def evaluate_endpoint_resegmentation(filename, seg_volume,
resegmentation_radius,
threshold=0.5):
"""Evaluates endpoint resegmentation.
Args:
filename: path to the file containing resegmentation results
seg_volume: volume object with the original segmentation
resegmentation_radius: (z, y, x) radius of the resegmentation subvolume
threshold: threshold at which to create objects from the predicted
object map
Returns:
EndpointResegmentationResult proto
Raises:
InvalidBaseSegmentatonError: when no base segmentation object with the
expected ID matches the resegmentation data
"""
id1, _, x, y, z = parse_resegmentation_filename(filename)
result = resegmentation_pb2.EndpointSegmentationResult()
result.id = id1
start = result.start
start.x, start.y, start.z = x, y, z
sr = result.segmentation_radius
sr.z, sr.y, sr.x = resegmentation_radius
with gfile.Open(filename, 'rb') as f:
data = np.load(f)
prob = storage.dequantize_probability(data['probs'])
prob = np.nan_to_num(prob) # nans indicate unvisited voxels
sr = result.segmentation_radius
orig_seg = seg_volume[0,
(z - sr.z):(z + sr.z + 1),
(y - sr.y):(y + sr.y + 1),
(x - sr.x):(x + sr.x + 1)][0, ...]
seg1 = orig_seg == id1
if not np.any(seg1):
raise InvalidBaseSegmentatonError()
new_seg = prob[0, ...] >= threshold
result.num_voxels = int(np.sum(new_seg))
overlaps = pywrapsegment_util.ComputeOverlapCounts(
orig_seg.ravel(), new_seg.astype(np.uint64).ravel())
for k, v in overlaps.items():
old, new = k
if not new:
continue
result.overlaps[old].num_overlapping = v
result.overlaps[old].num_original = int(np.sum(orig_seg == old))
if old == id1:
result.source.CopyFrom(result.overlaps[old])
return result
def evaluate_pair_resegmentation(filename, seg_volume,
resegmentation_radius,
analysis_radius,
voxel_size,
threshold=0.5):
"""Evaluates segment pair resegmentation.
Args:
filename: path to the file containing resegmentation results
seg_volume: VolumeStore object with the original segmentation
resegmentation_radius: (z, y, x) radius of the resegmentation subvolume
analysis_radius: (z, y, x) radius of the subvolume in which to perform
analysis
voxel_size: (z, y, x) voxel size in physical units
threshold: threshold at which to create objects from the predicted
object map
Returns:
PairResegmentationResult proto
Raises:
IncompleteResegmentationError: when the resegmentation data does not
represent two finished segments
InvalidBaseSegmentatonError: when no base segmentation object with the
excepted ID matches the resegmentation data
"""
id1, id2, x, y, z = parse_resegmentation_filename(filename)
result = resegmentation_pb2.PairResegmentationResult()
result.id_a, result.id_b = id1, id2
p = result.point
p.x, p.y, p.z = x, y, z
sr = result.segmentation_radius
sr.z, sr.y, sr.x = resegmentation_radius
with gfile.Open(filename, 'rb') as f:
data = np.load(f)
prob = storage.dequantize_probability(data['probs'])
prob = np.nan_to_num(prob) # nans indicate unvisited voxels
dels = data['deletes']
moves = data['histories'] # z, y, x
start_points = data['start_points'] # x, y, z
if prob.shape[0] != 2:
raise IncompleteResegmentationError()
assert prob.ndim == 4
# Corner of the resegmentation subvolume in the global coordinate system.
corner = np.array([p.x - sr.x, p.y - sr.y, p.z - sr.z])
# In case of multiple segmentation attempts, the last recorded start
# point is the one we care about.
origin_a = np.array(start_points[0][-1], dtype=np.int) + corner
origin_b = np.array(start_points[1][-1], dtype=np.int) + corner
oa = result.eval.from_a.origin
oa.x, oa.y, oa.z = origin_a
ob = result.eval.from_b.origin
ob.x, ob.y, ob.z = origin_b
# Record basic infromation about the resegmentation run.
analysis_r = np.array(analysis_radius)
r = result.eval.radius
r.z, r.y, r.x = analysis_r
seg = seg_volume[0,
(z - analysis_r[0]):(z + analysis_r[0] + 1),
(y - analysis_r[1]):(y + analysis_r[1] + 1),
(x - analysis_r[2]):(x + analysis_r[2] + 1)][0, ...]
seg1 = seg == id1
seg2 = seg == id2
result.eval.num_voxels_a = int(np.sum(seg1))
result.eval.num_voxels_b = int(np.sum(seg2))
if result.eval.num_voxels_a == 0 or result.eval.num_voxels_b == 0:
raise InvalidBaseSegmentatonError()
# Record information about the size of the original segments.
result.eval.max_edt_a = float(
ndimage.distance_transform_edt(seg1, sampling=voxel_size).max())
result.eval.max_edt_b = float(
ndimage.distance_transform_edt(seg2, sampling=voxel_size).max())
# Offset of the analysis subvolume within the resegmentation subvolume.
delta = np.array(resegmentation_radius) - analysis_r
prob = prob[:,
delta[0]:(delta[0] + 2 * analysis_r[0] + 1),
delta[1]:(delta[1] + 2 * analysis_r[1] + 1),
delta[2]:(delta[2] + 2 * analysis_r[2] + 1)]
reseg = prob >= threshold
result.eval.iou = compute_iou(reseg)
# Record information about the size of the reconstructed segments.
evaluate_segmentation_result(
reseg[0, ...], dels[0], moves[0], delta, analysis_r, seg1, seg2,
voxel_size, result.eval.from_a)
evaluate_segmentation_result(
reseg[1, ...], dels[1], moves[1], delta, analysis_r, seg1, seg2,
voxel_size, result.eval.from_b)
return result