From 901c950a752fb8d953b445c2a34cba04202fedb1 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Tue, 27 Feb 2024 14:47:51 +0100
Subject: [PATCH] [common] Move reusable files to new common package
---
src/medbase/__init__.py | 0
src/{mednet => medbase}/data/__init__.py | 0
src/{mednet => medbase}/data/augmentations.py | 0
src/{mednet => medbase}/data/datamodule.py | 0
src/{mednet => medbase}/data/image_utils.py | 0
src/{mednet => medbase}/data/split.py | 2 +-
src/{mednet => medbase}/data/typing.py | 0
src/medbase/engine/__init__.py | 0
src/{mednet => medbase}/engine/callbacks.py | 0
src/{mednet => medbase}/engine/device.py | 0
src/{mednet => medbase}/engine/loggers.py | 0
src/{mednet => medbase}/engine/trainer.py | 0
src/medbase/utils/__init__.py | 0
src/{mednet => medbase}/utils/checkpointer.py | 0
src/{mednet => medbase}/utils/resources.py | 2 +-
src/medbase/utils/summary.py | 61 +++++++++++++++++++
src/{mednet => medbase}/utils/tensorboard.py | 0
src/mednet/config/data/hivtb/datamodule.py | 11 ++--
src/mednet/config/data/indian/datamodule.py | 5 +-
.../config/data/montgomery/datamodule.py | 11 ++--
.../data/montgomery_shenzhen/datamodule.py | 5 +-
.../montgomery_shenzhen_indian/datamodule.py | 5 +-
.../datamodule.py | 5 +-
.../datamodule.py | 5 +-
.../config/data/nih_cxr14/datamodule.py | 9 +--
.../data/nih_cxr14_padchest/datamodule.py | 5 +-
src/mednet/config/data/padchest/datamodule.py | 11 ++--
src/mednet/config/data/shenzhen/datamodule.py | 11 ++--
src/mednet/config/data/tbpoc/datamodule.py | 11 ++--
src/mednet/config/data/tbx11k/datamodule.py | 9 +--
src/mednet/engine/predictor.py | 3 +-
src/mednet/engine/saliency/completeness.py | 5 +-
src/mednet/engine/saliency/generator.py | 3 +-
src/mednet/models/alexnet.py | 2 +-
src/mednet/models/densenet.py | 2 +-
src/mednet/models/loss_weights.py | 2 +
src/mednet/models/model.py | 2 +-
src/mednet/models/pasa.py | 2 +-
src/mednet/models/separate.py | 3 +-
src/mednet/scripts/predict.py | 6 +-
src/mednet/scripts/saliency/completeness.py | 5 +-
src/mednet/scripts/saliency/generate.py | 6 +-
src/mednet/scripts/train.py | 7 ++-
src/mednet/scripts/train_analysis.py | 2 +-
tests/conftest.py | 5 +-
tests/test_cli.py | 14 ++---
tests/test_database_split.py | 3 +-
tests/test_image_utils.py | 3 +-
tests/test_summary.py | 19 ++++++
tests/test_transforms.py | 5 +-
50 files changed, 186 insertions(+), 81 deletions(-)
create mode 100644 src/medbase/__init__.py
rename src/{mednet => medbase}/data/__init__.py (100%)
rename src/{mednet => medbase}/data/augmentations.py (100%)
rename src/{mednet => medbase}/data/datamodule.py (100%)
rename src/{mednet => medbase}/data/image_utils.py (100%)
rename src/{mednet => medbase}/data/split.py (98%)
rename src/{mednet => medbase}/data/typing.py (100%)
create mode 100644 src/medbase/engine/__init__.py
rename src/{mednet => medbase}/engine/callbacks.py (100%)
rename src/{mednet => medbase}/engine/device.py (100%)
rename src/{mednet => medbase}/engine/loggers.py (100%)
rename src/{mednet => medbase}/engine/trainer.py (100%)
create mode 100644 src/medbase/utils/__init__.py
rename src/{mednet => medbase}/utils/checkpointer.py (100%)
rename src/{mednet => medbase}/utils/resources.py (99%)
create mode 100644 src/medbase/utils/summary.py
rename src/{mednet => medbase}/utils/tensorboard.py (100%)
create mode 100644 tests/test_summary.py
