions = neuroglancer.CoordinateSpace(
names=['z', 'y', 'x'],
units='nm',
scales=raw.voxel_size)
self.dimensions = neuroglancer.CoordinateSpace(
names=['c^', 'z', 'y', 'x'],
units=[''] + 3*['nm'],
scales=raw.voxel_size)
# if len(raw.shape) > 3:
# volume_shape = raw.shape[1:]
# else:
volume_shape = raw.shape
print(f"Creating segmentation layer with shape {volume_shape}")
#self.segmentation = np.arange(np.product(volume_shape),dtype=np.uint32)
#self.segmentation = self.segmentation.reshape(volume_shape)
self.segmentation = np.zeros(volume_shape, dtype=np.uint32)
self.segmentation_volume = neuroglancer.LocalVolume(
data=self.segmentation,
dimensions=self.raw_dimensions)
self.viewer = neuroglancer.Viewer()
self.viewer.actions.add('label_fg', self._label_fg)
self.viewer.actions.add('label_bg', self._label_bg)
self.viewer.actions.add('update_seg', self._update_segmentation)
with self.viewer.config_state.txn() as s:
s.input_event_bindings.data_view['shift+mousedown0'] = 'label_fg'
s.input_event_bindings.data_view['shift+mousedown1'] = 'label_bg'
s.input_event_bindings.data_view['keyu'] = 'update_seg'
with self.viewer.txn() as s:
add_layer(s, self.raw, 'raw')
add_layer(s, self.embedding, 'embedding')
s.layers['embedding'].visible = False
s.layers['points'] = neuroglancer.LocalAnnotationLayer(
self.dimensions)
s.layers['segmentation'] = neuroglancer.SegmentationLayer(
source=self.segmentation_volume)
def _visualize_training(self, run):
# returns a neuroglancer link to visualize snapshots and validations
snapshot_container = self.snapshot_container(run.name)
validation_container = self.validation_container(run.name)
snapshot_zarr = zarr.open(snapshot_container.container)
validation_zarr = zarr.open(validation_container.container)
snapshots = []
validations = []
def generate_groups(container):
def add_element(name, obj):
if isinstance(obj, zarr.hierarchy.Array):
container.append(name)
return add_element
snapshot_zarr.visititems(
lambda name, obj: generate_groups(snapshots)(name, obj)
)
validation_zarr.visititems(
lambda name, obj: generate_groups(validations)(name, obj)
)
viewer = neuroglancer.Viewer()
with viewer.txn() as s:
snapshot_layers = {}
for snapshot in snapshots:
snapshot_layers[snapshot] = ZarrArray.open_from_array_identifier(
snapshot_container.array_identifier(snapshot), name=snapshot
)._neuroglancer_layer()
validation_layers = {}
for validation in validations:
validation_layers[validation] = ZarrArray.open_from_array_identifier(
validation_container.array_identifier(validation), name=validation
)._neuroglancer_layer()
for layer_name, (layer, kwargs) in itertools.chain(
snapshot_layers.items(), validation_layers.items()
):
s.layers.append(
name=layer_name,
layer=layer,
**kwargs,
)
s.layout = neuroglancer.row_layout(
[
neuroglancer.LayerGroupViewer(layers=list(snapshot_layers.keys())),
neuroglancer.LayerGroupViewer(
layers=list(validation_layers.keys())
),
]
)
return f"http://neuroglancer-demo.appspot.com/#!{json.dumps(viewer.state.to_json())}"
def __init__(self, synapse_path, top_method='min', num_top_partners=10):
with open(synapse_path, 'r') as f:
synapse_data = json.load(f)['data']
self.synapses_by_id, self.synapse_partner_counts = get_synapses_by_id(
synapse_data)
self.top_method = top_method
self.num_top_partners = num_top_partners
dimensions = neuroglancer.CoordinateSpace(
names=['x', 'y', 'z'],
units='nm',
scales=[8, 8, 8],
)
viewer = self.viewer = neuroglancer.Viewer()
viewer.actions.add('select-custom', self._handle_select)
with viewer.config_state.txn() as s:
s.input_event_bindings.data_view['dblclick0'] = 'select-custom'
with viewer.txn() as s:
