def _test_performance(self):
roi_begin = [10, 1000, 1000]
roi_end = [60, 1512, 1512]
bb = tuple(slice(rb, re) for rb, re in zip(roi_begin, roi_end))
times = []
graph_file = './tmpdir/subgraph.n5'
for _ in range(10):
if os.path.exists('./tmpdir'):
rmtree('./tmpdir')
os.mkdir('./tmpdir')
f_graph = z5py.File(graph_file, use_zarr_format=False)
t0 = time.time()
ndist.computeMergeableRegionGraph(self.labels_path,
self.labels_key, roi_begin,
roi_end, graph_file, 'block0')
times.append(time.time() - t0)
print("Mean extraction time:", np.mean(times), "s")
# load the graph from file
nodes, edges = self.load_graph(f_graph, 'block0')
# check that nodes were extracted correctly
labels = z5py.File(self.labels_path)[self.labels_key][bb]
self.check_nodes(labels, nodes)
self.check_rag(labels, nodes, edges)
def extract_subgraph(block_id):
block = blocking.getBlockWithHalo(block_id, halo)
outer_block, inner_block = block.outerBlock, block.innerBlock
# we only need the halo into one direction,
# hence we use the outer-block only for the end coordinate
begin = inner_block.begin
end = outer_block.end
block_key = 'sub_graphs/s0/block_%i' % block_id
ndist.computeMergeableRegionGraph(self.labels_path,
self.labels_key, begin, end,
graph_path, block_key)
def extract_subgraph(block_id):
print("Extracting subgraph", block_id, "/", blocking.numberOfBlocks)
block = blocking.getBlockWithHalo(block_id, halo)
outer_block, inner_block = block.outerBlock, block.innerBlock
# we only need the halo into one direction,
# hence we use the outer-block only for the end coordinate
begin = inner_block.begin
end = outer_block.end
# TODO groups for different scale levels
block_key = 'sub_graphs/s0/block_%i' % block_id
ndist.computeMergeableRegionGraph(path, labels_key, begin, end,
graph_path, block_key)
def test_subgraph(self):
roi_begin = [0, 0, 0]
roi_end = [50, 512, 512]
bb = tuple(slice(rb, re) for rb, re in zip(roi_begin, roi_end))
# distributed graph extraction
graph_path = './tmpdir/graph.n5'
graph_key = 'block0'
ndist.computeMergeableRegionGraph(self.labels_path, self.labels_key,
roi_begin, roi_end, graph_path,
graph_key)
# check that nodes were extracted correctly
labels = z5py.File(self.labels_path)[self.labels_key]
self.check_subgraph(graph_path, graph_key, labels, bb)
def _graph_block(block_id, blocking, input_path, input_key, graph_path,
ignore_label):
fu.log("start processing block %i" % block_id)
block = blocking.getBlock(block_id)
# we only need the halo into one direction,
# hence we use the outer-block only for the end coordinate
subgraph_key = 's0/sub_graphs'
ndist.computeMergeableRegionGraph(input_path, input_key,
block.begin, block.end,
graph_path, subgraph_key,
ignore_label,
increaseRoi=True,
serializeToVarlen=True)
# log block success
fu.log_block_success(block_id)
def extract_subgraph_from_roi(block_id, blocking, labels_path, labels_key,
graph_path):
print("Processign block", block_id)
t0 = time.time()
halo = [1, 1, 1]
block = blocking.getBlockWithHalo(block_id, halo)
outer_block, inner_block = block.outerBlock, block.innerBlock
# we only need the halo into one direction,
# hence we use the outer-block only for the end coordinate
begin = inner_block.begin
end = outer_block.end
block_key = 'sub_graphs/s0/block_%i' % block_id
ndist.computeMergeableRegionGraph(labels_path, labels_key, begin, end,
graph_path, block_key)
print("done", block_id)
return time.time() - t0