diff --git a/pyproject.toml b/pyproject.toml
index 240f1cf217c38ef6ea5ef3e7d6ccb85f41fa3ebc..20ffe906fcf346f40a844e71cb5bd972b9056354 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -171,16 +171,20 @@ combined-disc = "deepdraw.binseg.configs.datasets.combined.od"
combined-cup = "deepdraw.binseg.configs.datasets.combined.oc"
# montgomery county - cxr
montgomery = "deepdraw.binseg.configs.datasets.montgomery.default"
+montgomery-gt = "deepdraw.binseg.configs.datasets.montgomery.default_gtcrop"
montgomery-xtest = "deepdraw.binseg.configs.datasets.montgomery.xtest"
# shenzhen - cxr
shenzhen = "deepdraw.binseg.configs.datasets.shenzhen.default"
shenzhen-small = "deepdraw.binseg.configs.datasets.shenzhen.default_256"
+shenzhen-gt = "deepdraw.binseg.configs.datasets.shenzhen.default_gtcrop"
shenzhen-xtest = "deepdraw.binseg.configs.datasets.shenzhen.xtest"
# jsrt - cxr
jsrt = "deepdraw.binseg.configs.datasets.jsrt.default"
+jsrt-gt = "deepdraw.binseg.configs.datasets.jsrt.default_gtcrop"
jsrt-xtest = "deepdraw.binseg.configs.datasets.jsrt.xtest"
# cxr8 - cxr
cxr8 = "deepdraw.binseg.configs.datasets.cxr8.default"
+cxr8-gt = "deepdraw.binseg.configs.datasets.cxr8.default_gtcrop"
cxr8-xtest = "deepdraw.binseg.configs.datasets.cxr8.xtest"
[project.entry-points."detect.config"]
diff --git a/src/deepdraw/binseg/configs/datasets/cxr8/__init__.py b/src/deepdraw/binseg/configs/datasets/cxr8/__init__.py
index 7c02e4820770ac878add95503d2fc147609e3f92..d4ee2c022333fd8270fe2433e99b8644d2498182 100644
--- a/src/deepdraw/binseg/configs/datasets/cxr8/__init__.py
+++ b/src/deepdraw/binseg/configs/datasets/cxr8/__init__.py
@@ -55,3 +55,51 @@ def _maker_augmented(protocol, n):
)
],
)
+
+
+def _maker_augmented_gt_box(protocol, n):
+ from .....common.data.transforms import ColorJitter as _jitter
+ from .....common.data.transforms import Compose as _compose
+ from .....common.data.transforms import GaussianBlur as _blur
+ from .....common.data.transforms import GroundTruthCrop as _gtcrop
+ from .....common.data.transforms import RandomHorizontalFlip as _hflip
+ from .....common.data.transforms import RandomRotation as _rotation
+ from .....common.data.transforms import Resize as _resize
+ from ....data.cxr8 import dataset as raw
+ from .. import make_subset
+
+ def mk_aug_subset(subsets, train_transforms, all_transforms):
+ retval = {}
+
+ for key in subsets.keys():
+ retval[key] = make_subset(subsets[key], transforms=all_transforms)
+ if key == "train":
+ retval["__train__"] = make_subset(
+ subsets[key],
+ transforms=train_transforms,
+ )
+ else:
+ if key == "validation":
+ retval["__valid__"] = retval[key]
+
+ if ("__train__" in retval) and ("__valid__" not in retval):
+ retval["__valid__"] = retval["__train__"]
+
+ return retval
+
+ return mk_aug_subset(
+ subsets=raw.subsets(protocol),
+ all_transforms=[_gtcrop(extra_area=0.2), _resize((n, n))],
+ train_transforms=[
+ _compose(
+ [
+ _gtcrop(extra_area=0.2),
+ _resize((n, n)),
+ _rotation(degrees=15, p=0.5),
+ _hflip(p=0.5),
+ _jitter(p=0.5),
+ _blur(p=0.5),
+ ]
+ )
+ ],
+ )
diff --git a/src/deepdraw/binseg/configs/datasets/cxr8/default_gtcrop.py b/src/deepdraw/binseg/configs/datasets/cxr8/default_gtcrop.py
new file mode 100644
index 0000000000000000000000000000000000000000..7a18a56718b71dee302b80e3e4ec963f09e1e539
--- /dev/null
+++ b/src/deepdraw/binseg/configs/datasets/cxr8/default_gtcrop.py
@@ -0,0 +1,14 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""CXR8 Dataset (default protocol)
+
+* Split reference: [GAAL-2020]_
+* Configuration resolution: 256 x 256
+* See :py:mod:`deepdraw.binseg.data.cxr8` for dataset details
+"""
+
+from . import _maker_augmented_gt_box
+
+dataset = _maker_augmented_gt_box("default", 256)
diff --git a/src/deepdraw/binseg/configs/datasets/jsrt/__init__.py b/src/deepdraw/binseg/configs/datasets/jsrt/__init__.py
index c785fe8fdae2ad1fa765a3c584b1bfb82a17788f..d8b3c90c02517f0d4235b85c773fb66d47cc4c28 100644
--- a/src/deepdraw/binseg/configs/datasets/jsrt/__init__.py
