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Add channel dim in ComputeHoVerMaps and ComputeHoVerMapsd #5183

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Merged
bhashemian merged 4 commits into from
Sep 21, 2022
Merged

Add channel dim in ComputeHoVerMaps and ComputeHoVerMapsd #5183

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bf22324
add channel dim
KumoLiu Sep 20, 2022
a6e13fc
update doc string
KumoLiu Sep 20, 2022
06d49a8
Merge branch 'dev' into update-dim-in-computehovermaps
bhashemian Sep 20, 2022
39d7ba6
update according to comment
KumoLiu Sep 20, 2022
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4 changes: 3 additions & 1 deletion monai/transforms/intensity/array.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2293,6 +2293,7 @@ def __call__(self, image: NdarrayOrTensor):
class ComputeHoVerMaps(Transform):
"""Compute horizontal and vertical maps from an instance mask
It generates normalized horizontal and vertical distances to the center of mass of each region.
Input data with the size of [1xHxW[xD]], which channel dim will temporarily removed for calculating coordinates.

Args:
dtype: the data type of output Tensor. Defaults to `"float32"`.
Expand All @@ -2311,6 +2312,7 @@ def __call__(self, mask: NdarrayOrTensor):

h_map = instance_mask.astype(self.dtype, copy=True)
v_map = instance_mask.astype(self.dtype, copy=True)
instance_mask = instance_mask.squeeze(0) # remove channel dim

for region in skimage.measure.regionprops(instance_mask):
v_dist = region.coords[:, 0] - region.centroid[0]
Expand All @@ -2325,5 +2327,5 @@ def __call__(self, mask: NdarrayOrTensor):
h_map[h_map == region.label] = h_dist
v_map[v_map == region.label] = v_dist

hv_maps = convert_to_tensor(np.stack([h_map, v_map]), track_meta=get_track_meta())
hv_maps = convert_to_tensor(np.concatenate([h_map, v_map]), track_meta=get_track_meta())
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Nic-Ma marked this conversation as resolved.
return hv_maps
10 changes: 5 additions & 5 deletions tests/test_compute_ho_ver_maps.py
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Expand Up @@ -22,11 +22,11 @@
_, has_skimage = optional_import("skimage", "0.19.0", min_version)


INSTANCE_MASK = np.zeros((16, 16), dtype="int16")
INSTANCE_MASK[5:8, 4:11] = 1
INSTANCE_MASK[3:5, 6:9] = 1
INSTANCE_MASK[8:10, 6:9] = 1
INSTANCE_MASK[13:, 13:] = 2
INSTANCE_MASK = np.zeros((1, 16, 16), dtype="int16")
INSTANCE_MASK[:, 5:8, 4:11] = 1
INSTANCE_MASK[:, 3:5, 6:9] = 1
INSTANCE_MASK[:, 8:10, 6:9] = 1
INSTANCE_MASK[:, 13:, 13:] = 2
H_MAP = torch.zeros((16, 16), dtype=torch.float32)
H_MAP[5:8, 4] = -1.0
H_MAP[5:8, 5] = -2.0 / 3.0
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10 changes: 5 additions & 5 deletions tests/test_compute_ho_ver_maps_d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,11 @@
_, has_skimage = optional_import("skimage", "0.19.0", min_version)


INSTANCE_MASK = np.zeros((16, 16), dtype="int16")
INSTANCE_MASK[5:8, 4:11] = 1
INSTANCE_MASK[3:5, 6:9] = 1
INSTANCE_MASK[8:10, 6:9] = 1
INSTANCE_MASK[13:, 13:] = 2
INSTANCE_MASK = np.zeros((1, 16, 16), dtype="int16")
INSTANCE_MASK[:, 5:8, 4:11] = 1
INSTANCE_MASK[:, 3:5, 6:9] = 1
INSTANCE_MASK[:, 8:10, 6:9] = 1
INSTANCE_MASK[:, 13:, 13:] = 2
H_MAP = torch.zeros((16, 16), dtype=torch.float32)
H_MAP[5:8, 4] = -1.0
H_MAP[5:8, 5] = -2.0 / 3.0
Expand Down