diff --git a/src/medbase/__init__.py b/src/medbase/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/mednet/data/__init__.py b/src/medbase/data/__init__.py
similarity index 100%
rename from src/mednet/data/__init__.py
rename to src/medbase/data/__init__.py
diff --git a/src/mednet/data/augmentations.py b/src/medbase/data/augmentations.py
similarity index 100%
rename from src/mednet/data/augmentations.py
rename to src/medbase/data/augmentations.py
diff --git a/src/mednet/data/datamodule.py b/src/medbase/data/datamodule.py
similarity index 100%
rename from src/mednet/data/datamodule.py
rename to src/medbase/data/datamodule.py
diff --git a/src/mednet/data/image_utils.py b/src/medbase/data/image_utils.py
similarity index 100%
rename from src/mednet/data/image_utils.py
rename to src/medbase/data/image_utils.py
diff --git a/src/mednet/data/split.py b/src/medbase/data/split.py
similarity index 98%
rename from src/mednet/data/split.py
rename to src/medbase/data/split.py
index 3bf8b8ca..0bcdf300 100644
--- a/src/mednet/data/split.py
+++ b/src/medbase/data/split.py
@@ -12,7 +12,7 @@ import typing
import torch
-from .typing import DatabaseSplit, RawDataLoader
+from medbase.data.typing import DatabaseSplit, RawDataLoader
logger = logging.getLogger(__name__)
diff --git a/src/mednet/data/typing.py b/src/medbase/data/typing.py
similarity index 100%
rename from src/mednet/data/typing.py
rename to src/medbase/data/typing.py
diff --git a/src/medbase/engine/__init__.py b/src/medbase/engine/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/mednet/engine/callbacks.py b/src/medbase/engine/callbacks.py
similarity index 100%
rename from src/mednet/engine/callbacks.py
rename to src/medbase/engine/callbacks.py
diff --git a/src/mednet/engine/device.py b/src/medbase/engine/device.py
similarity index 100%
rename from src/mednet/engine/device.py
rename to src/medbase/engine/device.py
diff --git a/src/mednet/engine/loggers.py b/src/medbase/engine/loggers.py
similarity index 100%
rename from src/mednet/engine/loggers.py
rename to src/medbase/engine/loggers.py
diff --git a/src/mednet/engine/trainer.py b/src/medbase/engine/trainer.py
similarity index 100%
rename from src/mednet/engine/trainer.py
rename to src/medbase/engine/trainer.py
diff --git a/src/medbase/utils/__init__.py b/src/medbase/utils/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/mednet/utils/checkpointer.py b/src/medbase/utils/checkpointer.py
similarity index 100%
rename from src/mednet/utils/checkpointer.py
rename to src/medbase/utils/checkpointer.py
diff --git a/src/mednet/utils/resources.py b/src/medbase/utils/resources.py
similarity index 99%
rename from src/mednet/utils/resources.py
rename to src/medbase/utils/resources.py
index 5b8844a1..58167711 100644
--- a/src/mednet/utils/resources.py
+++ b/src/medbase/utils/resources.py
@@ -18,7 +18,7 @@ import warnings
import numpy
import psutil
-from ..engine.device import SupportedPytorchDevice
+from medbase.engine.device import SupportedPytorchDevice
logger = logging.getLogger(__name__)
diff --git a/src/medbase/utils/summary.py b/src/medbase/utils/summary.py
new file mode 100644
index 00000000..bff705e3
--- /dev/null
+++ b/src/medbase/utils/summary.py
@@ -0,0 +1,61 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+# Adapted from https://github.com/pytorch/pytorch/issues/2001#issuecomment-405675488
+
+from functools import reduce
+
+import torch
+
+from torch.nn.modules.module import _addindent
+
+
+# ignore this space!
