def __init__(self):
self.voxel_size = Coordinate((40, 4, 4))
self.nodes = [
# corners
Node(id=1, location=np.array((-200, -200, -200))),
Node(id=2, location=np.array((-200, -200, 199))),
Node(id=3, location=np.array((-200, 199, -200))),
Node(id=4, location=np.array((-200, 199, 199))),
Node(id=5, location=np.array((199, -200, -200))),
Node(id=6, location=np.array((199, -200, 199))),
Node(id=7, location=np.array((199, 199, -200))),
Node(id=8, location=np.array((199, 199, 199))),
# center
Node(id=9, location=np.array((0, 0, 0))),
Node(id=10, location=np.array((-1, -1, -1))),
]
self.graph_spec = GraphSpec(roi=Roi((-100, -100, -100), (300, 300, 300)))
self.array_spec = ArraySpec(
roi=Roi((-200, -200, -200), (400, 400, 400)), voxel_size=self.voxel_size
)
self.graph = Graph(self.nodes, [], self.graph_spec)
def __init__(self, graph):
self.graph = graph
self.graph_spec = GraphSpec(roi=Roi((-10, -10, -10), (30, 30, 30)),
directed=False)
self.component_1_nodes = [
Node(i, np.array([0, i, 0])) for i in range(10)
] + [Node(i + 10, np.array([i, 5, 0])) for i in range(10)]
self.component_1_edges = ([Edge(i, i + 1) for i in range(9)] +
[Edge(i + 10, i + 11)
for i in range(9)] + [Edge(5, 15)])
self.component_2_nodes = [
Node(i + 20, np.array([i, 4, 0])) for i in range(10)
]
self.component_2_edges = [Edge(i + 20, i + 21) for i in range(9)]
def __init__(self):
self.voxel_size = Coordinate((1, 1, 1))
self.nodes = [
# corners
Node(id=1, location=np.array((0, 4, 4))),
Node(id=2, location=np.array((9, 4, 4)))
]
self.edges = [
Edge(1, 2)
]
self.graph_spec = GraphSpec(roi=Roi((0, 0, 0), (10, 10, 10)))
self.graph = Graph(self.nodes, self.edges, self.graph_spec)
def process(self, batch, request: BatchRequest):
outputs = Batch()
voxel_size = batch[self.embeddings].spec.voxel_size
offset = batch[self.embeddings].spec.roi.get_begin()
embeddings = batch[self.embeddings].data
candidates = batch[self.mask].data
_, depth, height, width = embeddings.shape
coordinates = np.meshgrid(
np.arange(0, (depth - 0.5) * self.coordinate_scale[0],
self.coordinate_scale[0]),
np.arange(0, (height - 0.5) * self.coordinate_scale[1],
self.coordinate_scale[1]),
np.arange(0, (width - 0.5) * self.coordinate_scale[2],
self.coordinate_scale[2]),
indexing="ij",
)
for i in range(len(coordinates)):
coordinates[i] = coordinates[i].astype(np.float32)
embedding = np.concatenate([embeddings, coordinates], 0)
embedding = np.transpose(embedding, axes=[1, 2, 3, 0])
embedding = embedding.reshape(depth * width * height, -1)
candidates = candidates.reshape(depth * width * height)
embedding = embedding[candidates == 1, :]
emst = mlp.emst(embedding)["output"]
nodes = set()
edges = []
for u, v, distance in emst:
u = int(u)
pos_u = embedding[u][-3:] / self.coordinate_scale * voxel_size
v = int(v)
pos_v = embedding[v][-3:] / self.coordinate_scale * voxel_size
nodes.add(Node(u, location=pos_u + offset))
nodes.add(Node(v, location=pos_v + offset))
edges.append(Edge(u, v, attrs={self.distance_attr: distance}))
graph_spec = request[self.mst]
graph_spec.directed = False
outputs[self.mst] = Graph(nodes, edges, graph_spec)
logger.debug(
f"OUTPUTS CONTAINS MST WITH {len(list(outputs[self.mst].nodes))} NODES"
)
return outputs
def array_to_graph(self, array):
# Override with local function
sklearn.feature_extraction.image._make_edges_3d = _make_edges_3d
s = array.data.shape
# Identify connectivity
t1 = time.time()
adj_mat = grid_to_graph(n_x=s[0], n_y=s[1], n_z=s[2], mask=array.data)
t2 = time.time()
logger.debug(f"GRID TO GRAPH TOOK {t2-t1} SECONDS!")