+++ b/src/deepdraw/binseg/configs/datasets/jsrt/__init__.py
@@ -55,3 +55,51 @@ def _maker_augmented(protocol):
)
],
)
+
+
+def _maker_augmented_gt_box(protocol):
+ from .....common.data.transforms import ColorJitter as _jitter
+ from .....common.data.transforms import Compose as _compose
+ from .....common.data.transforms import GaussianBlur as _blur
+ from .....common.data.transforms import GroundTruthCrop as _gtcrop
+ from .....common.data.transforms import RandomHorizontalFlip as _hflip
+ from .....common.data.transforms import RandomRotation as _rotation
+ from .....common.data.transforms import Resize as _resize
+ from ....data.jsrt import dataset as raw
+ from .. import make_subset
+
+ def mk_aug_subset(subsets, train_transforms, all_transforms):
+ retval = {}
+
+ for key in subsets.keys():
+ retval[key] = make_subset(subsets[key], transforms=all_transforms)
+ if key == "train":
+ retval["__train__"] = make_subset(
+ subsets[key],
+ transforms=train_transforms,
+ )
+ else:
+ if key == "validation":
+ retval["__valid__"] = retval[key]
+
+ if ("__train__" in retval) and ("__valid__" not in retval):
+ retval["__valid__"] = retval["__train__"]
+
+ return retval
+
+ return mk_aug_subset(
+ subsets=raw.subsets(protocol),
+ all_transforms=[_gtcrop(extra_area=0.2), _resize((256, 256))],
+ train_transforms=[
+ _compose(
+ [
+ _gtcrop(extra_area=0.2),
+ _resize((256, 256)),
+ _rotation(degrees=15, p=0.5),
+ _hflip(p=0.5),
+ _jitter(p=0.5),
+ _blur(p=0.5),
+ ]
+ )
+ ],
+ )
diff --git a/src/deepdraw/binseg/configs/datasets/jsrt/default_gtcrop.py b/src/deepdraw/binseg/configs/datasets/jsrt/default_gtcrop.py
new file mode 100644
index 0000000000000000000000000000000000000000..0261bb61a13af98bb5dcd5580a12c424098fd884
--- /dev/null
+++ b/src/deepdraw/binseg/configs/datasets/jsrt/default_gtcrop.py
@@ -0,0 +1,15 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Japanese Society of Radiological Technology dataset for Lung Segmentation
+(default protocol)
+
+* Split reference: [GAAL-2020]_
+* Configuration resolution: 256 x 256
+* See :py:mod:`deepdraw.binseg.data.jsrt` for dataset details
+"""
+
+from . import _maker_augmented_gt_box
+
+dataset = _maker_augmented_gt_box("default")
diff --git a/src/deepdraw/binseg/configs/datasets/montgomery/__init__.py b/src/deepdraw/binseg/configs/datasets/montgomery/__init__.py
index e9463dfa57ca58584da87bfec00bc187ab8d4b91..834fe01fbf57d3fbbc7c33151cea009ece1bf015 100644
--- a/src/deepdraw/binseg/configs/datasets/montgomery/__init__.py
+++ b/src/deepdraw/binseg/configs/datasets/montgomery/__init__.py
@@ -57,3 +57,57 @@ def _maker_augmented(protocol):
)
],
)
+
+
+def _maker_augmented_gt_box(protocol):
+ from .....common.data.transforms import ColorJitter as _jitter
+ from .....common.data.transforms import Compose as _compose
+ from .....common.data.transforms import GaussianBlur as _blur
+ from .....common.data.transforms import GroundTruthCrop as _gtcrop
+ from .....common.data.transforms import RandomHorizontalFlip as _hflip
+ from .....common.data.transforms import RandomRotation as _rotation
+ from .....common.data.transforms import Resize as _resize
+ from .....common.data.transforms import ShrinkIntoSquare as _shrinkintosq
+ from ....data.montgomery import dataset as raw
+ from .. import make_subset
+
+ def mk_aug_subset(subsets, train_transforms, all_transforms):
+ retval = {}
+
+ for key in subsets.keys():
+ retval[key] = make_subset(subsets[key], transforms=all_transforms)
+ if key == "train":
+ retval["__train__"] = make_subset(
+ subsets[key],
+ transforms=train_transforms,
+ )
+ else:
+ if key == "validation":
+ retval["__valid__"] = retval[key]
+
+ if ("__train__" in retval) and ("__valid__" not in retval):
+ retval["__valid__"] = retval["__train__"]
+
+ return retval
+
+ return mk_aug_subset(
+ subsets=raw.subsets(protocol),
+ all_transforms=[
+ _shrinkintosq(),
+ _gtcrop(extra_area=0.2),
+ _resize((256, 256)),
+ ],
+ train_transforms=[
+ _compose(
+ [
