Skip to content

Commit

Permalink
add support for treating background as an object
Browse files Browse the repository at this point in the history
add option to avoid predicting all 0s for affs and lsds in background.
  • Loading branch information
pattonw committed Feb 14, 2024
1 parent 39915ac commit ee3f7cc
Show file tree
Hide file tree
Showing 3 changed files with 21 additions and 3 deletions.
1 change: 1 addition & 0 deletions dacapo/experiments/tasks/affinities_task.py
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ def __init__(self, task_config):
affs_weight_clipmax=task_config.affs_weight_clipmax,
lsd_weight_clipmin=task_config.lsd_weight_clipmin,
lsd_weight_clipmax=task_config.lsd_weight_clipmax,
background_as_object=task_config.background_as_object,
)
self.loss = AffinitiesLoss(
len(task_config.neighborhood), task_config.lsds_to_affs_weight_ratio
Expand Down
10 changes: 10 additions & 0 deletions dacapo/experiments/tasks/affinities_task_config.py
Original file line number Diff line number Diff line change
Expand Up @@ -52,3 +52,13 @@ class AffinitiesTaskConfig(TaskConfig):
default=0.95,
metadata={"help_text": "The maximum value for lsds weights."},
)
background_as_object: bool = attr.ib(
default=False,
metadata={
"help_text": (
"Whether to treat the background as a separate object. "
"If set to false background should get an affinity near 0. If "
"set to true, the background should also have high affinity with other background."
)
},
)
13 changes: 10 additions & 3 deletions dacapo/experiments/tasks/predictors/affinities_predictor.py
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ def __init__(
affs_weight_clipmax: float = 0.95,
lsd_weight_clipmin: float = 0.05,
lsd_weight_clipmax: float = 0.95,
background_as_object: bool = False,
):
self.neighborhood = neighborhood
self.lsds = lsds
Expand All @@ -51,6 +52,8 @@ def __init__(
self.lsd_weight_clipmin = lsd_weight_clipmin
self.lsd_weight_clipmax = lsd_weight_clipmax

self.background_as_object = background_as_object

def extractor(self, voxel_size):
if self._extractor is None:
self._extractor = LsdExtractor(
Expand Down Expand Up @@ -105,10 +108,12 @@ def create_target(self, gt):
label_data = label_data[0]
else:
axes = ["c"] + axes
affinities = seg_to_affgraph(label_data, self.neighborhood).astype(np.float32)
affinities = seg_to_affgraph(
label_data + int(self.background_as_object), self.neighborhood
).astype(np.float32)
if self.lsds:
descriptors = self.extractor(gt.voxel_size).get_descriptors(
segmentation=label_data,
segmentation=label_data + int(self.background_as_object),
voxel_size=gt.voxel_size,
)
return NumpyArray.from_np_array(
Expand Down Expand Up @@ -208,7 +213,9 @@ def gt_region_for_roi(self, target_spec):
for a, b in zip(pad_pos, self.lsd_pad(target_spec.voxel_size))
]
)
gt_spec.roi = gt_spec.roi.grow(pad_neg, pad_pos)
gt_spec.roi = gt_spec.roi.grow(pad_neg, pad_pos).snap_to_grid(
target_spec.voxel_size
)
gt_spec.dtype = None
return gt_spec

Expand Down

0 comments on commit ee3f7cc

Please sign in to comment.