+def _repr(model: torch.nn.Module) -> tuple[str, int]:
+ # We treat the extra repr like the sub-module, one item per line
+ extra_lines = []
+ extra_repr = model.extra_repr()
+ # empty string will be split into list ['']
+ if extra_repr:
+ extra_lines = extra_repr.split("\n")
+ child_lines = []
+ total_params = 0
+ for key, module in model._modules.items():
+ mod_str, num_params = _repr(module)
+ mod_str = _addindent(mod_str, 2)
+ child_lines.append("(" + key + "): " + mod_str)
+ total_params += num_params
+ lines = extra_lines + child_lines
+
+ for _, p in model._parameters.items():
+ if hasattr(p, "dtype"):
+ total_params += reduce(lambda x, y: x * y, p.shape)
+
+ main_str = model._get_name() + "("
+ if lines:
+ # simple one-liner info, which most builtin Modules will use
+ if len(extra_lines) == 1 and not child_lines:
+ main_str += extra_lines[0]
+ else:
+ main_str += "\n " + "\n ".join(lines) + "\n"
+
+ main_str += ")"
+ main_str += f", {total_params:,} params"
+ return main_str, total_params
+
+
+def summary(model: torch.nn.Module) -> tuple[str, int]:
+ """Count the number of parameters in each model layer.
+
+ Parameters
+ ----------
+ model
+ Model to summarize.
+
+ Returns
+ -------
+ tuple[int, str]
+ A tuple containing a multiline string representation of the network and the number of parameters.
+ """
+ return _repr(model)
diff --git a/src/mednet/utils/tensorboard.py b/src/medbase/utils/tensorboard.py
similarity index 100%
rename from src/mednet/utils/tensorboard.py
rename to src/medbase/utils/tensorboard.py
diff --git a/src/mednet/config/data/hivtb/datamodule.py b/src/mednet/config/data/hivtb/datamodule.py
index 6c674085..21f773b2 100644
--- a/src/mednet/config/data/hivtb/datamodule.py
+++ b/src/mednet/config/data/hivtb/datamodule.py
@@ -12,11 +12,12 @@ import pathlib
import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ....data.datamodule import CachingDataModule
-from ....data.image_utils import remove_black_borders
-from ....data.split import make_split
-from ....data.typing import RawDataLoader as _BaseRawDataLoader
-from ....data.typing import Sample
+from medbase.data.datamodule import CachingDataModule
+from medbase.data.image_utils import remove_black_borders
+from medbase.data.split import make_split
+from medbase.data.typing import RawDataLoader as _BaseRawDataLoader
+from medbase.data.typing import Sample
+
from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
diff --git a/src/mednet/config/data/indian/datamodule.py b/src/mednet/config/data/indian/datamodule.py
index fa285170..f6825bba 100644
--- a/src/mednet/config/data/indian/datamodule.py
+++ b/src/mednet/config/data/indian/datamodule.py
@@ -8,9 +8,10 @@ Database reference: [INDIAN-2013]_
import pathlib
+from medbase.data.datamodule import CachingDataModule
+from medbase.data.split import make_split
+
from ....config.data.shenzhen.datamodule import RawDataLoader
-from ....data.datamodule import CachingDataModule
-from ....data.split import make_split
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
diff --git a/src/mednet/config/data/montgomery/datamodule.py b/src/mednet/config/data/montgomery/datamodule.py
index 98d591ae..64b2f7ff 100644
--- a/src/mednet/config/data/montgomery/datamodule.py
+++ b/src/mednet/config/data/montgomery/datamodule.py
@@ -12,11 +12,12 @@ import pathlib
import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ....data.datamodule import CachingDataModule
-from ....data.image_utils import remove_black_borders
-from ....data.split import make_split
-from ....data.typing import RawDataLoader as _BaseRawDataLoader
-from ....data.typing import Sample
+from medbase.data.datamodule import CachingDataModule
+from medbase.data.image_utils import remove_black_borders
+from medbase.data.split import make_split
+from medbase.data.typing import Sample
+from medbase.data.typing import RawDataLoader as _BaseRawDataLoader
+
from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
diff --git a/src/mednet/config/data/montgomery_shenzhen/datamodule.py b/src/mednet/config/data/montgomery_shenzhen/datamodule.py
index f726a431..16dfec25 100644
--- a/src/mednet/config/data/montgomery_shenzhen/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen/datamodule.py
@@ -5,8 +5,9 @@
import pathlib
-from ....data.datamodule import ConcatDataModule
-from ....data.split import make_split
+from medbase.data.datamodule import ConcatDataModule
+from medbase.data.split import make_split
+
from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
index f75eb1e5..bfeb1a33 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
@@ -7,8 +7,9 @@ databases.