+ _shrinkintosq(),
+ _gtcrop(extra_area=0.2),
+ _resize((256, 256)),
+ _rotation(degrees=15, p=0.5),
+ _hflip(p=0.5),
+ _jitter(p=0.5),
+ _blur(p=0.5),
+ ]
+ )
+ ],
+ )
diff --git a/src/deepdraw/binseg/configs/datasets/montgomery/default_gtcrop.py b/src/deepdraw/binseg/configs/datasets/montgomery/default_gtcrop.py
new file mode 100644
index 0000000000000000000000000000000000000000..718e086d97d0000802fb163bb97df1802f028fb1
--- /dev/null
+++ b/src/deepdraw/binseg/configs/datasets/montgomery/default_gtcrop.py
@@ -0,0 +1,14 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Montgomery County dataset for Lung Segmentation (default protocol)
+
+* Split reference: [GAAL-2020]_
+* Configuration resolution: 256 x 256
+* See :py:mod:`deepdraw.binseg.data.montgomery` for dataset details
+"""
+
+from . import _maker_augmented_gt_box
+
+dataset = _maker_augmented_gt_box("default")
diff --git a/src/deepdraw/binseg/configs/datasets/shenzhen/__init__.py b/src/deepdraw/binseg/configs/datasets/shenzhen/__init__.py
index 5499e4a81393341dc365f30d174e541b34157179..9ea76c32c57ad4a78762ca2dd44e9f164a98c577 100644
--- a/src/deepdraw/binseg/configs/datasets/shenzhen/__init__.py
+++ b/src/deepdraw/binseg/configs/datasets/shenzhen/__init__.py
@@ -57,3 +57,57 @@ def _maker_augmented(protocol, n):
)
],
)
+
+
+def _maker_augmented_gt_box(protocol, n):
+ from .....common.data.transforms import ColorJitter as _jitter
+ from .....common.data.transforms import Compose as _compose
+ from .....common.data.transforms import GaussianBlur as _blur
+ from .....common.data.transforms import GroundTruthCrop as _gtcrop
+ from .....common.data.transforms import RandomHorizontalFlip as _hflip
+ from .....common.data.transforms import RandomRotation as _rotation
+ from .....common.data.transforms import Resize as _resize
+ from .....common.data.transforms import ShrinkIntoSquare as _shrinkintosq
+ from ....data.shenzhen import dataset as raw
+ from .. import make_subset
+
+ def mk_aug_subset(subsets, train_transforms, all_transforms):
+ retval = {}
+
+ for key in subsets.keys():
+ retval[key] = make_subset(subsets[key], transforms=all_transforms)
+ if key == "train":
+ retval["__train__"] = make_subset(
+ subsets[key],
+ transforms=train_transforms,
+ )
+ else:
+ if key == "validation":
+ retval["__valid__"] = retval[key]
+
+ if ("__train__" in retval) and ("__valid__" not in retval):
+ retval["__valid__"] = retval["__train__"]
+
+ return retval
+
+ return mk_aug_subset(
+ subsets=raw.subsets(protocol),
+ all_transforms=[
+ _shrinkintosq(),
+ _gtcrop(extra_area=0.2),
+ _resize((n, n)),
+ ],
+ train_transforms=[
+ _compose(
+ [
+ _shrinkintosq(),
+ _gtcrop(extra_area=0.2),
+ _resize((n, n)),
+ _rotation(degrees=15, p=0.5),
+ _hflip(p=0.5),
+ _jitter(p=0.5),
+ _blur(p=0.5),
+ ]
+ )
+ ],
+ )
diff --git a/src/deepdraw/binseg/configs/datasets/shenzhen/default_gtcrop.py b/src/deepdraw/binseg/configs/datasets/shenzhen/default_gtcrop.py
new file mode 100644
index 0000000000000000000000000000000000000000..31a5b782c3bbdec5f8993fe1f5c2d7b72be3ffdd
--- /dev/null
+++ b/src/deepdraw/binseg/configs/datasets/shenzhen/default_gtcrop.py
@@ -0,0 +1,14 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Shenzhen dataset for Lung Segmentation (default protocol)
+
+* Split reference: [GAAL-2020]_
+* Configuration resolution: 256 x 256
+* See :py:mod:`deepdraw.binseg.data.shenzhen` for dataset details
+"""
+
+from . import _maker_augmented_gt_box
+
+dataset = _maker_augmented_gt_box("default", 256)
diff --git a/src/deepdraw/common/data/transforms.py b/src/deepdraw/common/data/transforms.py
index a26aeb784d1ded0b27beb4f3af216b4fb3211583..8bddfb1a2828443af0cbe08f88ce83796e7d6d43 100644
--- a/src/deepdraw/common/data/transforms.py
+++ b/src/deepdraw/common/data/transforms.py
@@ -430,3 +430,110 @@ class GetBoundingBox:
target["labels"] = labels
return [args[self.image], target]
+
+
+class GroundTruthCrop:
+ """Crop image in a square keeping only the area with the ground truth.
