Merge branch 'master' into 1155-savitzky-golay-kernel

Project-MONAI · Jan 13, 2021 · 759daf5 · 759daf5
2 parents db07bb3 + 3cb82cf
commit 759daf5
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Showing 18 changed files with 290 additions and 25 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -13,7 +13,7 @@ ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:20.10-py3
 
 FROM ${PYTORCH_IMAGE}
 
-MAINTAINER MONAI Consortium <monai.miccai2019@gmail.com>
+LABEL maintainer="monai.miccai2019@gmail.com"
 
 WORKDIR /opt/monai
 

diff --git a/docs/source/transforms.rst b/docs/source/transforms.rst
@@ -510,6 +510,18 @@ Utility
     :members:
     :special-members: __call__
 
+`ConvertToMultiChannelBasedOnBratsClasses`
+""""""""""""""""""""""""""""""""""""""""""
+.. autoclass:: ConvertToMultiChannelBasedOnBratsClasses
+    :members:
+    :special-members: __call__
+
+`AddExtremePointsChannel`
+"""""""""""""""""""""""""
+.. autoclass:: AddExtremePointsChannel
+    :members:
+    :special-members: __call__
+
 `TorchVision`
 """""""""""""
 .. autoclass:: TorchVision
@@ -981,6 +993,18 @@ Utility (Dict)
     :members:
     :special-members: __call__
 
+`ConvertToMultiChannelBasedOnBratsClassesd`
+"""""""""""""""""""""""""""""""""""""""""""
+.. autoclass:: ConvertToMultiChannelBasedOnBratsClassesd
+    :members:
+    :special-members: __call__
+
+`AddExtremePointsChanneld`
+""""""""""""""""""""""""""
+.. autoclass:: AddExtremePointsChanneld
+    :members:
+    :special-members: __call__
+
 `TorchVisiond`
 """"""""""""""
 .. autoclass:: TorchVisiond

diff --git a/monai/networks/utils.py b/monai/networks/utils.py
@@ -301,13 +301,13 @@ def train_mode(*nets: nn.Module):
     """
 
     # Get original state of network(s)
-    eval = [n for n in nets if not n.training]
+    eval_list = [n for n in nets if not n.training]
 