import pathlib
-from ....data.datamodule import ConcatDataModule
-from ....data.split import make_split
+from medbase.data.datamodule import ConcatDataModule
+from medbase.data.split import make_split
+
from ..indian.datamodule import CONFIGURATION_KEY_DATADIR as INDIAN_KEY_DATADIR
from ..indian.datamodule import DataModule as IndianDataModule
from ..indian.datamodule import RawDataLoader as IndianLoader
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
index 060f6231..268ba2a2 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
@@ -7,8 +7,9 @@ datasets.
import pathlib
-from ....data.datamodule import ConcatDataModule
-from ....data.split import make_split
+from medbase.data.datamodule import ConcatDataModule
+from medbase.data.split import make_split
+
from ..indian.datamodule import CONFIGURATION_KEY_DATADIR as INDIAN_KEY_DATADIR
from ..indian.datamodule import DataModule as IndianDataModule
from ..indian.datamodule import RawDataLoader as IndianLoader
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
index db2f7901..932e6571 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
@@ -7,8 +7,9 @@ datasets.
import pathlib
-from ....data.datamodule import ConcatDataModule
-from ....data.split import make_split
+from medbase.data.datamodule import ConcatDataModule
+from medbase.data.split import make_split
+
from ..indian.datamodule import CONFIGURATION_KEY_DATADIR as INDIAN_KEY_DATADIR
from ..indian.datamodule import DataModule as IndianDataModule
from ..indian.datamodule import RawDataLoader as IndianLoader
diff --git a/src/mednet/config/data/nih_cxr14/datamodule.py b/src/mednet/config/data/nih_cxr14/datamodule.py
index 6d6b283e..8e72d6d4 100644
--- a/src/mednet/config/data/nih_cxr14/datamodule.py
+++ b/src/mednet/config/data/nih_cxr14/datamodule.py
@@ -12,10 +12,11 @@ import pathlib
import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ....data.datamodule import CachingDataModule
-from ....data.split import make_split
-from ....data.typing import RawDataLoader as _BaseRawDataLoader
-from ....data.typing import Sample
+from medbase.data.datamodule import CachingDataModule
+from medbase.data.split import make_split
+from medbase.data.typing import Sample
+from medbase.data.typing import RawDataLoader as _BaseRawDataLoader
+
from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
diff --git a/src/mednet/config/data/nih_cxr14_padchest/datamodule.py b/src/mednet/config/data/nih_cxr14_padchest/datamodule.py
index bfd17daf..3de000c1 100644
--- a/src/mednet/config/data/nih_cxr14_padchest/datamodule.py
+++ b/src/mednet/config/data/nih_cxr14_padchest/datamodule.py
@@ -5,8 +5,9 @@
import pathlib
-from ....data.datamodule import ConcatDataModule
-from ....data.split import make_split
+from medbase.data.datamodule import ConcatDataModule
+from medbase.data.split import make_split
+
from ..nih_cxr14.datamodule import RawDataLoader as CXR14Loader
from ..padchest.datamodule import RawDataLoader as PadchestLoader
diff --git a/src/mednet/config/data/padchest/datamodule.py b/src/mednet/config/data/padchest/datamodule.py
index 97c80a13..99545ee2 100644
--- a/src/mednet/config/data/padchest/datamodule.py
+++ b/src/mednet/config/data/padchest/datamodule.py
@@ -13,11 +13,12 @@ import numpy
import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ....data.datamodule import CachingDataModule
-from ....data.image_utils import remove_black_borders
-from ....data.split import make_split
-from ....data.typing import RawDataLoader as _BaseRawDataLoader
-from ....data.typing import Sample
