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Modifies the squaring bbox and tweaks PIL input shapes #1030

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merged 7 commits into from
Dec 11, 2024
Merged

Modifies the squaring bbox and tweaks PIL input shapes #1030

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090e0ef
Rm single crop expansion (l/r) for always both (l+r)
MaxGamill-Sheffield Dec 1, 2024
68cadb7
update and add single constrained test
MaxGamill-Sheffield Dec 1, 2024
45d6046
remove passing square condition
MaxGamill-Sheffield Dec 10, 2024
f3f53ff
add square and bbox iun img bounds asserts
MaxGamill-Sheffield Dec 10, 2024
5b2f473
Merge branch 'main' into maxgamill-sheffield/unet-crop-fix
MaxGamill-Sheffield Dec 10, 2024
af613a5
tests(unet_masking): Correct ids and add expected fail
ns-rse Dec 10, 2024
0625a55
Merge pull request #1046 from AFM-SPM/ns-rse/enhance-bbox-test
MaxGamill-Sheffield Dec 11, 2024
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47 changes: 34 additions & 13 deletions tests/test_unet_masking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@

from topostats.unet_masking import dice_loss, iou_loss, make_bounding_box_square, pad_bounding_box, predict_unet

# pylint: disable=too-many-positional-arguments


@pytest.mark.parametrize(
("y_true", "y_pred", "smooth", "expected_loss"),
Expand Down Expand Up @@ -149,18 +151,29 @@ def test_predict_unet(mock_model_5_by_5_single_class: MagicMock) -> None:
("crop_min_row", "crop_min_col", "crop_max_row", "crop_max_col", "image_shape", "expected_indices"),
[
pytest.param(0, 0, 100, 100, (100, 100), (0, 0, 100, 100), id="not a crop"),
pytest.param(3, 4, 8, 8, (10, 10), (3, 4, 8, 9), id="free space single min col decrease"),
pytest.param(4, 3, 8, 8, (10, 10), (4, 3, 9, 8), id="free space single min row decrease"),
pytest.param(4, 4, 7, 8, (10, 10), (4, 4, 8, 8), id="free space single max col increase"),
pytest.param(4, 4, 8, 7, (10, 10), (4, 4, 8, 8), id="free space single max row increase"),
pytest.param(4, 2, 8, 8, (10, 10), (3, 2, 9, 8), id="free space double min col decrease"),
pytest.param(2, 4, 8, 8, (10, 10), (2, 3, 8, 9), id="free space double min row decrease"),
pytest.param(4, 4, 8, 6, (10, 10), (4, 3, 8, 7), id="free space double max col increase"),
pytest.param(4, 4, 6, 8, (10, 10), (3, 4, 7, 8), id="free space double max row increase"),
pytest.param(1, 1, 6, 2, (10, 10), (1, 1, 6, 6), id="constrained left"),
pytest.param(1, 6, 7, 8, (10, 10), (1, 2, 7, 8), id="constrained right"),
pytest.param(1, 1, 2, 6, (10, 10), (1, 1, 6, 6), id="constrained top"),
pytest.param(6, 1, 8, 7, (10, 10), (2, 1, 8, 7), id="constrained bottom"),
pytest.param(3, 4, 8, 8, (10, 10), (3, 4, 8, 9), id="free space single max col increase"),
pytest.param(4, 3, 8, 8, (10, 10), (4, 3, 9, 8), id="free space single max row increase"),
pytest.param(4, 4, 7, 8, (10, 10), (4, 4, 8, 8), id="free space single max row increase"),
pytest.param(4, 4, 8, 7, (10, 10), (4, 4, 8, 8), id="free space single max col increase"),
pytest.param(4, 2, 8, 8, (10, 10), (3, 2, 9, 8), id="free space double min row decrease, max row increase"),
pytest.param(2, 4, 8, 8, (10, 10), (2, 3, 8, 9), id="free space double min col decrease, max col increase"),
pytest.param(4, 4, 8, 6, (10, 10), (4, 3, 8, 7), id="free space double min col decrease, max col increase"),
pytest.param(4, 4, 6, 8, (10, 10), (3, 4, 7, 8), id="free space double min row decrease, max row increase"),
pytest.param(1, 1, 6, 2, (10, 10), (1, 0, 6, 5), id="constrained left"),
pytest.param(1, 6, 7, 8, (10, 10), (1, 3, 7, 9), id="constrained right"),
pytest.param(1, 1, 2, 6, (10, 10), (0, 1, 5, 6), id="constrained top"),
pytest.param(6, 1, 8, 7, (10, 10), (3, 1, 9, 7), id="constrained bottom"),
pytest.param(117, 20, 521, 603, (608, 608), (24, 20, 607, 603), id="constrained top and bottom"),
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@ns-rse ns-rse Dec 3, 2024 •
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Now I've tried looking at this in detail I find the dimensions quite hard to think about, are there smaller image_shape and co-ordinates that would be constrained top and bottom?

