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fix(transforms): new dir struct, catch module errs
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10 files changed

+103
-97
lines changed

‎cellseg_models_pytorch/transforms/__init__.py‎

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from ._composition import apply_each, compose, to_tensor, to_tensorv3
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from .img_transforms import (
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blur_transforms,
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center_crop,
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hue_saturation_transforms,
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non_rigid_transforms,
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non_spatial_transforms,
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random_crop,
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resize,
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rigid_transforms,
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)
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from .inst_transforms import (
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binarize_transform,
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cellpose_transform,
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contour_transform,
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dist_transform,
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edgeweight_transform,
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hovernet_transform,
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omnipose_transform,
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smooth_dist_transform,
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stardist_opt_transform,
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stardist_transform,
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)
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from .norm_transforms import (
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imgnorm_transform,
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minmaxnorm_transform,
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percentilenorm_transform,
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)
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IMG_TRANSFORMS = {
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"blur": blur_transforms,
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"center_crop": center_crop,
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"hue_sat": hue_saturation_transforms,
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"non_rigid": non_rigid_transforms,
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"rigid": rigid_transforms,
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"non_spatial": non_spatial_transforms,
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"resize": resize,
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"random_crop": random_crop,
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}
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INST_TRANSFORMS = {
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"cellpose": cellpose_transform,
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"omnipose": omnipose_transform,
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"hovernet": hovernet_transform,
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"stardist": stardist_transform,
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"stardist_opt": stardist_opt_transform,
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"contour": contour_transform,
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"dist": dist_transform,
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"edgeweight": edgeweight_transform,
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"smooth_dist": smooth_dist_transform,
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"binarize": binarize_transform,
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}
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NORM_TRANSFORMS = {
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"norm": imgnorm_transform,
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"percentile": percentilenorm_transform,
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"minmax": minmaxnorm_transform,
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}
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__all__ = [
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"IMG_TRANSFORMS",
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"NORM_TRANSFORMS",
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"INST_TRANSFORMS",
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"rigid_transforms",
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"non_rigid_transforms",
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"non_spatial_transforms",
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"hue_saturation_transforms",
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"blur_transforms",
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"random_crop",
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"center_crop",
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"resize",
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"compose",
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"apply_each",
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"to_tensor",
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"to_tensorv3",
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"cellpose_transform",
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"omnipose_transform",
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"hovernet_transform",
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"stardist_transform",
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"stardist_orig_transform",
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"dist_transform",
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"smooth_dist_transform",
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"contour_transform",
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"edgeweight_transform",
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"binarize_transform",
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"imgnorm_transform",
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"percentilenorm_transform",
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"minmaxnorm_transform",
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]

‎cellseg_models_pytorch/transforms/albu_transforms/__init__.py‎

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try:
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from ._composition import apply_each, compose, to_tensor, to_tensorv3
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from .img_transforms import (
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blur_transforms,
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center_crop,
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hue_saturation_transforms,
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non_rigid_transforms,
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non_spatial_transforms,
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random_crop,
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resize,
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rigid_transforms,
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)
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from .inst_transforms import (
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binarize_transform,
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cellpose_transform,
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contour_transform,
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dist_transform,
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edgeweight_transform,
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hovernet_transform,
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omnipose_transform,
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smooth_dist_transform,
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stardist_opt_transform,
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stardist_transform,
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)
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from .norm_transforms import (
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imgnorm_transform,
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minmaxnorm_transform,
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percentilenorm_transform,
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)
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IMG_TRANSFORMS = {
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"blur": blur_transforms,
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"center_crop": center_crop,
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"hue_sat": hue_saturation_transforms,
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"non_rigid": non_rigid_transforms,
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"rigid": rigid_transforms,
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"non_spatial": non_spatial_transforms,
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"resize": resize,
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"random_crop": random_crop,
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}
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INST_TRANSFORMS = {
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"cellpose": cellpose_transform,
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"omnipose": omnipose_transform,
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"hovernet": hovernet_transform,
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"stardist": stardist_transform,
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"stardist_opt": stardist_opt_transform,
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"contour": contour_transform,
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"dist": dist_transform,
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"edgeweight": edgeweight_transform,
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"smooth_dist": smooth_dist_transform,
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"binarize": binarize_transform,
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}
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NORM_TRANSFORMS = {
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"norm": imgnorm_transform,
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"percentile": percentilenorm_transform,
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"minmax": minmaxnorm_transform,
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}
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__all__ = [
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"IMG_TRANSFORMS",
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"NORM_TRANSFORMS",
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"INST_TRANSFORMS",
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"rigid_transforms",
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"non_rigid_transforms",
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"non_spatial_transforms",
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"hue_saturation_transforms",
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"blur_transforms",
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"random_crop",
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"center_crop",
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"resize",
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"compose",
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"apply_each",
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"to_tensor",
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"to_tensorv3",
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"cellpose_transform",
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"omnipose_transform",
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"hovernet_transform",
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"stardist_transform",
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"stardist_orig_transform",
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"dist_transform",
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"smooth_dist_transform",
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"contour_transform",
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"edgeweight_transform",
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"binarize_transform",
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"imgnorm_transform",
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"percentilenorm_transform",
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"minmaxnorm_transform",
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]
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except ModuleNotFoundError:
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raise ModuleNotFoundError(
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"To use the `csmp.transforms.albu_transforms` module, "
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"the albumentations lib is needed. Install with `pip install albumentations`"
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)