+
+ This transform can crop all images given a ground-truth mask as reference.
+ Notice that the crop will result in a square image at the end, which means
+ that it will keep the bigger dimension and adjust the smaller one to fit
+ into a square. There's an option to add extra area around the gt bounding
+ box. If resulting dimensions are larger than the boundaries of the image,
+ minimal padding will be done to keep the image in a square shape.
+
+ Parameters
+ ----------
+
+ reference : :py:class:`int`, Optional
+ Which reference part of the sample to use for getting coordinates.
+ If not set, use the second object on the sample (typically, the mask).
+
+ extra_area : :py:class:`float`, Optional
+ Multiplier that will add the extra area around the ground-truth
+ bounding box. Example: 0.1 will result in a crop with dimensions of
+ the largest side increased by 10%. If not set, the default will be 0
+ (only the ground-truth box).
+ """
+
+ def __init__(self, reference=1, extra_area=0.0):
+ self.reference = reference
+ self.extra_area = extra_area
+
+ def __call__(self, *args):
+ ref = args[self.reference]
+
+ max_w, max_h = ref.size
+
+ where = numpy.where(ref)
+ y0 = numpy.min(where[0])
+ y1 = numpy.max(where[0])
+ x0 = numpy.min(where[1])
+ x1 = numpy.max(where[1])
+
+ w = x1 - x0
+ h = y1 - y0
+
+ extra_x = self.extra_area * w / 2
+ extra_y = self.extra_area * h / 2
+
+ new_w = (1 + self.extra_area) * w
+ new_h = (1 + self.extra_area) * h
+
+ diff = abs(new_w - new_h) / 2
+
+ if new_w == new_h:
+ x0_new = x0.copy() - extra_x
+ x1_new = x1.copy() + extra_x
+ y0_new = y0.copy() - extra_y
+ y1_new = y1.copy() + extra_y
+
+ elif new_w > new_h:
+ x0_new = x0.copy() - extra_x
+ x1_new = x1.copy() + extra_x
+ y0_new = y0.copy() - extra_y - diff
+ y1_new = y1.copy() + extra_y + diff
+
+ else:
+ x0_new = x0.copy() - extra_x - diff
+ x1_new = x1.copy() + extra_x + diff
+ y0_new = y0.copy() - extra_y
+ y1_new = y1.copy() + extra_y
+
+ border = (x0_new, y0_new, max_w - x1_new, max_h - y1_new)
+
+ def _expand_img(
+ pil_img, background_color, x0_pad=0, x1_pad=0, y0_pad=0, y1_pad=0
+ ):
+ width = pil_img.size[0] + x0_pad + x1_pad
+ height = pil_img.size[1] + y0_pad + y1_pad
+
+ result = PIL.Image.new(
+ pil_img.mode, (width, height), background_color
+ )
+ result.paste(pil_img, (x0_pad, y0_pad))
+ return result
+
+ def _black_background(i):
+ return (0, 0, 0) if i.mode == "RGB" else 0
+
+ d_x0 = numpy.rint(max([0 - x0_new, 0])).astype(int)
+ d_y0 = numpy.rint(max([0 - y0_new, 0])).astype(int)
+ d_x1 = numpy.rint(max([x1_new - max_w, 0])).astype(int)
+ d_y1 = numpy.rint(max([y1_new - max_h, 0])).astype(int)
+
+ new_args = [
+ _expand_img(
+ k,
+ _black_background(k),
+ x0_pad=d_x0,
+ x1_pad=d_x1,
+ y0_pad=d_y0,
+ y1_pad=d_y1,
+ )
+ for k in args
+ ]
+
+ new_args = [PIL.ImageOps.crop(k, border) for k in new_args]
+
+ return new_args