s.projection_orientation = [
0.63240087, 0.01582051, 0.05692779, 0.77238464
]
s.dimensions = dimensions
s.position = [3000, 3000, 3000]
s.layers['image'] = neuroglancer.ImageLayer(
source=
'precomputed://gs://neuroglancer-public-data/flyem_fib-25/image',
)
s.layers['ground_truth'] = neuroglancer.SegmentationLayer(
source=
'precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth',
)
s.layers['partners'] = neuroglancer.SegmentationLayer(
source=
'precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth',
)
s.layers['synapses'] = neuroglancer.LocalAnnotationLayer(
dimensions=dimensions,
linked_segmentation_layer='ground_truth')
s.layout = neuroglancer.row_layout([
neuroglancer.LayerGroupViewer(
layout='xy',
layers=['image', 'ground_truth', 'partners', 'synapses'],
),
neuroglancer.LayerGroupViewer(
layout='3d',
layers=['ground_truth', 'synapses'],
),
neuroglancer.LayerGroupViewer(
layout='3d',
layers=['partners', 'synapses'],
),
])
self.selected_segments = frozenset()
self.viewer.shared_state.add_changed_callback(
lambda: self.viewer.defer_callback(self.on_state_changed))
def __init__(self,
reference_image,
moving_image,
segmentation,
points_file,
reference_voxel_size,
moving_voxel_size,
min_distance=1.0,
n_workers=multiprocessing.cpu_count()):
"""Constructor
:param reference_image: align to this image
:param moving_image: align this image
:param segmentation: the segmentation associated with the reference
image or None if no segmentation.
:param points_file: where to load and store points
:param reference_voxel_size: a 3-tuple giving the X, Y and Z voxel
size in nanometers.
:param moving_voxel_size: the voxel size for the moving image
:param min_distance: the minimum allowed distance between any two points
:param n_workers: # of workers to use when warping
"""
self.reference_image = reference_image
self.moving_image = moving_image
self.segmentation = segmentation
self.n_workers = n_workers
self.moving_images[id(self)] = moving_image
self.decimation = max(1, np.min(reference_image.shape) // 5)
n_elems = int(np.prod(self.reference_image.shape))
alignment_raw = multiprocessing.RawArray('f', n_elems)
self.alignment_raw[id(self)] = alignment_raw
self.reference_viewer = neuroglancer.Viewer()
self.moving_viewer = neuroglancer.Viewer()
self.points_file = points_file
self.warper = None
self.reference_voxel_size = reference_voxel_size
self.moving_voxel_size = moving_voxel_size
self.reference_brightness = 1.0
self.moving_brightness = 1.0
self.min_distance = min_distance
self.load_points()
self.init_state()
self.refresh_brightness()
def __init__(self, num_to_prefetch=10):
self.viewer = neuroglancer.Viewer()
self.num_to_prefetch = num_to_prefetch
self.todo = [] # items are lists of segment IDs
self.index = 0
self.batch = 1
self.apply_equivs = False
self.set_init_state()
def run_vol(vol_idx):
neuroglancer.set_static_content_source(url='https://neuroglancer-demo.appspot.com')
with h5py.File(os.path.expanduser('~/data/div_detect/full_records.h5'), 'r') as rec_file:
record = rec_file['records'][vol_idx,:, :, :, 1]
viewer = neuroglancer.Viewer(voxel_size=[1, 1, 1])
viewer.add(vol_to_int8(record),
name='record')
#viewer.add(b, name='b')
return viewer
def visualize_trees(graphs: Dict[str, nx.DiGraph]):
viewer = neuroglancer.Viewer()
with viewer.txn() as s:
s.layers["blegh"] = neuroglancer.ImageLayer(
source=neuroglancer.LocalVolume(data=np.zeros([1, 1, 1]).transpose(
[2, 1, 0]),
voxel_size=[1, 1, 1]))
node_id = itertools.count(start=1)
for name, graph in graphs.items():
add_trees(s, graph, node_id, name=name, visible=True)
print(viewer)
input("Hit ENTER to quit!")