cellseg_models_pytorch/transforms/_composition.py renamed to cellseg_models_pytorch/transforms/albu_transforms/_composition.py

File renamed without changes.

cellseg_models_pytorch/transforms/img_transforms.py renamed to cellseg_models_pytorch/transforms/albu_transforms/img_transforms.py

File renamed without changes.

cellseg_models_pytorch/transforms/inst_transforms.py renamed to cellseg_models_pytorch/transforms/albu_transforms/inst_transforms.py

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@@ -4,9 +4,8 @@
44

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from cellseg_models_pytorch.utils import fix_duplicates
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from ..utils import binarize
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from ._composition import OnlyInstMapTransform
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from .functional import (
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from ...utils import binarize
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from ..functional import (
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gen_contour_maps,
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gen_dist_maps,
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gen_flow_maps,
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gen_weight_maps,
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smooth_distance,
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)
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from ._composition import OnlyInstMapTransform
2020

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__all__ = [
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"cellpose_transform",

cellseg_models_pytorch/transforms/norm_transforms.py renamed to cellseg_models_pytorch/transforms/albu_transforms/norm_transforms.py

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@@ -3,7 +3,7 @@
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import numpy as np
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from albumentations.core.transforms_interface import ImageOnlyTransform
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from ..utils import minmax_normalize, normalize, percentile_normalize
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from ...utils import minmax_normalize, normalize, percentile_normalize
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__all__ = ["imgnorm_transform", "percentilenorm_transform", "minmaxnorm_transform"]
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‎cellseg_models_pytorch/transforms/tests/test_full_pipeline.py‎

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import pytest
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import torch
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from cellseg_models_pytorch.transforms import (
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from cellseg_models_pytorch.transforms.albu_transforms import (
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apply_each,
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blur_transforms,
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cellpose_transform,

‎cellseg_models_pytorch/transforms/tests/test_img_transforms.py‎

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@@ -1,7 +1,7 @@
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import pytest
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import torch
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from cellseg_models_pytorch.transforms import (
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from cellseg_models_pytorch.transforms.albu_transforms import (
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blur_transforms,
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center_crop,
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compose,

‎cellseg_models_pytorch/transforms/tests/test_inst_transforms.py‎

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import numpy as np
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import pytest
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from cellseg_models_pytorch.transforms import (
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from cellseg_models_pytorch.transforms.albu_transforms import (
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apply_each,
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binarize_transform,
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cellpose_transform,

‎cellseg_models_pytorch/transforms/tests/test_norm_transforms.py‎

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import numpy as np
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import pytest
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4-
from cellseg_models_pytorch.transforms import (
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from cellseg_models_pytorch.transforms.albu_transforms import (
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compose,
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imgnorm_transform,
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minmaxnorm_transform,

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