def _write_block(block_id):
block = blocking.getBlock(block_id)
bb = tuple(slice(beg, end) for beg, end in zip(block.begin, block.end))
# check if we have a mask and if we do if we
# have pixels in the mask
if mask is not None:
m = mask[bb].astype('bool')
if m.sum() == 0:
return None
offset = offsets[block_id]
# load the data from this block
d = out[bb]
if mask is None:
if with_background:
d[d != 0] += offset
else:
d += offset
d = nt.take(mapping, d)
else:
if with_background:
m[d == 0] = 0
values = (d[m] + offset)
values = nt.take(mapping, values)
d[m] = values
out[bb] = d
def run_lmc(merge_boutons, beta=.7):
path = './test_data.h5'
graph, feats, sizes, z_edges, boundaries = compute_graph_and_weights(
path, return_edge_sizes=True)
costs = compute_edge_costs(feats,
edge_sizes=sizes,
weighting_scheme='z',
z_edge_mask=z_edges,
beta=beta)
costs, lifted_uvs, lifted_costs = _lifted_problem(graph, costs, path)
print("Running lifted multicut ...")
node_labels = lifted_multicut_gaec(graph, costs, lifted_uvs, lifted_costs)
print("... done")
if merge_boutons:
node_labels = _merge_bouton_labels(node_labels, path)
with h5py.File('./test_data.h5', 'r') as f:
ws = f['watershed'][:]
import nifty.tools as nt
seg = nt.take(node_labels, ws)
return seg, boundaries
def debug_subresult(block_id=1):
from cremi_tools.viewer.volumina import view
path = '/g/kreshuk/data/arendt/platyneris_v1/membrane_training_data/validation/segmentation/val_block_01.n5'
tmp_folder = './tmp_plat_val'
block_prefix = os.path.join(path, 's0', 'sub_graphs', 'block_')
graph = ndist.Graph(os.path.join(path, 'graph'))
block_path = block_prefix + str(block_id)
nodes = ndist.loadNodes(block_path)
nodes = nodes[1:]
inner_edges, outer_edges, sub_uvs = graph.extractSubgraphFromNodes(nodes)
block_res_path = os.path.join(
tmp_folder, 'subproblem_results/s0_block%i.npy' % block_id)
res = np.load(block_res_path)
merge_edges = np.ones(graph.numberOfEdges, dtype='bool')
merge_edges[res] = False
merge_edges[outer_edges] = False
uv_ids = graph.uvIds()
n_nodes = int(uv_ids.max()) + 1
ufd = nufd.ufd(n_nodes)
ufd.merge(uv_ids[merge_edges])
node_labels = ufd.elementLabeling()
ws = z5py.File(path)['volumes/watershed'][:]
seg = nt.take(node_labels, ws)
view([ws, seg])
def _apply_node_labels(seg, node_labels, allow_empty_assignments):
# choose the appropriate mapping:
# - 1d np.array -> just apply it
# - 2d np.array -> extract the local dict and apply
# - dict -> extract the local dict and apply
apply_array = False if isinstance(
node_labels, dict) else (True if node_labels.ndim == 1 else False)
if apply_array:
seg = nt.take(node_labels, seg)
else:
# this copys the dict and hence is extremely RAM hungry
# so we make the dict as small as possible
this_labels = np.unique(seg)
if isinstance(node_labels, dict):