def main():
app = QtWidgets.QApplication(sys.argv)
args = parse_args()
if args.static_content_source is not None:
neuroglancer.set_static_content_source(
url=args.static_content_source)
neuroglancer.set_server_bind_address(
args.bind_address, bind_port=args.port)
viewer = neuroglancer.Viewer()
print("Neuroglancer URL: %s" % str(viewer))
window = ApplicationWindow(viewer)
window.show()
sys.exit(app.exec())
def run(args):
neuroglancer.cli.handle_server_arguments(args)
state = args.state
state.selected_layer.visible = False
state.statistics.visible = False
if args.layout is not None:
state.layout = args.layout
if args.show_axis_lines is not None:
state.show_axis_lines = args.show_axis_lines
if args.show_default_annotations is not None:
state.show_default_annotations = args.show_default_annotations
if args.projection_scale_multiplier is not None:
state.projection_scale *= args.projection_scale_multiplier
state.gpu_memory_limit = args.gpu_memory_limit
state.system_memory_limit = args.system_memory_limit
state.concurrent_downloads = args.concurrent_downloads
if args.no_webdriver:
viewers = [neuroglancer.Viewer() for _ in range(args.jobs)]
print('Open the following URLs to begin rendering')
for viewer in viewers:
print(viewer)
def refresh_browser_callback():
print('Browser unresponsive, consider reloading')
capture_image([(viewer, refresh_browser_callback) for viewer in viewers], args, state)
else:
def _make_webdriver():
webdriver = neuroglancer.webdriver.Webdriver(
headless=args.headless,
docker=args.docker_chromedriver,
debug=args.debug_chromedriver,
)
def refresh_browser_callback():
print('Browser unresponsive, reloading')
webdriver.reload_browser()
return webdriver, refresh_browser_callback
webdrivers = [_make_webdriver() for _ in range(args.jobs)]
try:
capture_image([(webdriver.viewer, refresh_browser_callback)
for webdriver, refresh_browser_callback in webdrivers], args, state)
finally:
for webdriver, _ in webdrivers:
try:
webdriver.__exit__()
except:
pass
def __init__(self, state_path, bodies, labels, segmentation_url, image_url,
num_to_prefetch):
self.state = State(state_path)
self.num_to_prefetch = num_to_prefetch
self.viewer = neuroglancer.Viewer()
self.bodies = bodies
self.state.load()
self.total_voxels = sum(x.num_voxels for x in bodies)
self.cumulative_voxels = np.cumsum([x.num_voxels for x in bodies])
with self.viewer.txn() as s:
s.layers['image'] = neuroglancer.ImageLayer(source=image_url)
s.layers['segmentation'] = neuroglancer.SegmentationLayer(
source=segmentation_url)
s.navigation.zoom_factor = 66
s.perspective_zoom = 1280
s.show_slices = False
s.concurrent_downloads = 256
s.gpu_memory_limit = 2 * 1024 * 1024 * 1024
s.layout = '3d'
key_bindings = [
['bracketleft', 'prev-index'],
['bracketright', 'next-index'],
['home', 'first-index'],
['end', 'last-index'],
['control+keys', 'save'],
]
label_keys = ['keyd', 'keyf', 'keyg', 'keyh']
for label, label_key in zip(labels, label_keys):
key_bindings.append([label_key, 'label-%s' % label])
def label_func(s, label=label):
self.set_label(s, label)
self.viewer.actions.add('label-%s' % label, label_func)
self.viewer.actions.add('prev-index', self._prev_index)
self.viewer.actions.add('next-index', self._next_index)
self.viewer.actions.add('first-index', self._first_index)
self.viewer.actions.add('last-index', self._last_index)
self.viewer.actions.add('save', self.save)
with self.viewer.config_state.txn() as s:
for key, command in key_bindings:
s.input_event_bindings.viewer[key] = command
s.status_messages['help'] = (
'KEYS: ' + ' | '.join('%s=%s' % (key, command)
for key, command in key_bindings))
self.index = -1
self.set_index(self._find_one_after_last_labeled_index())
def __init__(self):
# Address
# neuroglancer.set_server_bind_address('127.0.0.1')
# neuroglancer.set_static_content_source(url='http://localhost:8080')
# Data
img = tifffile.imread('sample.tif')
img = img * 10 / 256
img = img.astype('uint8')
img = np.transpose(img, (1, 0, 2, 3))
self.img = img
# Same viewer every function call
viewer = self.viewer = neuroglancer.Viewer()
def visualize_npy(npy_file: Path, voxel_size):
voxel_size = daisy.Coordinate(voxel_size)
viewer = neuroglancer.Viewer()
with viewer.txn() as s:
v = np.load(npy_file)
m = daisy.Array(
v,
daisy.Roi(daisy.Coordinate([0, 0, 0]), daisy.Coordinate(v.shape)),
daisy.Coordinate([1, 1, 1]),
)
add_layer(s, m, f"npy array")
print(viewer)
input("Hit ENTER to quit!")