# Identify order of the voxels
t1 = time.time()
voxel_locs = compute_voxel_locs(
mask=array.data,
offset=array.spec.roi.get_begin(),
scale=array.spec.voxel_size,
)
t2 = time.time()
logger.debug(f"COMPUTING VOXEL LOCS TOOK {t2-t1} SECONDS!")
t1 = time.time()
nodes = [
Node(node_id, voxel_loc) for node_id, voxel_loc in enumerate(voxel_locs)
]
for a, b in zip(adj_mat.row, adj_mat.col):
assert all(
abs(voxel_locs[a] - voxel_locs[b]) <= array.spec.voxel_size
), f"{voxel_locs[a] - voxel_locs[b]}, {array.spec.voxel_size}"
edges = [Edge(a, b) for a, b in zip(adj_mat.row, adj_mat.col) if a != b]
graph = Graph(nodes, edges, GraphSpec(array.spec.roi, directed=False))
t2 = time.time()
logger.debug(f"BUILDING GRAPH TOOK {t2-t1} SECONDS!")
return graph
def process(self, batch, request: BatchRequest):
outputs = Batch()
voxel_size = batch[self.embeddings].spec.voxel_size
roi = batch[self.embeddings].spec.roi
offset = batch[self.embeddings].spec.roi.get_begin()
spatial_dims = len(voxel_size)
embeddings = batch[self.embeddings].data
embeddings = embeddings.reshape((-1,) + embeddings.shape[-spatial_dims:])
maxima = batch[self.mask].data
maxima = maxima.reshape((-1,) + maxima.shape[-spatial_dims:])[0]
try:
minimax_edges = maximin.maximin_tree_query_hd(
embeddings.astype(np.float64),
maxima.astype(np.uint8),
decimate=self.decimate,
)
except OSError as e:
logger.warning(
f"embeddings have shape: {embeddings.shape} and mask has shape: {maxima.shape}"
)
raise e
maximin_id = itertools.count(start=0)
nodes = set()
edges = []
ids = {}
for a, b, cost in minimax_edges:
a_id = ids.setdefault(a, next(maximin_id))
b_id = ids.setdefault(b, next(maximin_id))
a_loc = np.array(a) * voxel_size + offset
b_loc = np.array(b) * voxel_size + offset
assert roi.contains(a_loc), f"Roi {roi} does not contain {a_loc}"
assert roi.contains(b_loc), f"Roi {roi} does not contain {b_loc}"
nodes.add(Node(a_id, location=a_loc))
nodes.add(Node(b_id, location=b_loc))
edges.append(Edge(a_id, b_id, attrs={self.distance_attr: cost}))
graph_spec = request[self.mst]
graph_spec.directed = False
outputs[self.mst] = Graph(nodes, edges, graph_spec)
return outputs
def provide(self, request: BatchRequest) -> Batch:
timing = Timing(self, "provide")
timing.start()
batch = Batch()
for points_key in self.points:
if points_key not in request:
continue
# Retrieve all points in the requested region using a kdtree for speed
point_ids = self._query_kdtree(
self.data.tree,
(
np.array(request[points_key].roi.get_begin()),
np.array(request[points_key].roi.get_end()),
),
)
# To account for boundary crossings we must retrieve neighbors of all points
# in the graph. This is too slow for large queries and less important
points_subgraph = self._subgraph_points(
point_ids,
with_neighbors=len(point_ids) < len(self._graph.nodes) // 2)
nodes = [
Node(id=node, location=attrs["location"], attrs=attrs)
for node, attrs in points_subgraph.nodes.items()
]
edges = [Edge(u, v) for u, v in points_subgraph.edges]
return_graph = Graph(nodes, edges,
GraphSpec(roi=request[points_key].roi))
# Handle boundary cases
return_graph = return_graph.trim(request[points_key].roi)
batch = Batch()
batch.points[points_key] = return_graph
logger.debug(
"Graph points source provided {} points for roi: {}".format(
len(list(batch.points[points_key].nodes)),
request[points_key].roi))
logger.debug(
f"Providing {len(list(points_subgraph.nodes))} nodes to {points_key}"
)
timing.stop()
batch.profiling_stats.add(timing)
return batch
def _get_points(self, point_filter):
filtered = self.data[point_filter][:,:self.ndims]
if self.id_dim is not None:
ids = self.data[point_filter][:,self.id_dim]
else:
ids = np.arange(len(self.data))[point_filter]
return [
Node(id=i, location=p)
for i, p in zip(ids, filtered)
]
def setup(self):