I think if image_shape is always square, which isn't necessarily the case since I recall @SylviaWhittle writing code to handle none-square images, then we'd only ever see a constraint on one side. Something that would be constrained top and bottom would be a wide rectangular bounding box within a wide rectangular image.

EDIT: I added just such a set of test parameters to the above mentioned commit and marked it as pytest.mark.xfail() with a reason explaining why. If cherry picking it will be included.

pytest.param(
1,
1,
2,
4,
(2, 4),
(0, 1, 2, 4),
id="rectangular image with large rectangular box",
marks=pytest.mark.xfail(reason="square bounding box not possible"),
),
],
)
def test_make_bounding_box_square(
Expand All @@ -171,8 +184,16 @@ def test_make_bounding_box_square(
image_shape: tuple[int, int],
expected_indices: tuple[int, int, int, int],
) -> None:
"""Test the make_bounding_box_square method."""
"""Test the make_bounding_box_square method returns square objects within image shape with known coordinates."""
result = make_bounding_box_square(crop_min_row, crop_min_col, crop_max_row, crop_max_col, image_shape)
# check bbox within image bounds
assert result[0] >= 0
assert result[1] >= 0
assert result[2] <= image_shape[0]
assert result[3] <= image_shape[1]
# check if square
assert (result[2] - result[0]) == (result[3] - result[1])
# check bbox coords match
assert result == expected_indices


Expand Down
16 changes: 9 additions & 7 deletions topostats/grains.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
# pylint: disable=too-many-arguments
# pylint: disable=bare-except
# pylint: disable=dangerous-default-value
# pylint: disable=too-many-positional-arguments
# pylint: disable=too-many-lines
# pylint: disable=too-many-public-methods

Expand Down Expand Up @@ -699,13 +700,14 @@ def improve_grain_segmentation_unet(
)

# Make the bounding box square within the confines of the image
bounding_box = make_bounding_box_square(
crop_min_row=bounding_box[0],
crop_min_col=bounding_box[1],
crop_max_row=bounding_box[2],
crop_max_col=bounding_box[3],
image_shape=(image.shape[0], image.shape[1]),
)
if (bounding_box[2] - bounding_box[0]) != (bounding_box[3] - bounding_box[1]):
bounding_box = make_bounding_box_square(
crop_min_row=bounding_box[0],
crop_min_col=bounding_box[1],
crop_max_row=bounding_box[2],
crop_max_col=bounding_box[3],
image_shape=(image.shape[0], image.shape[1]),
)

# Grab the cropped image. Using slice since the bounding box from skimage is
# half-open, so the max_row and max_col are not included in the region.
Expand Down
53 changes: 25 additions & 28 deletions topostats/unet_masking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,9 @@

LOGGER = logging.getLogger(LOGGER_NAME)