def __init__(self, imgs, points, quit_cb, save_cb):
"""Initializer
:param imgs: a sequence of three-tuples: image, name, shader. The
possible shaders are nuggt.utils.ngutils.{gray, red, green, blue}_shader
:param points: an Nx3 array of points where points[:, 0] is the z
coordinate, points[:, 1] is the y coordinate and points[:, 2] is the
x coordinate
:param quit_cb: a function to be called when quitting.
:param save_cb: a function to be called when saving
"""
self.idx = 0
self.points = points
self.quit_cb = quit_cb
self.save_cb = save_cb
self.viewer = neuroglancer.Viewer()
self._yea = np.zeros(len(points), bool)
self._nay = np.zeros(len(points), bool)
with self.viewer.txn() as txn:
for img, name, shader in imgs:
layer(txn, name, img.astype(np.float32), shader, 1.0)
self.display_points()
self.go_to()
self.viewer.actions.add("quit", self.on_quit)
self.viewer.actions.add("yea", self.on_yea)
self.viewer.actions.add("nay", self.on_nay)
self.viewer.actions.add("go-to", self.on_go_to)
self.viewer.actions.add("next", self.on_next)
self.viewer.actions.add("next-unmarked", self.on_next_unmarked)
self.viewer.actions.add("previous", self.on_previous)
self.viewer.actions.add("previous-unmarked", self.on_previous_unmarked)
self.viewer.actions.add("center", self.on_center)
if save_cb is not None:
self.viewer.actions.add("save", self.on_save)
with self.viewer.config_state.txn() as s:
v = s.input_event_bindings.viewer
v["control+keyq"] = "quit"
v["shift+keyy"] = "yea"
v["shift+keyn"] = "nay"
v["shift+keyg"] = "go-to"
v["shift+bracketleft"] = "previous"
v["control+bracketleft"] = "previous-unmarked"
v["shift+bracketright"] = "next"
v["control+bracketright"] = "next-unmarked"
v["shift+keyc"] = "center"
if save_cb is not None:
v["control+keys"] = "save"
def create_neuroglancer_viewer(model:Model) -> neuroglancer.Viewer:
"""
Create a viewer for a Neuroglancer instance
:param model: has the details for the static Neuroglancer elements
:return: a Neuroglancer viewer that can be used to display volumes
"""
if not model.neuroglancer_initialized.get():
neuroglancer.set_static_content_source(
url=model.static_content_source.get())
neuroglancer.set_server_bind_address(
model.bind_address.get(),
model.port_number.get())
model.neuroglancer_initialized.set(True)
return neuroglancer.Viewer()
def main():
app = QtWidgets.QApplication(sys.argv)
args = parse_args()
if args.static_content_source is not None:
print(
"Please do not use --static-content-source."
