U-Net implementation in PyTorch for FLAIR abnormality segmentation in brain MRI

Overview

U-Net for brain segmentation

U-Net implementation in PyTorch for FLAIR abnormality segmentation in brain MRI based on a deep learning segmentation algorithm used in Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm.

This repository is an all Python port of official MATLAB/Keras implementation in brain-segmentation. Weights for trained models are provided and can be used for inference or fine-tuning on a different dataset. If you use code or weights shared in this repository, please consider citing:

@article{buda2019association,
  title={Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm},
  author={Buda, Mateusz and Saha, Ashirbani and Mazurowski, Maciej A},
  journal={Computers in Biology and Medicine},
  volume={109},
  year={2019},
  publisher={Elsevier},
  doi={10.1016/j.compbiomed.2019.05.002}
}

docker

docker build -t brainseg .
nvidia-docker run --rm --shm-size 8G -it -v `pwd`:/workspace brainseg

PyTorch Hub

Loading model using PyTorch Hub: pytorch.org/hub/mateuszbuda_brain-segmentation-pytorch_unet

import torch
model = torch.hub.load('mateuszbuda/brain-segmentation-pytorch', 'unet',
    in_channels=3, out_channels=1, init_features=32, pretrained=True)

data

dataset

Dataset used for development and evaluation was made publicly available on Kaggle: kaggle.com/mateuszbuda/lgg-mri-segmentation. It contains MR images from TCIA LGG collection with segmentation masks approved by a board-certified radiologist at Duke University.

model

A segmentation model implemented in this repository is U-Net as described in Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm with added batch normalization.

unet

results

TCGA_DU_6404_19850629 TCGA_HT_7879_19981009 TCGA_CS_4944_20010208
94% DSC 91% DSC 89% DSC

Qualitative results for validation cases from three different institutions with DSC of 94%, 91%, and 89%. Green outlines correspond to ground truth and red to model predictions. Images show FLAIR modality after preprocessing.

dsc

Distribution of DSC for 10 randomly selected validation cases. The red vertical line corresponds to mean DSC (91%) and the green one to median DSC (92%). Results may be biased since model selection was based on the mean DSC on these validation cases.

inference

  1. Download and extract the dataset from Kaggle.
  2. Run docker container.
  3. Run inference.py script with specified paths to weights and images. Trained weights for input images of size 256x256 are provided in ./weights/unet.pt file. For more options and help run: python3 inference.py --help.

train

  1. Download and extract the dataset from Kaggle.
  2. Run docker container.
  3. Run train.py script. Default path to images is ./kaggle_3m. For more options and help run: python3 train.py --help.

Training can be also run using Kaggle kernel shared together with the dataset: kaggle.com/mateuszbuda/brain-segmentation-pytorch. Due to memory limitations for Kaggle kernels, input images are of size 224x224 instead of 256x256.

Running this code on a custom dataset would likely require adjustments in dataset.py. Should you need help with this, just open an issue.

Comments
  • Reproducibility issue

    Reproducibility issue

    Hello, thank you for sharing nice work. I'm sorry but I can't get the dice score you got. Is it able to reproduce the evaluation result without changing any code?

    opened by whikwon 5
  • where do you implement concatenation

    where do you implement concatenation

    Hi,

    From the image of the architecture in README.md, it seems that a concatenation was implemented. But from your unet.py, I couldn't find where do concatenation was implemented? I have trouble implementing the concatenation in U-net, Could you please help me understand it?

    Great Thanks.

    opened by bsun0802 2
  • Bump tensorflow from 1.12.2 to 2.7.2

    Bump tensorflow from 1.12.2 to 2.7.2

    Bumps tensorflow from 1.12.2 to 2.7.2.

    Release notes

    Sourced from tensorflow's releases.

    TensorFlow 2.7.2

    Release 2.7.2

    This releases introduces several vulnerability fixes:

    TensorFlow 2.7.1

    Release 2.7.1

    This releases introduces several vulnerability fixes:

    • Fixes a floating point division by 0 when executing convolution operators (CVE-2022-21725)
    • Fixes a heap OOB read in shape inference for ReverseSequence (CVE-2022-21728)
    • Fixes a heap OOB access in Dequantize (CVE-2022-21726)
    • Fixes an integer overflow in shape inference for Dequantize (CVE-2022-21727)
    • Fixes a heap OOB access in FractionalAvgPoolGrad (CVE-2022-21730)
    • Fixes an overflow and divide by zero in UnravelIndex (CVE-2022-21729)
    • Fixes a type confusion in shape inference for ConcatV2 (CVE-2022-21731)
    • Fixes an OOM in ThreadPoolHandle (CVE-2022-21732)
    • Fixes an OOM due to integer overflow in StringNGrams (CVE-2022-21733)
    • Fixes more issues caused by incomplete validation in boosted trees code (CVE-2021-41208)
    • Fixes an integer overflows in most sparse component-wise ops (CVE-2022-23567)
    • Fixes an integer overflows in AddManySparseToTensorsMap (CVE-2022-23568)

    ... (truncated)

    Changelog

    Sourced from tensorflow's changelog.