     try:
         # set to train mode
         with torch.set_grad_enabled(True):
             yield [n.train() for n in nets]
     finally:
-        # Return required networks to eval
-        for n in eval:
+        # Return required networks to eval_list
+        for n in eval_list:
             n.eval()
diff --git a/monai/transforms/__init__.py b/monai/transforms/__init__.py
@@ -139,7 +139,21 @@
     ThresholdIntensityDict,
 )
 from .io.array import LoadImage, LoadNifti, LoadNumpy, LoadPNG
-from .io.dictionary import LoadDatad, LoadImaged, LoadNiftid, LoadNumpyd, LoadPNGd
+from .io.dictionary import (
+    LoadDatad,
+    LoadImaged,
+    LoadImageD,
+    LoadImageDict,
+    LoadNiftid,
+    LoadNiftiD,
+    LoadNiftiDict,
+    LoadNumpyd,
+    LoadNumpyD,
+    LoadNumpyDict,
+    LoadPNGd,
+    LoadPNGD,
+    LoadPNGDict,
+)
 from .post.array import (
     Activations,
     AsDiscrete,
@@ -150,12 +164,24 @@
 )
 from .post.dictionary import (
     Activationsd,
+    ActivationsD,
+    ActivationsDict,
     AsDiscreted,
+    AsDiscreteD,
+    AsDiscreteDict,
     Ensembled,
     KeepLargestConnectedComponentd,
+    KeepLargestConnectedComponentD,
+    KeepLargestConnectedComponentDict,
     LabelToContourd,
+    LabelToContourD,
+    LabelToContourDict,
     MeanEnsembled,
+    MeanEnsembleD,
+    MeanEnsembleDict,
     VoteEnsembled,
+    VoteEnsembleD,
+    VoteEnsembleDict,
 )
 from .spatial.array import (
     Affine,
@@ -180,26 +206,55 @@
 )
 from .spatial.dictionary import (
     Flipd,
+    FlipD,
+    FlipDict,
     Orientationd,
+    OrientationD,
+    OrientationDict,
     Rand2DElasticd,
+    Rand2DElasticD,
+    Rand2DElasticDict,
     Rand3DElasticd,
+    Rand3DElasticD,
+    Rand3DElasticDict,
     RandAffined,
+    RandAffineD,
+    RandAffineDict,
     RandFlipd,
+    RandFlipD,
+    RandFlipDict,
     RandRotate90d,
+    RandRotate90D,
+    RandRotate90Dict,
     RandRotated,
+    RandRotateD,
+    RandRotateDict,
     RandZoomd,
+    RandZoomD,
+    RandZoomDict,
     Resized,
+    ResizeD,
+    ResizeDict,
     Rotate90d,
+    Rotate90D,
+    Rotate90Dict,
     Rotated,
+    RotateD,
+    RotateDict,
     Spacingd,
+    SpacingD,
+    SpacingDict,
     Zoomd,
+    ZoomD,
+    ZoomDict,
 )
 from .utility.array import (
     AddChannel,
     AddExtremePointsChannel,
     AsChannelFirst,
     AsChannelLast,
     CastToType,
+    ConvertToMultiChannelBasedOnBratsClasses,
     DataStats,
     FgBgToIndices,
     Identity,
@@ -216,27 +271,65 @@
 )
 from .utility.dictionary import (
     AddChanneld,
+    AddChannelD,
+    AddChannelDict,
     AddExtremePointsChanneld,
+    AddExtremePointsChannelD,
+    AddExtremePointsChannelDict,
     AsChannelFirstd,
+    AsChannelFirstD,
+    AsChannelFirstDict,
     AsChannelLastd,
+    AsChannelLastD,
+    AsChannelLastDict,
     CastToTyped,
+    CastToTypeD,
+    CastToTypeDict,
     ConcatItemsd,
+    ConcatItemsD,
+    ConcatItemsDict,
     ConvertToMultiChannelBasedOnBratsClassesd,
+    ConvertToMultiChannelBasedOnBratsClassesD,
+    ConvertToMultiChannelBasedOnBratsClassesDict,
     CopyItemsd,
+    CopyItemsD,
+    CopyItemsDict,
     DataStatsd,
+    DataStatsD,
+    DataStatsDict,
     DeleteItemsd,
+    DeleteItemsD,
+    DeleteItemsDict,
     FgBgToIndicesd,
+    FgBgToIndicesD,
+    FgBgToIndicesDict,
     Identityd,
+    IdentityD,
+    IdentityDict,
     LabelToMaskd,
+    LabelToMaskD,
+    LabelToMaskDict,
     Lambdad,
+    LambdaD,
+    LambdaDict,
     RepeatChanneld,
+    RepeatChannelD,
+    RepeatChannelDict,
     SelectItemsd,
     SimulateDelayd,
+    SimulateDelayD,
+    SimulateDelayDict,
     SplitChanneld,
+    SplitChannelD,
+    SplitChannelDict,
     SqueezeDimd,
+    SqueezeDimD,
+    SqueezeDimDict,
     ToNumpyd,
     TorchVisiond,
     ToTensord,
+    ToTensorD,
+    ToTensorDict,
 )
 from .utils import (
     apply_transform,

diff --git a/monai/transforms/io/dictionary.py b/monai/transforms/io/dictionary.py
@@ -24,7 +24,21 @@
 from monai.transforms.compose import MapTransform
 from monai.transforms.io.array import LoadImage, LoadNifti, LoadNumpy, LoadPNG
 