+from medbase.data.datamodule import CachingDataModule
+from medbase.data.image_utils import remove_black_borders
+from medbase.data.split import make_split
+from medbase.data.typing import Sample
+from medbase.data.typing import RawDataLoader as _BaseRawDataLoader
+
from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
diff --git a/src/mednet/config/data/shenzhen/datamodule.py b/src/mednet/config/data/shenzhen/datamodule.py
index c2838ce2..ae1b4639 100644
--- a/src/mednet/config/data/shenzhen/datamodule.py
+++ b/src/mednet/config/data/shenzhen/datamodule.py
@@ -12,11 +12,12 @@ import pathlib
import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ....data.datamodule import CachingDataModule
-from ....data.image_utils import remove_black_borders
-from ....data.split import make_split
-from ....data.typing import RawDataLoader as _BaseRawDataLoader
-from ....data.typing import Sample
+from medbase.data.datamodule import CachingDataModule
+from medbase.data.image_utils import remove_black_borders
+from medbase.data.split import make_split
+from medbase.data.typing import Sample
+from medbase.data.typing import RawDataLoader as _BaseRawDataLoader
+
from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
diff --git a/src/mednet/config/data/tbpoc/datamodule.py b/src/mednet/config/data/tbpoc/datamodule.py
index 3e7dcaa2..5b4b6011 100644
--- a/src/mednet/config/data/tbpoc/datamodule.py
+++ b/src/mednet/config/data/tbpoc/datamodule.py
@@ -8,11 +8,12 @@ import pathlib
import PIL.Image
from torchvision.transforms.functional import to_tensor
-from ....data.datamodule import CachingDataModule
-from ....data.image_utils import remove_black_borders
-from ....data.split import make_split
-from ....data.typing import RawDataLoader as _BaseRawDataLoader
-from ....data.typing import Sample
+from medbase.data.datamodule import CachingDataModule
+from medbase.data.image_utils import remove_black_borders
+from medbase.data.split import make_split
+from medbase.data.typing import Sample
+from medbase.data.typing import RawDataLoader as _BaseRawDataLoader
+
from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
diff --git a/src/mednet/config/data/tbx11k/datamodule.py b/src/mednet/config/data/tbx11k/datamodule.py
index 993f9e50..c6b28ef9 100644
--- a/src/mednet/config/data/tbx11k/datamodule.py
+++ b/src/mednet/config/data/tbx11k/datamodule.py
@@ -13,10 +13,11 @@ import typing_extensions
from torch.utils.data._utils.collate import default_collate_fn_map
from torchvision.transforms.functional import to_tensor
-from ....data.datamodule import CachingDataModule
-from ....data.split import make_split
-from ....data.typing import RawDataLoader as _BaseRawDataLoader
-from ....data.typing import Sample
+from medbase.data.datamodule import CachingDataModule
+from medbase.data.split import make_split
+from medbase.data.typing import RawDataLoader as _BaseRawDataLoader
+from medbase.data.typing import Sample
+
from ....utils.rc import load_rc
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
diff --git a/src/mednet/engine/predictor.py b/src/mednet/engine/predictor.py
index 1ba6f05a..fce844a1 100644
--- a/src/mednet/engine/predictor.py
+++ b/src/mednet/engine/predictor.py
@@ -7,13 +7,14 @@ import logging
import lightning.pytorch
import torch.utils.data
+from medbase.engine.device import DeviceManager
+
from ..models.typing import (
BinaryPrediction,
BinaryPredictionSplit,
MultiClassPrediction,
MultiClassPredictionSplit,
)
-from .device import DeviceManager
logger = logging.getLogger(__name__)
