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Merged
bhashemian merged 4 commits into from
Nov 18, 2021
Merged

Improve TileOnGrid #3355

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fc861f6
Fix casting for tile step
bhashemian Nov 17, 2021
2c610cf
Merge branch 'dev' into improve-tile-on-grid
bhashemian Nov 18, 2021
9fd7e96
Merge branch 'dev' into improve-tile-on-grid
bhashemian Nov 18, 2021
a2f0c1e
Merge branch 'dev' into improve-tile-on-grid
wyli Nov 18, 2021
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18 changes: 9 additions & 9 deletions monai/apps/pathology/transforms/spatial/array.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.

from typing import Optional, Sequence, Tuple, Union, cast
from typing import Optional, Sequence, Tuple, Union

import numpy as np
import torch
Expand Down Expand Up @@ -113,14 +113,16 @@ def __init__(
):
self.tile_count = tile_count
self.tile_size = tile_size
self.step = step
self.random_offset = random_offset
self.pad_full = pad_full
self.background_val = background_val
self.filter_mode = filter_mode

if self.step is None:
self.step = self.tile_size # non-overlapping grid
if step is None:
# non-overlapping grid
self.step = self.tile_size
else:
self.step = step

self.offset = (0, 0)
self.random_idxs = np.array((0,))
Expand All @@ -131,7 +133,6 @@ def __init__(
def randomize(self, img_size: Sequence[int]) -> None:

c, h, w = img_size
tile_step = cast(int, self.step)

self.offset = (0, 0)
if self.random_offset:
Expand All @@ -147,8 +148,8 @@ def randomize(self, img_size: Sequence[int]) -> None:
h = h + pad_h
w = w + pad_w

h_n = (h - self.tile_size + tile_step) // tile_step
w_n = (w - self.tile_size + tile_step) // tile_step
h_n = (h - self.tile_size + self.step) // self.step
w_n = (w - self.tile_size + self.step) // self.step
tile_total = h_n * w_n

if self.tile_count is not None and tile_total > self.tile_count:
Expand All @@ -160,7 +161,6 @@ def __call__(self, image: np.ndarray) -> np.ndarray:

# add random offset
self.randomize(img_size=image.shape)
tile_step = cast(int, self.step)

if self.random_offset and (self.offset[0] > 0 or self.offset[1] > 0):
image = image[:, self.offset[0] :, self.offset[1] :]
Expand All @@ -177,7 +177,7 @@ def __call__(self, image: np.ndarray) -> np.ndarray:
)

# extact tiles
xstep, ystep = tile_step, tile_step
xstep, ystep = self.step, self.step
xsize, ysize = self.tile_size, self.tile_size
clen, xlen, ylen = image.shape
cstride, xstride, ystride = image.strides
Expand Down