Feature/2231 transforms by rijobro · Pull Request #2278 · Project-MONAI/MONAI

rijobro · 2021-05-28T17:03:09Z

Description

I've sorted transforms into TorchTransforms and/or NumpyTransforms.

TorchTransform: convert input to torch, do transform, convert back to original
NumpyTransform: convert input to numpy, do transform, convert back to original
Both TorchTransform and NumpyTransform: no need for conversion (e.g., img[None])

I've also added some enums to try and unify the input types:

class DataObjects:
    """Common classes used for arrays/tensors and then their usage in dict/mappings."""

    Images = Union[torch.Tensor, np.ndarray]
    Dict = Dict[Hashable, Any]
    Mapping = Mapping[Hashable, Any]

We can keep a track of progress with:

from monai import transforms
from inspect import getmembers, isclass
for n,obj in getmembers(transforms):
    if isclass(obj) and issubclass(obj,transforms.Transform) and not issubclass(obj,transforms.MapTransform):
        print(n)

And we can add in is not TorchTransform and is not NumpyTransform, etc. to see which are yet to be considered.

Status

Ready/Work in progress/Hold

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: Richard Brown <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

…atedChannel Signed-off-by: Richard Brown <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

rijobro · 2021-06-02T16:19:15Z

@wyli @Nic-Ma @ericspod I think this commit might be interesting.

I made RandRicianNoise available for both numpy and torch inputs. I realised we couldn't fix the seed for the torch random generators, so I followed this StackOverflow post.

Now we can use self.R and self.R_torch for random generation with numpy and torch, respectively.

Signed-off-by: Richard Brown <[email protected]>

rijobro · 2021-08-23T10:41:13Z

Current state of proposed transforms as I start merging them into MONAI:

TorchOrNumpy:  Activations
TorchOrNumpy:  AddChannel
TorchOrNumpy:  AddCoordinateChannels
Torch:         AddExtremePointsChannel
TorchOrNumpy:  AdjustContrast
Torch:         Affine
Torch:         AffineGrid
TorchOrNumpy:  AsChannelFirst
TorchOrNumpy:  AsChannelLast
TorchOrNumpy:  AsDiscrete
Uncategorised: BatchInverseTransform
TorchOrNumpy:  BorderPad
TorchOrNumpy:  BoundingRect
TorchOrNumpy:  CastToType
TorchOrNumpy:  CenterScaleCrop
TorchOrNumpy:  CenterSpatialCrop
TorchOrNumpy:  ClassesToIndices
TorchOrNumpy:  ConvertToMultiChannelBasedOnBratsClasses
TorchOrNumpy:  CropForeground
TorchOrNumpy:  DataStats
Torch:         DetectEnvelope
TorchOrNumpy:  DivisiblePad
Torch:         EnsureChannelFirst
Uncategorised: EnsureType
TorchOrNumpy:  FgBgToIndices
Torch:         Flip
Torch:         GaussianSharpen
Torch:         GaussianSmooth
TorchOrNumpy:  GibbsNoise
TorchOrNumpy:  Identity
TorchOrNumpy:  KSpaceSpikeNoise
Torch:         KeepLargestConnectedComponent
Torch:         LabelToContour
TorchOrNumpy:  LabelToMask
TorchOrNumpy:  MaskIntensity
TorchOrNumpy:  MeanEnsemble
TorchOrNumpy:  NormalizeIntensity
Numpy:         Orientation
TorchOrNumpy:  Pad
TorchOrNumpy:  PadListDataCollate
Torch:         ProbNMS
Torch:         Rand2DElastic
Torch:         Rand3DElastic
TorchOrNumpy:  RandAdjustContrast
Torch:         RandAffine
Torch:         RandAffineGrid
Torch:         RandAxisFlip
TorchOrNumpy:  RandBiasField
TorchOrNumpy:  RandCoarseDropout
TorchOrNumpy:  RandCropByLabelClasses
TorchOrNumpy:  RandCropByPosNegLabel
TorchOrNumpy:  RandDeformGrid
Torch:         RandFlip
TorchOrNumpy:  RandGaussianNoise
Torch:         RandGaussianSharpen
Torch:         RandGaussianSmooth
TorchOrNumpy:  RandGibbsNoise
Numpy:         RandHistogramShift
TorchOrNumpy:  RandKSpaceSpikeNoise
Uncategorised: RandLambda
TorchOrNumpy:  RandRicianNoise
Torch:         RandRotate
TorchOrNumpy:  RandRotate90
TorchOrNumpy:  RandScaleCrop
TorchOrNumpy:  RandScaleIntensity
TorchOrNumpy:  RandShiftIntensity
TorchOrNumpy:  RandSpatialCrop
TorchOrNumpy:  RandSpatialCropSamples
TorchOrNumpy:  RandStdShiftIntensity
TorchOrNumpy:  RandWeightedCrop
Torch:         RandZoom
TorchOrNumpy:  RemoveRepeatedChannel
TorchOrNumpy:  RepeatChannel
Torch:         Resample
Torch:         Resize
TorchOrNumpy:  ResizeWithPadOrCrop
Torch:         Rotate
TorchOrNumpy:  Rotate90
TorchOrNumpy:  SaveImage
Torch:         SavitzkyGolaySmooth
TorchOrNumpy:  ScaleIntensity
TorchOrNumpy:  ScaleIntensityRange
TorchOrNumpy:  ScaleIntensityRangePercentiles
TorchOrNumpy:  ShiftIntensity
TorchOrNumpy:  SimulateDelay
Torch:         Spacing
TorchOrNumpy:  SpatialCrop
TorchOrNumpy:  SpatialPad
TorchOrNumpy:  SplitChannel
TorchOrNumpy:  SqueezeDim
TorchOrNumpy:  StdShiftIntensity
TorchOrNumpy:  ThresholdIntensity
TorchOrNumpy:  ToNumpy
Torch:         ToTensor
TorchOrNumpy:  Transpose
TorchOrNumpy:  VoteEnsemble
Torch:         Zoom

