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torms3torms3
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feat: cortex augmentation
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‎deepem/data/augment/cortex/aug_16nm.py

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from augmentor import *
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def get_augmentation(
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is_train,
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box=None,
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missing=7,
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blur=7,
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lost=True,
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random=False,
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recompute=False,
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border=[],
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**kwargs
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):
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augs = list()
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# Box
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if is_train:
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if box == 'noise':
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augs.append(
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NoiseBox(sigma=(1, 3), dims=(3, 13), margin=(1, 3, 3),
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density=0.3, skip=0.1)
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)
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elif box == 'fill':
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augs.append(
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FillBox(dims=(3, 13), margin=(1, 3, 3),
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density=0.3, skip=0.1)
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)
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# Brightness & contrast purterbation
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augs.append(
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MixedGrayscale2D(
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contrast_factor=0.5,
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brightness_factor=0.5,
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prob=1, skip=0.3))
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# Missing section & misalignment
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to_blend = list()
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# Misalingments
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trans = Compose([Misalign((0, 3), margin=1),
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Misalign((0, 8), margin=1),
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Misalign((0, 13), margin=1)])
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# Out-of-alignments
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slip = Compose([SlipMisalign((0, 3), interp=True, margin=1),
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SlipMisalign((0, 8), interp=True, margin=1),
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SlipMisalign((0, 13), interp=True, margin=1)])
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to_blend.append(Blend([trans, slip], props=[0.7, 0.3]))
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if is_train:
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to_blend.append(Blend([
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MisalignPlusMissing((2, 8), value=0, random=random),
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MisalignPlusMissing((2, 8), value=0, random=False)
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]))
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else:
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to_blend.append(MisalignPlusMissing((2, 8), value=0, random=False))
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if missing > 0:
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if is_train:
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to_blend.append(Blend([
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=False),
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=random),
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MissingSection(maxsec=missing, individual=False, value=0, random=random),
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]))
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else:
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to_blend.append(
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=False)
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)
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if lost:
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if is_train:
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to_blend.append(Blend([
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LostSection(1),
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LostPlusMissing(value=0, random=random),
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LostPlusMissing(value=0, random=False)
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]))
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augs.append(Blend(to_blend))
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# Out-of-focus
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if blur > 0:
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augs.append(MixedBlurrySection(maxsec=blur))
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# Warping
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if is_train:
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augs.append(Warp(skip=0.3, do_twist=False, rot_max=45.0, scale_max=1.1))
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# Flip & rotate
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augs.append(FlipRotate())
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# Create border
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if border:
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augs.append(Border(targets=border))
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# Recompute connected components
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if recompute:
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augs.append(Label())
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return Compose(augs)