# do we allow for assignments that are not in the assignment table?
if allow_empty_assignments:
this_assignment = {
label: node_labels.get(label, label)
for label in this_labels
}
else:
this_assignment = {
label: node_labels[label]
for label in this_labels
}
else:
this_assignment = node_labels[:,
1][np.in1d(node_labels[:, 0],
this_labels)]
this_assignment = {
label: this_assignment[ii]
for ii, label in enumerate(this_labels)
}
seg = nt.takeDict(this_assignment, seg)
return seg
def make_new_segmentation(segmentation, blocks, block_coordinates,
label_offsets, node_labeling, coordinate_offset):
# we will write some parts of the volumes multiple times,
# but that should be ok, because the ids will agree due to the merging
for block, block_coord, label_offset in zip(blocks, block_coordinates,
label_offsets):
local_begin = tuple(c.start - off
for c, off in zip(block_coord, coordinate_offset))
local_end = tuple(c.stop - off
for c, off in zip(block_coord, coordinate_offset))
roi = tuple(
slice(beg, end) for beg, end in zip(local_begin, local_end))
segmentation[roi] = nt.take(node_labeling, block + label_offset)
def write_ganglion_segmentation():
seg_path = os.path.join(
'/g/arendt/EM_6dpf_segmentation/platy-browser-data/data',
'0.6.5/images/local/sbem-6dpf-1-whole-segmented-cells.n5')
tab_path = os.path.join(
'/g/arendt/EM_6dpf_segmentation/platy-browser-data/data',
'0.6.6/tables/sbem-6dpf-1-whole-segmented-cells/ganglia_ids.csv')
tab = pd.read_csv(tab_path, sep='\t')
seg_key = 'setup0/timepoint0/s0'
with z5py.File(seg_path) as f:
ds = f[seg_key]
max_id = int(ds.attrs['maxId']) + 1
label_ids = tab['label_id'].values.astype('uint32')
ganglion_labels = tab['ganglion_id'].values.astype('uint32')
label_mapping = np.zeros(max_id, 'uint32')
label_mapping[label_ids] = ganglion_labels
seg_key = 'setup0/timepoint0/s3'
out_path = './sbem-6dpf-1-whole-segmented-ganglia.n5'
print("Reading segmentation ...")
with z5py.File(seg_path, 'r') as f:
ds = f[seg_key]
ds.n_threads = 16
seg = ds[:].astype('uint32')
print("To ganglion segmentation ...")
seg = nt.take(label_mapping, seg)
seg = seg.astype('int16')
print(seg.shape)
print("Writing segmentation ...")
n_scales = 4
res = [.2, .16, .16]
chunks = (128, ) * 3
downscale_factors = n_scales * [[2, 2, 2]]
make_bdv(seg,
out_path,
downscale_factors,
resolution=res,
unit='micrometer',
chunks=chunks,
n_threads=16)
with z5py.File(out_path) as f:
ds = f['setup0/timepoint0/s0']
ds.attrs['maxId'] = max_id
def _write_block_with_offsets(ds_in, ds_out, blocking, block_id, node_labels,
offsets):
fu.log("start processing block %i" % block_id)
off = offsets[block_id]
block = blocking.getBlock(block_id)
bb = vu.block_to_bb(block)
seg = ds_in[bb]
seg[seg != 0] += off
# choose the appropriate function for array or dictionary
if isinstance(node_labels, np.ndarray):
seg = nt.take(node_labels, seg)
else:
seg = nt.takeDict(node_labels, seg)
ds_out[bb] = seg
fu.log_block_success(block_id)
def check_result(self, node_labels):
node_labels = self.node_labels
with z5py.File(self.output_path) as f:
ds = f[self.output_key]
ds.n_threads = 8
res = ds[:]
with z5py.File(self.input_path) as f:
ds = f[self.input_path]
ds.n_threads = 8
exp = ds[:]
exp = nt.take(node_labels, exp)
self.assertEqual(res.shape, exp.shape)
self.assertTrue(np.array_equal(res, exp))
def trace_from_boutons(threshold):
path = './test_data.h5'
with h5py.File(path, 'r') as f:
bouton_labels = f['bouton_overlaps'][:]
print("Computing graph and features ...")