diff --git a/src/mednet/engine/saliency/completeness.py b/src/mednet/engine/saliency/completeness.py
index eb2832bc..7c3cb3c6 100644
--- a/src/mednet/engine/saliency/completeness.py
+++ b/src/mednet/engine/saliency/completeness.py
@@ -17,9 +17,10 @@ from pytorch_grad_cam.metrics.road import (
)
from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget
-from ...data.typing import Sample
+from medbase.data.typing import Sample
+from medbase.engine.device import DeviceManager
+
from ...models.typing import SaliencyMapAlgorithm
-from ..device import DeviceManager
logger = logging.getLogger(__name__)
diff --git a/src/mednet/engine/saliency/generator.py b/src/mednet/engine/saliency/generator.py
index e1c03af7..f440eb08 100644
--- a/src/mednet/engine/saliency/generator.py
+++ b/src/mednet/engine/saliency/generator.py
@@ -12,8 +12,9 @@ import torch
import torch.nn
import tqdm
+from medbase.engine.device import DeviceManager
+
from ...models.typing import SaliencyMapAlgorithm
-from ..device import DeviceManager
logger = logging.getLogger(__name__)
diff --git a/src/mednet/models/alexnet.py b/src/mednet/models/alexnet.py
index 3e58463e..22c41547 100644
--- a/src/mednet/models/alexnet.py
+++ b/src/mednet/models/alexnet.py
@@ -12,7 +12,7 @@ import torch.utils.data
import torchvision.models as models
import torchvision.transforms
-from ..data.typing import TransformSequence
+from medbase.data.typing import TransformSequence
from .model import Model
from .separate import separate
from .transforms import RGB, SquareCenterPad
diff --git a/src/mednet/models/densenet.py b/src/mednet/models/densenet.py
index c54d5d9a..3feb2ade 100644
--- a/src/mednet/models/densenet.py
+++ b/src/mednet/models/densenet.py
@@ -12,7 +12,7 @@ import torch.utils.data
import torchvision.models as models
import torchvision.transforms
-from ..data.typing import TransformSequence
+from medbase.data.typing import TransformSequence
from .model import Model
from .separate import separate
from .transforms import RGB, SquareCenterPad
diff --git a/src/mednet/models/loss_weights.py b/src/mednet/models/loss_weights.py
index 2cf5e292..382a7ae5 100644
--- a/src/mednet/models/loss_weights.py
+++ b/src/mednet/models/loss_weights.py
@@ -9,6 +9,8 @@ from collections import Counter
import torch
import torch.utils.data
+from medbase.data.typing import DataLoader
+
logger = logging.getLogger(__name__)
diff --git a/src/mednet/models/model.py b/src/mednet/models/model.py
index 560b1115..e1b264be 100644
--- a/src/mednet/models/model.py
+++ b/src/mednet/models/model.py
@@ -12,7 +12,7 @@ import torch.optim.optimizer
import torch.utils.data
import torchvision.transforms
-from ..data.typing import TransformSequence
+from medbase.data.typing import TransformSequence
from .loss_weights import get_positive_weights
from .typing import Checkpoint
diff --git a/src/mednet/models/pasa.py b/src/mednet/models/pasa.py
index cb7ebfea..0e1d24f1 100644
--- a/src/mednet/models/pasa.py
+++ b/src/mednet/models/pasa.py
@@ -12,7 +12,7 @@ import torch.optim.optimizer
import torch.utils.data
import torchvision.transforms
-from ..data.typing import TransformSequence
+from medbase.data.typing import TransformSequence
from .model import Model
from .separate import separate
from .transforms import Grayscale, SquareCenterPad
diff --git a/src/mednet/models/separate.py b/src/mednet/models/separate.py
index c79820bf..6c7afabb 100644
--- a/src/mednet/models/separate.py
+++ b/src/mednet/models/separate.py
@@ -7,7 +7,8 @@ import typing
import torch