wyli · 2021-11-05T10:46:36Z

feature merged into dev

rijobro and others added 14 commits May 27, 2021 13:52

torch default for Flip

7d5e639

Signed-off-by: Richard Brown <[email protected]>

correct doc

b01d6bc

Signed-off-by: Richard Brown <[email protected]>

return type

218a93c

Signed-off-by: Richard Brown <[email protected]>

typing

7911ee5

Signed-off-by: Richard Brown <[email protected]>

use types instead of bools

1d38104

Signed-off-by: Richard Brown <[email protected]>

Merge remote-tracking branch 'MONAI/dev' into torch_default_flip

9a6a1ad

update var name

6ade9c3

Signed-off-by: Richard Brown <[email protected]>

abstract common functionality

427ee2f

Signed-off-by: Richard Brown <[email protected]>

torch default

5105508

Signed-off-by: Richard Brown <[email protected]>

Merge branch 'torch_default' into feature/2231-transforms

ce26166

to_numpy, to_tensor, transpose

5680d9e

Signed-off-by: Richard Brown <[email protected]>

add todotransform

d921834

Signed-off-by: Richard Brown <[email protected]>

Merge branch 'dev' into feature/2231-transforms

dc68510

full ci/cd for feature branches

59a7ce7

Signed-off-by: Wenqi Li <[email protected]>

wyli force-pushed the feature/2231-transforms branch from 1c35763 to 59a7ce7 Compare May 30, 2021 15:13

wyli added the Module: transform data transforms for preprocessing and postprocessing. label May 30, 2021