self.points = [
Node(0, np.array([0, 10, 0])),
Node(1, np.array([0, 30, 0])),
Node(2, np.array([0, 50, 0])),
Node(3, np.array([0, 70, 0])),
Node(4, np.array([0, 90, 0])),
]
self.provides(
GraphKeys.TEST_POINTS,
GraphSpec(roi=Roi((-100, -100, -100), (300, 300, 300))),
)
self.provides(
ArrayKeys.TEST_LABELS,
ArraySpec(
roi=Roi((-100, -100, -100), (300, 300, 300)),
voxel_size=Coordinate((4, 1, 1)),
interpolatable=False,
),
)
def provide(self, request: BatchRequest) -> Batch:
random.seed(request.random_seed)
np.random.seed(request.random_seed)
timing = Timing(self, "provide")
timing.start()
batch = Batch()
roi = request[self.points].roi
region_shape = roi.get_shape()
trees = []
for _ in range(self.n_obj):
for _ in range(100):
root = np.random.random(len(region_shape)) * region_shape
tree = self._grow_tree(
root, Roi((0,) * len(region_shape), region_shape)
)
if self.num_nodes[0] <= len(tree.nodes) <= self.num_nodes[1]:
break
trees.append(tree)
# logger.info("{} trees got, expected {}".format(len(trees), self.n_obj))
trees_graph = nx.disjoint_union_all(trees)
points = {
node_id: Node(np.floor(node_attrs["pos"]) + roi.get_begin())
for node_id, node_attrs in trees_graph.nodes.items()
}
batch[self.points] = Graph(points, request[self.points], list(trees_graph.edges))
timing.stop()
batch.profiling_stats.add(timing)
# self._plot_tree(tree)
return batch
def _parse_swc(self, filename: Path):
"""Read one point per line. If ``ndims`` is 0, all values in one line
are considered as the location of the point. If positive, only the
first ``ndims`` are used. If negative, all but the last ``-ndims`` are
used.
"""
if "cube" in filename.name:
return 0
tree = parse_swc(
filename,
self.transform_file,
resolution=[self.scale[i] for i in self.transpose],
transpose=self.transpose,
)
assert len(list(nx.weakly_connected_components(tree))) == 1
points = []
for node, attrs in tree.nodes.items():
if not self.ignore_human_nodes or attrs["human_placed"]:
points.append(
Node(
id=node,
location=attrs["location"],
attrs=attrs,
))
human_edges = set()
if self.ignore_human_nodes:
for u, v in tree.edges:
if u not in points or v not in points:
human_edges.add(Edge(u, v))
edges = set(Edge(u, v) for (u, v) in tree.edges)
if not self.directed:
edges = edges | set(Edge(v, u) for u, v in tree.edges())
self._add_points_to_source(points, edges - human_edges)
return len(list(nx.weakly_connected_components(tree)))
def setup(self):
self.nodes = [
Node(id=0, location=np.array([0, 0, 0])),
Node(id=1, location=np.array([0, 10, 0])),
Node(id=2, location=np.array([0, 20, 0])),
Node(id=3, location=np.array([0, 30, 0])),
Node(id=4, location=np.array([0, 40, 0])),
Node(id=5, location=np.array([0, 50, 0])),
]
self.provides(
GraphKeys.TEST_GRAPH,
GraphSpec(roi=Roi((-100, -100, -100), (200, 200, 200))),
)
self.provides(
ArrayKeys.TEST_LABELS,
ArraySpec(
roi=Roi((-100, -100, -100), (200, 200, 200)),
voxel_size=Coordinate((4, 1, 1)),
interpolatable=False,
),
)
def __read_syn_points(self, roi):
""" read json file from dvid source, in json format to create for every location given """
if GraphKey.PRESYN in self.points_voxel_size:
voxel_size = self.points_voxel_size[GraphKey.PRESYN]
elif GraphKey.POSTSYN in self.points_voxel_size:
voxel_size = self.points_voxel_size[GraphKey.POSTSYN]
syn_file_json = self.__load_json_annotations(
array_shape_voxel=roi.get_shape() // voxel_size,
array_offset_voxel=roi.get_offset() // voxel_size,
array_name=self.datasets[GraphKey.PRESYN])
presyn_points_dict, postsyn_points_dict = {}, {}
location_to_location_id_dict, location_id_to_partner_locations = {}, {}
for node_nr, node in enumerate(syn_file_json):
# collect information
kind = str(node['Kind'])
location = np.asarray(
(node['Pos'][2], node['Pos'][1], node['Pos'][0])) * voxel_size