# pylint: disable=too-many-positional-arguments
# pylint: disable=too-many-locals


# DICE Loss
def dice_loss(y_true: npt.NDArray[np.float32], y_pred: npt.NDArray[np.float32], smooth: float = 1e-5) -> tf.Tensor:
Expand Down Expand Up @@ -199,7 +202,7 @@ def predict_unet(
# Resize the channel mask to the original image size, but we want boolean so use nearest neighbour
# Sylvia: Pylint incorrectly thinks that Image.NEAREST is not a member of Image. IDK why.
# pylint: disable=no-member
channel_mask_PIL = channel_mask_PIL.resize((original_image.shape[0], original_image.shape[1]), Image.NEAREST)
channel_mask_PIL = channel_mask_PIL.resize((original_image.shape[1], original_image.shape[0]), Image.NEAREST)
resized_predicted_mask[:, :, channel_index] = np.array(channel_mask_PIL).astype(bool)

return resized_predicted_mask
Expand Down Expand Up @@ -245,45 +248,39 @@ def make_bounding_box_square(
if crop_min_col - diff // 2 >= 0 and crop_max_col + diff - diff // 2 < image_shape[1]:
new_crop_min_col = crop_min_col - diff // 2
new_crop_max_col = crop_max_col + diff - diff // 2
# If we can't expand uniformly, expand in just one direction
# Check if we can expand right
elif crop_max_col + diff - diff // 2 < image_shape[1]:
# We can expand right
new_crop_min_col = crop_min_col
new_crop_max_col = crop_max_col + diff
elif crop_min_col - diff // 2 >= 0:
# We can expand left
new_crop_min_col = crop_min_col - diff
new_crop_max_col = crop_max_col
# If we can't expand uniformly, expand as much as possible in that dir
else:
# Crop expansion below 0
if crop_min_col - diff // 2 <= 0:
new_crop_min_col = 0
new_crop_max_col = crop_max_col + (diff - crop_min_col)
# Crop expansion beyond image size
else:
new_crop_max_col = image_shape[1] - 1
new_crop_min_col = crop_min_col - (diff - (image_shape[1] - 1 - crop_max_col))
# Set the new crop height to the original crop height since we are just updating the width
new_crop_min_row = crop_min_row
new_crop_max_row = crop_max_row
elif crop_width > crop_height:
else:
# The crop is wider than it is tall
diff = crop_width - crop_height
# Check if we can expand equally in each direction
if crop_min_row - diff // 2 >= 0 and crop_max_row + diff - diff // 2 < image_shape[0]:
new_crop_min_row = crop_min_row - diff // 2
new_crop_max_row = crop_max_row + diff - diff // 2
# If we can't expand uniformly, expand in just one direction
# Check if we can expand down
elif crop_max_row + diff - diff // 2 < image_shape[0]:
# We can expand down
new_crop_min_row = crop_min_row
new_crop_max_row = crop_max_row + diff
elif crop_min_row - diff // 2 >= 0:
# We can expand up
new_crop_min_row = crop_min_row - diff
new_crop_max_row = crop_max_row
# If we can't expand uniformly, expand as much as possible in that dir
else:
# Crop expansion below 0
if crop_min_row - diff // 2 <= 0:
new_crop_min_row = 0
new_crop_max_row = crop_max_row + (diff - crop_min_row)
# Crop expansion beyond image size
else:
new_crop_max_row = image_shape[0] - 1
new_crop_min_row = crop_min_row - (diff - (image_shape[0] - 1 - crop_max_row))
# Set the new crop width to the original crop width since we are just updating the height
new_crop_min_col = crop_min_col
new_crop_max_col = crop_max_col
else:
# If the crop is already square, return the original crop
new_crop_min_row = crop_min_row
new_crop_min_col = crop_min_col
new_crop_max_row = crop_max_row
new_crop_max_col = crop_max_col

return new_crop_min_row, new_crop_min_col, new_crop_max_row, new_crop_max_col

Expand Down
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