rijobro and others added 13 commits June 1, 2021 14:01

more transforms

4662522

Signed-off-by: Richard Brown <[email protected]>

Merge remote-tracking branch 'MONAI/dev' into feature/2231-transforms

257952b

SpatialCrop, CenterSpatialCrop, AsDiscrete, RepeatChannel, RemoveRepe…

9a6901c

…atedChannel Signed-off-by: Richard Brown <[email protected]>

MaskIntensity

494db1d

Signed-off-by: Richard Brown <[email protected]>

gibbsnoise, and restore device

ada481f

Signed-off-by: Richard Brown <[email protected]>

Merge branch 'dev' into feature/2231-transforms

b9d91ea

Signed-off-by: Wenqi Li <[email protected]>

rotate90, randrotate90

12d8ac7

Signed-off-by: Richard Brown <[email protected]>

rand_gibbs_noise

5f8c1c7

Signed-off-by: Richard Brown <[email protected]>

crop_foreground

0ec1ff1

Signed-off-by: Richard Brown <[email protected]>

format

207d18f

Signed-off-by: Richard Brown <[email protected]>

torch_seed and rician_noise

1b578a2

Signed-off-by: Richard Brown <[email protected]>

Merge remote-tracking branch 'MONAI/dev' into feature/2231-transforms

81bd74f

Signed-off-by: Richard Brown <[email protected]>

format

c0aad87

Signed-off-by: Richard Brown <[email protected]>

rijobro added 22 commits July 28, 2021 14:48

fix 1d SpatialCrop

9a7cf96

Signed-off-by: Richard Brown <[email protected]>

fix randbiasfield

9db3256

Signed-off-by: Richard Brown <[email protected]>

fix KSpaceSpikeNoise

ecbb200

Signed-off-by: Richard Brown <[email protected]>

fix RandBiasFieldd

c3323d5

Signed-off-by: Richard Brown <[email protected]>

fix generate_pos_neg_label_crop_centers

e645a3f

Signed-off-by: Richard Brown <[email protected]>

Merge remote-tracking branch 'MONAI/dev' into feature/2231-transforms

af49fd7

Merge remote-tracking branch 'MONAI/dev' into feature/2231-transforms

e31bfb0

Signed-off-by: Richard Brown <[email protected]>

fix generate_spatial_bounding_box

293f196

Signed-off-by: Richard Brown <[email protected]>

fix resize

d03911b

Signed-off-by: Richard Brown <[email protected]>

separate one_hot fns for np and torch (allows for torchscript)

40fa288

Signed-off-by: Richard Brown <[email protected]>

fix various tests

fd1af06

Signed-off-by: Richard Brown <[email protected]>

fix one_hot

be9ce91

Signed-off-by: Richard Brown <[email protected]>

fix one_hot 2

6401533

Signed-off-by: Richard Brown <[email protected]>

fix test_invers

c303989

Signed-off-by: Richard Brown <[email protected]>

fix pt1.6

34776d8

Signed-off-by: Richard Brown <[email protected]>

fix

0ead566

Signed-off-by: Richard Brown <[email protected]>

Merge remote-tracking branch 'MONAI/dev' into feature/2231-transforms

6d18280

pt1.7 fix

446d7ea

Signed-off-by: Richard Brown <[email protected]>

fix torch1.7

cb1f047

Signed-off-by: Richard Brown <[email protected]>

Merge remote-tracking branch 'MONAI/dev' into feature/2231-transforms

8d5af04

Signed-off-by: Richard Brown <[email protected]>

post merge fix

f30f72e

Signed-off-by: Richard Brown <[email protected]>

get number of conversions

228e3b4

Signed-off-by: Richard Brown <[email protected]>

This was referenced Aug 10, 2021

RandGaussianNoise and SavitzkyGolaySmooth Torch/NumpyTransforms #2740

Merged

Default to using Pytorch APIs for monai.transforms (ETA TBD) #2231

Closed

rijobro mentioned this pull request Aug 23, 2021

Tensor computation for Brats transforms #2819

Closed

wyli mentioned this pull request Sep 8, 2021

RandRotate90 and RandZoom to work with torch.Tensor #2913

Closed

wyli closed this Nov 5, 2021

wyli deleted the feature/2231-transforms branch December 2, 2021 12:43

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Feature/2231 transforms#2278

Feature/2231 transforms#2278
rijobro wants to merge 209 commits intodevfrom
feature/2231-transforms

rijobro commented May 28, 2021 •

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