location_id = int(node_nr)
# some synapses are wrongly annotated in dvid source, have 'Tag': null ???, they are skipped
try:
syn_id = int(node['Tags'][0][3:])
except:
continue
location_to_location_id_dict[str(location)] = location_id
partner_locations = []
try:
for relation in node['Rels']:
partner_locations.append((np.asarray([
relation['To'][2], relation['To'][1], relation['To'][0]
])) * voxel_size)
except:
partner_locations = []
location_id_to_partner_locations[int(node_nr)] = partner_locations
# check if property given, not always given
props = {}
if 'conf' in node['Prop']:
props['conf'] = float(node['Prop']['conf'])
if 'agent' in node['Prop']:
props['agent'] = str(node['Prop']['agent'])
if 'flagged' in node['Prop']:
str_value_flagged = str(node['Prop']['flagged'])
props['flagged'] = bool(
distutils.util.strtobool(str_value_flagged))
if 'multi' in node['Prop']:
str_value_multi = str(node['Prop']['multi'])
props['multi'] = bool(
distutils.util.strtobool(str_value_multi))
# create synPoint with information collected so far (partner_ids not completed yet)
if kind == 'PreSyn':
syn_point = Node(location=location,
location_id=location_id,
synapse_id=syn_id,
partner_ids=[],
props=props)
presyn_points_dict[int(node_nr)] = deepcopy(syn_point)
elif kind == 'PostSyn':
syn_(location=location,
location_id=location_id,
synapse_id=syn_id,
partner_ids=[],
props=props)
postsyn_points_dict[int(node_nr)] = deepcopy(syn_point)
# add partner ids
last_node_nr = len(syn_file_json) - 1
for current_syn_point_id in location_id_to_partner_locations.keys():
all_partner_ids = []
for partner_loc in location_id_to_partner_locations[
current_syn_point_id]:
if location_to_location_id_dict.has_key(str(partner_loc)):
all_partner_ids.append(
int(location_to_location_id_dict[str(partner_loc)]))
else:
last_node_nr = last_node_nr + 1
assert not location_to_location_id_dict.has_key(
str(partner_loc))
all_partner_ids.append(int(last_node_nr))
if current_syn_point_id in presyn_points_dict:
presyn_points_dict[
current_syn_point_id].partner_ids = all_partner_ids
elif current_syn_point_id in postsyn_points_dict:
postsyn_points_dict[
current_syn_point_id].partner_ids = all_partner_ids
else:
raise Exception(
"current syn_point id not found in any dictionary")
return presyn_points_dict, postsyn_points_dict
def process(self, batch, request: BatchRequest):
outputs = Batch()
voxel_size = batch[self.intensities].spec.voxel_size
roi = batch[self.intensities].spec.roi
offset = batch[self.intensities].spec.roi.get_begin()
spatial_dims = len(voxel_size)
intensities = batch[self.intensities].data
intensities = intensities.reshape((-1,) + intensities.shape[-spatial_dims:])[0]
maxima = batch[self.mask].data
maxima = maxima.reshape((-1,) + maxima.shape[-spatial_dims:])[0]
logger.warning(f"{self.mask} has {maxima.sum()} maxima")
if maxima.sum() < 2:
minimax_edges = []
if self.dense_mst is not None:
dense_minimax_edges = []
else:
if self.dense_mst is not None:
dense_minimax_edges, minimax_edges = maximin.maximin_tree_query_plus_decimated(
intensities.astype(np.float64),
maxima.astype(np.uint8),
threshold=self.threshold,
)
else:
minimax_edges = maximin.maximin_tree_query(
intensities.astype(np.float64),
maxima.astype(np.uint8),
decimate=self.decimate,
threshold=self.threshold,
)
maximin_id = itertools.count(start=0)
nodes = set()
edges = []
ids = {}
for a, b, cost in minimax_edges:
a_id = ids.setdefault(a, next(maximin_id))
b_id = ids.setdefault(b, next(maximin_id))
a_loc = np.array(a) * voxel_size + offset
b_loc = np.array(b) * voxel_size + offset
assert roi.contains(a_loc), f"Roi {roi} does not contain {a_loc}"
assert roi.contains(b_loc), f"Roi {roi} does not contain {b_loc}"
nodes.add(Node(a_id, location=a_loc))
nodes.add(Node(b_id, location=b_loc))