-__all__ = ["LoadImaged", "LoadDatad", "LoadNiftid", "LoadPNGd", "LoadNumpyd"]
+__all__ = [
+    "LoadImaged",
+    "LoadDatad",
+    "LoadNiftid",
+    "LoadPNGd",
+    "LoadNumpyd",
+    "LoadImageD",
+    "LoadImageDict",
+    "LoadNiftiD",
+    "LoadNiftiDict",
+    "LoadPNGD",
+    "LoadPNGDict",
+    "LoadNumpyD",
+    "LoadNumpyDict",
+]
 
 
 class LoadImaged(MapTransform):

diff --git a/monai/transforms/post/dictionary.py b/monai/transforms/post/dictionary.py
@@ -40,6 +40,18 @@
     "Ensembled",
     "MeanEnsembled",
     "VoteEnsembled",
+    "ActivationsD",
+    "ActivationsDict",
+    "AsDiscreteD",
+    "AsDiscreteDict",
+    "KeepLargestConnectedComponentD",
+    "KeepLargestConnectedComponentDict",
+    "LabelToContourD",
+    "LabelToContourDict",
+    "MeanEnsembleD",
+    "MeanEnsembleDict",
+    "VoteEnsembleD",
+    "VoteEnsembleDict",
 ]
 
 

diff --git a/monai/transforms/spatial/dictionary.py b/monai/transforms/spatial/dictionary.py
@@ -62,6 +62,34 @@
     "RandRotated",
     "Zoomd",
     "RandZoomd",
+    "SpacingD",
+    "SpacingDict",
+    "OrientationD",
+    "OrientationDict",
+    "Rotate90D",
+    "Rotate90Dict",
+    "RandRotate90D",
+    "RandRotate90Dict",
+    "ResizeD",
+    "ResizeDict",
+    "RandAffineD",
+    "RandAffineDict",
+    "Rand2DElasticD",
+    "Rand2DElasticDict",
+    "Rand3DElasticD",
+    "Rand3DElasticDict",
+    "FlipD",
+    "FlipDict",
+    "RandFlipD",
+    "RandFlipDict",
+    "RotateD",
+    "RotateDict",
+    "RandRotateD",
+    "RandRotateDict",
+    "ZoomD",
+    "ZoomDict",
+    "RandZoomD",
+    "RandZoomDict",
 ]
 
 GridSampleModeSequence = Union[Sequence[Union[GridSampleMode, str]], GridSampleMode, str]

diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
@@ -41,6 +41,7 @@
     "Lambda",
     "LabelToMask",
     "FgBgToIndices",
+    "ConvertToMultiChannelBasedOnBratsClasses",
     "AddExtremePointsChannel",
     "TorchVision",
 ]
@@ -556,6 +557,27 @@ def __call__(
         return fg_indices, bg_indices
 
 
+class ConvertToMultiChannelBasedOnBratsClasses(Transform):
+    """
+    Convert labels to multi channels based on brats18 classes:
+    label 1 is the necrotic and non-enhancing tumor core
+    label 2 is the the peritumoral edema
+    label 4 is the GD-enhancing tumor
+    The possible classes are TC (Tumor core), WT (Whole tumor)
+    and ET (Enhancing tumor).
+    """
+
+    def __call__(self, img: np.ndarray) -> np.ndarray:
+        result = []
+        # merge labels 1 (tumor non-enh) and 4 (tumor enh) to TC
+        result.append(np.logical_or(img == 1, img == 4))
+        # merge labels 1 (tumor non-enh) and 4 (tumor enh) and 2 (large edema) to WT
+        result.append(np.logical_or(np.logical_or(img == 1, img == 4), img == 2))
+        # label 4 is ET
+        result.append(img == 4)
+        return np.stack(result, axis=0).astype(np.float32)
+
+
 class AddExtremePointsChannel(Transform, Randomizable):
     """
     Add extreme points of label to the image as a new channel. This transform generates extreme