-from ..data.typing import Sample
+from medbase.data.typing import Sample
+
from .typing import BinaryPrediction, MultiClassPrediction
diff --git a/src/mednet/scripts/predict.py b/src/mednet/scripts/predict.py
index 5645685a..ffd42aff 100644
--- a/src/mednet/scripts/predict.py
+++ b/src/mednet/scripts/predict.py
@@ -134,9 +134,9 @@ def predict(
import shutil
import typing
- from ..engine.device import DeviceManager
- from ..engine.predictor import run
- from ..utils.checkpointer import get_checkpoint_to_run_inference
+ from medbase.engine.device import DeviceManager
+ from mednet.engine.predictor import run
+ from medbase.utils.checkpointer import get_checkpoint_to_run_inference
from .utils import (
device_properties,
execution_metadata,
diff --git a/src/mednet/scripts/saliency/completeness.py b/src/mednet/scripts/saliency/completeness.py
index e02aa3b6..28a33695 100644
--- a/src/mednet/scripts/saliency/completeness.py
+++ b/src/mednet/scripts/saliency/completeness.py
@@ -203,9 +203,10 @@ def completeness(
"""
import json
- from ...engine.device import DeviceManager
+ from medbase.engine.device import DeviceManager
+ from medbase.utils.checkpointer import get_checkpoint_to_run_inference
+
from ...engine.saliency.completeness import run
- from ...utils.checkpointer import get_checkpoint_to_run_inference
if device in ("cuda", "mps") and (parallel == 0 or parallel > 1):
raise RuntimeError(
diff --git a/src/mednet/scripts/saliency/generate.py b/src/mednet/scripts/saliency/generate.py
index 649ad96b..34fb8382 100644
--- a/src/mednet/scripts/saliency/generate.py
+++ b/src/mednet/scripts/saliency/generate.py
@@ -168,9 +168,11 @@ def generate(
The quality of saliency information depends on the saliency map
algorithm and trained model.
"""
- from ...engine.device import DeviceManager
+
+ from medbase.engine.device import DeviceManager
+ from medbase.utils.checkpointer import get_checkpoint_to_run_inference
+
from ...engine.saliency.generator import run
- from ...utils.checkpointer import get_checkpoint_to_run_inference
logger.info(f"Output folder: {output_folder}")
output_folder.mkdir(parents=True, exist_ok=True)
diff --git a/src/mednet/scripts/train.py b/src/mednet/scripts/train.py
index 42ecf1b8..df8b1fec 100644
--- a/src/mednet/scripts/train.py
+++ b/src/mednet/scripts/train.py
@@ -272,9 +272,10 @@ def train(
import torch
from lightning.pytorch import seed_everything
- from ..engine.device import DeviceManager
- from ..engine.trainer import run
- from ..utils.checkpointer import get_checkpoint_to_resume_training
+ from medbase.engine.device import DeviceManager
+ from medbase.engine.trainer import run
+ from medbase.utils.checkpointer import get_checkpoint_to_resume_training
+
from .utils import (
device_properties,
execution_metadata,
diff --git a/src/mednet/scripts/train_analysis.py b/src/mednet/scripts/train_analysis.py
index 80e74e44..3938e226 100644
--- a/src/mednet/scripts/train_analysis.py
+++ b/src/mednet/scripts/train_analysis.py
@@ -231,7 +231,7 @@ def train_analysis(
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
- from ..utils.tensorboard import scalars_to_dict
+ from medbase.utils.tensorboard import scalars_to_dict
data = scalars_to_dict(logdir)
diff --git a/tests/conftest.py b/tests/conftest.py
index a2127bcb..89b055ec 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -10,8 +10,9 @@ import numpy
import numpy.typing
import pytest
import torch
-from mednet.data.split import JSONDatabaseSplit
-from mednet.data.typing import DatabaseSplit
+