graph, feats = compute_graph_and_weights(path)
print("... done")
axon_labels = trace_axons_prototype(graph,
feats,
bouton_labels,
threshold=threshold)
with h5py.File('./test_data.h5', 'r') as f:
ws = f['watershed'][:]
import nifty.tools as nt
seg = nt.take(axon_labels, ws)
return seg
def check_results(seg, boundaries):
import napari
import nifty.tools as nt
with h5py.File('./test_data.h5', 'r') as f:
raw = f['raw'][:]
# boundaries = f['boundaries'][:]
ws = f['watershed'][:]
# boutons = f['boutons_corrected'][:]
b_overlaps = f['bouton_overlaps'][:]
overlaps_mapepd = nt.take(b_overlaps, ws)
with napari.gui_qt():
viewer = napari.Viewer()
viewer.add_image(raw)
viewer.add_image(boundaries, visible=False)
viewer.add_labels(ws, visible=False)
# viewer.add_labels(boutons, visible=False)
viewer.add_labels(overlaps_mapepd)
viewer.add_labels(seg)
def _apply_node_labels(seg, node_labels, allow_empty_assignments):
# choose the appropriate mapping:
# - 1d np.array -> just apply it
# - 2d np.array -> extract the local dict and apply
# - dict -> extract the local dict and apply
apply_array = False if isinstance(
node_labels, dict) else (True if node_labels.ndim == 1 else False)
if apply_array:
assert seg.max() < len(
node_labels), "Max id %i exceeds number of node labels %i" % (
seg.max(), len(node_labels))
seg = nt.take(node_labels, seg)
else:
# this copys the dict and hence is extremely RAM hungry
# so we make the dict as small as possible
this_labels = np.unique(seg)
if isinstance(node_labels, dict):
# do we allow for assignments that are not in the assignment table?
if allow_empty_assignments:
this_assignment = {
label: node_labels.get(label, label)
for label in this_labels
}
else:
this_assignment = {
label: node_labels[label]
for label in this_labels
}
else:
this_assignment = node_labels[:,
1][np.in1d(node_labels[:, 0],
this_labels)]
this_assignment = {
label: this_assignment[ii]
for ii, label in enumerate(this_labels)
}
# FIXME this casts to uint32 which can lead to nasty over-flows
seg = nt.takeDict(this_assignment, seg)
return seg
def _write_block(ds_in, ds_out, blocking, block_id, node_labels):
fu.log("start processing block %i" % block_id)
block = blocking.getBlock(block_id)
bb = vu.block_to_bb(block)
seg = ds_in[bb]
# check if this block is empty and don't write if it is
if np.sum(seg != 0) == 0:
fu.log_block_success(block_id)
return
# choose the appropriate function for array or dictionary
if isinstance(node_labels, np.ndarray):
# this should actually amount to the same as
# seg = node_labels[seg]
seg = nt.take(node_labels, seg)
else:
# this copys the dict and hence is extremely RAM hungry
# so we make the dict as small as possible
this_labels = nt.unique(seg)
this_assignment = {label: node_labels[label] for label in this_labels}
seg = nt.takeDict(this_assignment, seg)
ds_out[bb] = seg
fu.log_block_success(block_id)
def debug_costs():
from cremi_tools.viewer.volumina import view
from nifty.graph import undirectedGraph
path = '/g/kreshuk/data/arendt/platyneris_v1/membrane_training_data/validation/segmentation/val_block_01.n5'
costs = z5py.File(path)['costs'][:]
edges = z5py.File(path)['graph/edges'][:]
assert len(costs) == len(edges)
print(np.mean(costs), "+-", np.std(costs))
print(costs.min(), costs.max())
# import matplotlib.pyplot as plt
# n, bins, patches = plt.hist(costs, 50)
# plt.grid(True)
# plt.show()
n_nodes = int(edges.max()) + 1
graph = undirectedGraph(n_nodes)
graph.insertEdges(edges)
assert graph.numberOfEdges == len(costs)
node_labels = multicut_gaec(graph, costs)
ds = z5py.File(path)['volumes/watershed']
ds.n_threads = 8
ws = ds[:]
seg = nt.take(node_labels, ws)
bb = np.s_[25:75, 500:1624, 100:1624]
input_path = '/g/kreshuk/data/arendt/platyneris_v1/membrane_training_data/validation/predictions/val_block_0%i_unet_lr_v3_ds122.n5' % block_id
with z5py.File(input_path) as f:
ds = f['data']
ds.n_threads = 8
affs = ds[(slice(0, 3), ) + bb]
view([affs.transpose((1, 2, 3, 0)), ws[bb], seg[bb]])
def make_test_data():
in_path = '/g/kreshuk/data/cremi/example/sampleA.n5'
raw_key = 'volumes/raw/s0'
ws_key = 'volumes/segmentation/watershed'
seg_key = 'volumes/segmentation/multicut'
bd_key = 'volumes/boundaries'
with z5py.File(in_path, 'r') as f:
ds = f[ws_key]
ds.n_threasds = 8
halo = [25, 512, 512]
bb = tuple(slice(sh // 2 - ha, sh // 2 + ha)
for sh, ha in zip(ds.shape, halo))
ws = ds[bb]
ds = f[seg_key]
ds.n_threasds = 8
seg = ds[bb]
ds = f[bd_key]
ds.n_threads = 8
bd = ds[bb]
ds = f[raw_key]
ds.n_threads = 8
raw = ds[bb]
chunks = ds.chunks
print("Run ccs ...")