edges.append(Edge(a_id, b_id, attrs={self.distance_attr: 1 - cost}))
graph_spec = request[self.mst]
graph_spec.directed = False
outputs[self.mst] = Graph(nodes, edges, graph_spec)
if self.dense_mst is not None:
maximin_id = itertools.count(start=0)
nodes = set()
edges = []
ids = {}
for a, b, cost in dense_minimax_edges:
a_id = ids.setdefault(a, next(maximin_id))
b_id = ids.setdefault(b, next(maximin_id))
a_loc = np.array(a) * voxel_size + offset
b_loc = np.array(b) * voxel_size + offset
assert roi.contains(a_loc), f"Roi {roi} does not contain {a_loc}"
assert roi.contains(b_loc), f"Roi {roi} does not contain {b_loc}"
nodes.add(Node(a_id, location=a_loc))
nodes.add(Node(b_id, location=b_loc))
edges.append(Edge(a_id, b_id, attrs={self.distance_attr: 1 - cost}))
graph_spec = request[self.dense_mst]
graph_spec.directed = False
outputs[self.dense_mst] = Graph(nodes, edges, graph_spec)
return outputs
def _get_points(self, point_filter):
filtered = self.data[point_filter]
ids = np.arange(len(self.data))[point_filter]
return [Node(id=i, location=p) for i, p in zip(ids, filtered)]
def process(self, batch, request: BatchRequest):
outputs = Batch()
voxel_size = batch[self.embeddings].spec.voxel_size
offset = batch[self.embeddings].spec.roi.get_begin()
embeddings = batch[self.embeddings].data
candidates = batch[self.candidates].to_nx_graph()
_, depth, height, width = embeddings.shape
coordinates = np.meshgrid(
np.arange(
0, (depth - 0.5) * self.coordinate_scale[0], self.coordinate_scale[0]
),
np.arange(
0, (height - 0.5) * self.coordinate_scale[1], self.coordinate_scale[1]
),
np.arange(
0, (width - 0.5) * self.coordinate_scale[2], self.coordinate_scale[2]
),
indexing="ij",
)
for i in range(len(coordinates)):
coordinates[i] = coordinates[i].astype(np.float32)
embedding = np.concatenate([embeddings, coordinates], 0)
embedding = np.transpose(embedding, axes=[1, 2, 3, 0])
embedding = embedding.reshape(depth * width * height, -1)
nodes = set()
edges = []
for i, component in enumerate(nx.connected_components(candidates)):
candidates_array = np.zeros((depth, height, width), dtype=bool)
locs_to_ids = {}
for node in component:
attrs = candidates.nodes[node]
location = attrs["location"]
voxel_location = tuple(
int(x) for x in ((location - offset) // voxel_size)
)
locs_to_ids[voxel_location] = node
candidates_array[voxel_location] = True
candidates_array = candidates_array.reshape(-1)
component_embedding = embedding[candidates_array, :]
logger.info(
f"processing component {i} with "
f"{len(component)} candidates"
)
component_emst = mlp.emst(component_embedding)["output"]
for u, v, distance in component_emst:
u = int(u)
pos_u = component_embedding[u][-3:] / self.coordinate_scale * voxel_size
u_index = locs_to_ids[
tuple(int(np.round(x)) for x in (pos_u / voxel_size))
]
v = int(v)
pos_v = component_embedding[v][-3:] / self.coordinate_scale * voxel_size
v_index = locs_to_ids[
tuple(int(np.round(x)) for x in (pos_v / voxel_size))
]
nodes.add(Node(u_index, location=pos_u + offset))
nodes.add(Node(v_index, location=pos_v + offset))
edges.append(
Edge(u_index, v_index, attrs={self.distance_attr: distance})
)
graph_spec = request[self.mst]
graph_spec.directed = False
logger.info(
f"candidates has {candidates.number_of_nodes()} nodes and "
f"{candidates.number_of_edges()} edges and "
f"{len(list(nx.connected_components(candidates)))} components"
)
outputs[self.mst] = Graph(nodes, edges, graph_spec)
output_graph = outputs[self.mst].to_nx_graph()
logger.info(
f"output_graph has {output_graph.number_of_nodes()} nodes and "
f"{output_graph.number_of_edges()} edges and "
f"{len(list(nx.connected_components(output_graph)))} components"
)
logger.debug(
f"OUTPUTS CONTAINS MST WITH {len(list(outputs[self.mst].nodes))} NODES"
)
return outputs