‎deepem/data/augment/cortex/aug_4nm.py

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from augmentor import *
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def get_augmentation(
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is_train,
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box=None,
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missing=7,
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blur=7,
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lost=True,
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random=False,
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recompute=False,
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border=[],
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**kwargs
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):
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augs = list()
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# Box
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if is_train:
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if box == 'noise':
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augs.append(
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NoiseBox(sigma=(1, 3), dims=(10, 50), margin=(1, 10, 10),
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density=0.3, skip=0.1)
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)
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elif box == 'fill':
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augs.append(
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FillBox(dims=(10, 50), margin=(1, 10, 10),
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density=0.3, skip=0.1)
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)
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# Brightness & contrast purterbation
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augs.append(
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MixedGrayscale2D(
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contrast_factor=0.5,
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brightness_factor=0.5,
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prob=1, skip=0.3))
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# Missing section & misalignment
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to_blend = list()
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# Misalingments
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trans = Compose([Misalign((0, 10), margin=1),
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Misalign((0, 30), margin=1),
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Misalign((0, 50), margin=1)])
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# Out-of-alignments
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slip = Compose([SlipMisalign((0, 10), interp=True, margin=1),
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SlipMisalign((0, 30), interp=True, margin=1),
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SlipMisalign((0, 50), interp=True, margin=1)])
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to_blend.append(Blend([trans, slip], props=[0.7, 0.3]))
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if is_train:
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to_blend.append(Blend([
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MisalignPlusMissing((5, 30), value=0, random=random),
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MisalignPlusMissing((5, 30), value=0, random=False)
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]))
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else:
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to_blend.append(MisalignPlusMissing((5, 30), value=0, random=False))
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if missing > 0:
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if is_train:
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to_blend.append(Blend([
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=False),
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=random),
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MissingSection(maxsec=missing, individual=False, value=0, random=random),
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]))
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else:
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to_blend.append(
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=False)
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)
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if lost:
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if is_train:
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to_blend.append(Blend([
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LostSection(1),
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LostPlusMissing(value=0, random=random),
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LostPlusMissing(value=0, random=False)
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]))
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augs.append(Blend(to_blend))
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# Out-of-focus
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if blur > 0:
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augs.append(MixedBlurrySection(maxsec=blur))
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# Warping
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if is_train:
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augs.append(Warp(skip=0.3, do_twist=False, rot_max=45.0, scale_max=1.1))
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# Flip & rotate
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augs.append(FlipRotate())
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# Create border
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if border:
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augs.append(Border(targets=border))
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# Recompute connected components
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if recompute:
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augs.append(Label())
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return Compose(augs)

‎deepem/data/augment/cortex/aug_8nm.py

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from augmentor import *
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def get_augmentation(
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is_train,
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box=None,
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missing=7,
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blur=7,
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lost=True,
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random=False,
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recompute=False,
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border=[],
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**kwargs
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):
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augs = list()
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# Box
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if is_train:
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if box == 'noise':
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augs.append(
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NoiseBox(sigma=(1, 3), dims=(5, 25), margin=(1, 5, 5),
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density=0.3, skip=0.1)
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)
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elif box == 'fill':
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augs.append(
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FillBox(dims=(5, 25), margin=(1, 5, 5),
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density=0.3, skip=0.1)
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)
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# Brightness & contrast purterbation
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augs.append(
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MixedGrayscale2D(
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contrast_factor=0.5,
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brightness_factor=0.5,
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prob=1, skip=0.3))
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# Missing section & misalignment
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to_blend = list()
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# Misalingments
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trans = Compose([Misalign((0, 5), margin=1),
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Misalign((0, 15), margin=1),
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Misalign((0, 25), margin=1)])
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# Out-of-alignments
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slip = Compose([SlipMisalign((0, 5), interp=True, margin=1),
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SlipMisalign((0, 15), interp=True, margin=1),
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SlipMisalign((0, 25), interp=True, margin=1)])
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to_blend.append(Blend([trans, slip], props=[0.7, 0.3]))
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if is_train:
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to_blend.append(Blend([
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MisalignPlusMissing((3, 15), value=0, random=random),
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MisalignPlusMissing((3, 15), value=0, random=False)
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]))
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else:
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to_blend.append(MisalignPlusMissing((3, 15), value=0, random=False))
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if missing > 0:
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if is_train:
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to_blend.append(Blend([
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=False),
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=random),
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MissingSection(maxsec=missing, individual=False, value=0, random=random),
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]))
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else:
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to_blend.append(
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MixedMissingSection(maxsec=missing, individual=True, value=0, random=False)
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)
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if lost:
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if is_train:
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to_blend.append(Blend([
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LostSection(1),
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LostPlusMissing(value=0, random=random),
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LostPlusMissing(value=0, random=False)
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]))
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augs.append(Blend(to_blend))
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# Out-of-focus
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if blur > 0:
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augs.append(MixedBlurrySection(maxsec=blur))
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# Warping
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if is_train:
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augs.append(Warp(skip=0.3, do_twist=False, rot_max=45.0, scale_max=1.1))
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# Flip & rotate
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augs.append(FlipRotate())
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# Create border
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if border:
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augs.append(Border(targets=border))
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# Recompute connected components
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if recompute:
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augs.append(Label())
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return Compose(augs)

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