ws = vigra.analysis.labelVolumeWithBackground(ws.astype('uint32')).astype('uint64')
seg = vigra.analysis.labelVolumeWithBackground(seg.astype('uint32')).astype('uint64')
print("ccs done")
node_labels = max_overlaps(ws, seg)
unique_labels = np.unique(node_labels)
n_merge = 50
merge_to = 3
has_merge = []
node_labels_merged = node_labels.copy()
for ii in range(n_merge):
merge_id = np.random.choice(unique_labels)
while merge_id in has_merge:
merge_id = np.random.choice(unique_labels)
for jj in range(merge_to):
merge_to_id = np.random.choice(unique_labels)
while merge_to_id in has_merge:
merge_to_id = np.random.choice(unique_labels)
node_labels_merged[node_labels_merged == merge_to_id] = merge_id
unique_labels = np.unique(node_labels_merged)
has_merge.append(merge_id)
seg_merged = nt.take(node_labels_merged, ws)
assert seg_merged.shape == seg.shape
print("Write outputs")
out_path = './test_data.n5'
out_raw_key = 'volumes/raw/s0'
with z5py.File(out_path, 'a') as f:
ds = f.create_dataset('volumes/seg/ref', data=seg, chunks=chunks, compression='gzip')
ds.attrs['maxId'] = int(seg.max())
ds = f.create_dataset('volumes/seg/merged', data=seg_merged, chunks=chunks, compression='gzip')
ds.attrs['maxId'] = int(seg_merged.max())
ds = f.create_dataset('volumes/ws', data=ws, chunks=chunks, compression='gzip')
ds.attrs['maxId'] = int(ws.max())
f.create_dataset('node_labels/ref', data=node_labels, compression='gzip')
f.create_dataset('node_labels/merged', data=node_labels_merged, compression='gzip')
f.create_dataset('volumes/boundaries', data=bd, compression='gzip', chunks=chunks)
f.create_dataset(out_raw_key, data=raw, compression='gzip', chunks=chunks)
print("Make paintera dataset")
# make the paintera dataset
tmp_paintera = './tmp_paintera'
scale_factors = [[1, 2, 2], [1, 2, 2]]
halos = [[1, 2, 2], [1, 2, 2]]
target = 'local'
max_jobs = 16
downscale(out_path, out_raw_key, 'volumes/raw', scale_factors, halos,
tmp_paintera, target, max_jobs)
convert_to_paintera_format(out_path, 'volumes/raw', 'volumes/ws', 'volumes/paintera',
label_scale=0, resolution=[1, 1, 1],
tmp_folder=tmp_paintera, target=target,
max_jobs=max_jobs, max_threads=max_jobs,
assignment_path=out_path, assignment_key='node_labels/merged',
convert_to_label_multisets=True, restrict_sets=[-1, -1])