+from medbase.data.split import JSONDatabaseSplit
+from medbase.data.typing import DatabaseSplit
@pytest.fixture
diff --git a/tests/test_cli.py b/tests/test_cli.py
index e79d500d..ab6abe57 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -204,11 +204,11 @@ def test_upload_help():
@pytest.mark.slow
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_train_pasa_montgomery(temporary_basedir):
- from mednet.scripts.train import train
- from mednet.utils.checkpointer import (
+ from medbase.utils.checkpointer import (
CHECKPOINT_EXTENSION,
_get_checkpoint_from_alias,
)
+ from mednet.scripts.train import train
runner = CliRunner()
@@ -260,11 +260,11 @@ def test_train_pasa_montgomery(temporary_basedir):
@pytest.mark.slow
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_train_pasa_montgomery_from_checkpoint(temporary_basedir):
- from mednet.scripts.train import train
- from mednet.utils.checkpointer import (
+ from medbase.utils.checkpointer import (
CHECKPOINT_EXTENSION,
_get_checkpoint_from_alias,
)
+ from mednet.scripts.train import train
runner = CliRunner()
@@ -337,12 +337,12 @@ def test_train_pasa_montgomery_from_checkpoint(temporary_basedir):
@pytest.mark.slow
@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
-def test_predict_pasa_montgomery(temporary_basedir):
- from mednet.scripts.predict import predict
- from mednet.utils.checkpointer import (
+def test_predict_pasa_montgomery(temporary_basedir, datadir):
+ from medbase.utils.checkpointer import (
CHECKPOINT_EXTENSION,
_get_checkpoint_from_alias,
)
+ from mednet.scripts.predict import predict
runner = CliRunner()
diff --git a/tests/test_database_split.py b/tests/test_database_split.py
index 8f50ed99..7ebe400a 100644
--- a/tests/test_database_split.py
+++ b/tests/test_database_split.py
@@ -3,8 +3,7 @@
# SPDX-License-Identifier: GPL-3.0-or-later
"""Test code for datasets."""
-from mednet.data.split import JSONDatabaseSplit
-
+from medbase.data.split import JSONDatabaseSplit
def test_json_loading(datadir):
# tests if we can build a simple JSON loader for the Iris Flower dataset
diff --git a/tests/test_image_utils.py b/tests/test_image_utils.py
index ab431eca..d81501ad 100644
--- a/tests/test_image_utils.py
+++ b/tests/test_image_utils.py
@@ -5,7 +5,8 @@
import numpy
import PIL.Image
-from mednet.data.image_utils import remove_black_borders
+
+from medbase.data.image_utils import remove_black_borders
def test_remove_black_borders(datadir):
diff --git a/tests/test_summary.py b/tests/test_summary.py
new file mode 100644
index 00000000..4e420eb2
--- /dev/null
+++ b/tests/test_summary.py
@@ -0,0 +1,19 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+import unittest
+
+import mednet.config.models.pasa as pasa_config
+
+from medbase.utils.summary import summary
+
+
+class Tester(unittest.TestCase):
+ """Unit test for model architectures."""
+
+ def test_summary_driu(self):
+ model = pasa_config.model
+ s, param = summary(model)
+ self.assertIsInstance(s, str)
+ self.assertIsInstance(param, int)
diff --git a/tests/test_transforms.py b/tests/test_transforms.py
index 2d8faf1e..85f59958 100644
--- a/tests/test_transforms.py
+++ b/tests/test_transforms.py
@@ -5,8 +5,9 @@
import numpy
import PIL.Image
-import torchvision.transforms.functional as F # noqa: N812
-from mednet.data.augmentations import ElasticDeformation
+import torchvision.transforms.functional as F # noqa: N812
+
+from medbase.data.augmentations import ElasticDeformation
def test_elastic_deformation(datadir):
--
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