" It's no longer necessary and is disabled.",
file=sys.stderr)
neuroglancer.set_server_bind_address(args.bind_address,
bind_port=args.port)
viewer = neuroglancer.Viewer()
print("Neuroglancer URL: %s" % str(viewer))
window = ApplicationWindow(viewer)
window.show()
sys.exit(app.exec())
def __call__(self, datas: dict, selected: str = None):
"""
Parameters:
chunks: multiple chunks
"""
if selected is None:
selected = datas.keys()
elif isinstance(selected, str):
selected = selected.split(',')
# ng.set_static_content_source(
# url='https://neuromancer-seung-import.appspot.com')
ng.set_server_bind_address(bind_address='0.0.0.0', bind_port=self.port)
viewer = ng.Viewer()
with viewer.txn() as viewer_state:
for name in selected:
data = datas[name]
if data is None:
continue
elif isinstance(data, Synapses):
# this could be synapses
self._append_synapse_annotation_layer(
viewer_state, name, data)
elif isinstance(
data,
np.ndarray) and 2 == data.ndim and 3 == data.shape[1]:
# points
self._append_point_annotation_layer(
viewer_state, name, data)
elif data.is_image or (data.ndim == 3 and np.issubdtype(
data.dtype, np.floating)):
self._append_image_layer(viewer_state, name, data)
elif data.is_segmentation:
self._append_segmentation_layer(viewer_state, name, data)
elif data.is_probability_map:
self._append_probability_map_layer(viewer_state, name,
data)
else:
breakpoint()
raise ValueError(f'do not support this type: {type(data)}')
print('Open this url in browser: ')
viewer_url = viewer.get_viewer_url()
print(viewer_url)
key = None
while key != 'q':
key = input('Press q and enter/return to quit neuroglancer.')
def __init__(self, ref_img, ref_seg, moving_pts, ref_pts, moving_shape):
self.viewer = neuroglancer.Viewer()
za = np.linspace(0, moving_shape[0], 10)
ya = np.linspace(0, moving_shape[1], 10)
xa = np.linspace(0, moving_shape[2], 10)
self.warp_to_ref = Warper(moving_pts, ref_pts).approximate(za, ya, xa)
za = np.linspace(0, ref_img.shape[0], 10)
ya = np.linspace(0, ref_img.shape[1], 10)
xa = np.linspace(0, ref_img.shape[2] , 10)
self.warp_to_moving = \
Warper(ref_pts, moving_pts).approximate(za, ya, xa)
with self.viewer.txn() as txn:
layer(txn, "image", ref_img, gray_shader, 1.0)
seglayer(txn, "segmentation", ref_seg)
def __init__(self,
ip='localhost',
port=98100,
res=[6, 6, 30],
label_dtype=np.uint16):
super(NeuroG, self).__init__()
self.port = port
self.ip = ip
self.res = res
neuroglancer.set_server_bind_address(bind_address=self.ip,
bind_port=self.port)
self.viewer = neuroglancer.Viewer()
self.label_dtype = label_dtype
def main():
parser = argparse.ArgumentParser()
parser.add_argument("files_and_colors",
nargs="+",
help="File name followed by display name followed by"
"\"red\", \"green\", \"blue\" or \"gray\".")
parser.add_argument("--segmentation",
default=None,
help="Segmentation volume to display")
parser.add_argument("--ip-address",
default="127.0.0.1",
help="IP address of neuroglancer server.")
parser.add_argument("--port",
default=0,
type=int,
help="Port # of neuroglancer server.")
parser.add_argument("--static-content-source",
default=None,
help="The URL of the static content source, e.g. "
"http://localhost:8080 if being served via npm.")
args = parser.parse_args()
if args.static_content_source is not None:
neuroglancer.set_static_content_source(url=args.static_content_source)
neuroglancer.set_server_bind_address(args.ip_address, args.port)
viewer = neuroglancer.Viewer()
with viewer.txn() as txn:
for filename, name, colorname in zip(args.files_and_colors[::3],
args.files_and_colors[1::3],
args.files_and_colors[2::3]):
img = tifffile.imread(filename).astype(np.float32)
if colorname.lower() == "red":
shader = red_shader
elif colorname.lower() == "green":
shader = green_shader
elif colorname.lower() == "blue":
shader = blue_shader
else:
shader = gray_shader
layer(txn, name, img, shader, 1.0)
if args.segmentation != None:
seg = tifffile.imread(args.segmentation).astype(np.uint32)
seglayer(txn, "segmentation", seg)
print(viewer.get_viewer_url())
webbrowser.open(viewer.get_viewer_url())
while True:
time.sleep(5)