    Release 2.7.2

    This releases introduces several vulnerability fixes:

    Release 2.6.4

    This releases introduces several vulnerability fixes:

    • Fixes a code injection in saved_model_cli (CVE-2022-29216)
    • Fixes a missing validation which causes TensorSummaryV2 to crash (CVE-2022-29193)
    • Fixes a missing validation which crashes QuantizeAndDequantizeV4Grad (CVE-2022-29192)
    • Fixes a missing validation which causes denial of service via DeleteSessionTensor (CVE-2022-29194)
    • Fixes a missing validation which causes denial of service via GetSessionTensor (CVE-2022-29191)
    • Fixes a missing validation which causes denial of service via StagePeek (CVE-2022-29195)
    • Fixes a missing validation which causes denial of service via UnsortedSegmentJoin (CVE-2022-29197)
    • Fixes a missing validation which causes denial of service via LoadAndRemapMatrix (CVE-2022-29199)
    • Fixes a missing validation which causes denial of service via SparseTensorToCSRSparseMatrix (CVE-2022-29198)
    • Fixes a missing validation which causes denial of service via LSTMBlockCell (CVE-2022-29200)
    • Fixes a missing validation which causes denial of service via Conv3DBackpropFilterV2 (CVE-2022-29196)
    • Fixes a CHECK failure in depthwise ops via overflows (CVE-2021-41197)
    • Fixes issues arising from undefined behavior stemming from users supplying invalid resource handles (CVE-2022-29207)
    • Fixes a segfault due to missing support for quantized types (CVE-2022-29205)
    • Fixes a missing validation which results in undefined behavior in SparseTensorDenseAdd (CVE-2022-29206)

    ... (truncated)

    Commits
    • dd7b8a3 Merge pull request #56034 from tensorflow-jenkins/relnotes-2.7.2-15779
    • 1e7d6ea Update RELEASE.md
    • 5085135 Merge pull request #56069 from tensorflow/mm-cp-52488e5072f6fe44411d70c6af09e...
    • adafb45 Merge pull request #56060 from yongtang:curl-7.83.1
    • 01cb1b8 Merge pull request #56038 from tensorflow-jenkins/version-numbers-2.7.2-4733
    • 8c90c2f Update version numbers to 2.7.2
    • 43f3cdc Update RELEASE.md
    • 98b0a48 Insert release notes place-fill
    • dfa5cf3 Merge pull request #56028 from tensorflow/disable-tests-on-r2.7
    • 501a65c Disable timing out tests
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    dependencies 
    opened by dependabot[bot] 1
  • Bump tensorflow from 1.12.2 to 2.6.4

    Bump tensorflow from 1.12.2 to 2.6.4

    Bumps tensorflow from 1.12.2 to 2.6.4.

    Release notes

    Sourced from tensorflow's releases.

    TensorFlow 2.6.4

    Release 2.6.4

    This releases introduces several vulnerability fixes:

    TensorFlow 2.6.3

    Release 2.6.3

    This releases introduces several vulnerability fixes:

    • Fixes a floating point division by 0 when executing convolution operators (CVE-2022-21725)
    • Fixes a heap OOB read in shape inference for ReverseSequence (CVE-2022-21728)
    • Fixes a heap OOB access in Dequantize (CVE-2022-21726)
    • Fixes an integer overflow in shape inference for Dequantize (CVE-2022-21727)
    • Fixes a heap OOB access in FractionalAvgPoolGrad (CVE-2022-21730)
    • Fixes an overflow and divide by zero in UnravelIndex (CVE-2022-21729)
    • Fixes a type confusion in shape inference for ConcatV2 (CVE-2022-21731)
    • Fixes an OOM in ThreadPoolHandle (CVE-2022-21732)
    • Fixes an OOM due to integer overflow in StringNGrams (CVE-2022-21733)
    • Fixes more issues caused by incomplete validation in boosted trees code (CVE-2021-41208)
    • Fixes an integer overflows in most sparse component-wise ops (CVE-2022-23567)
    • Fixes an integer overflows in AddManySparseToTensorsMap (CVE-2022-23568)
    • Fixes a number of CHECK-failures in MapStage (CVE-2022-21734)

    ... (truncated)

    Changelog

    Sourced from tensorflow's changelog.

    Release 2.6.4

    This releases introduces several vulnerability fixes:

    Release 2.8.0

    Major Features and Improvements

    • tf.lite:

      • Added TFLite builtin op support for the following TF ops:
        • tf.raw_ops.Bucketize op on CPU.
        • tf.where op for data types tf.int32/tf.uint32/tf.int8/tf.uint8/tf.int64.
        • tf.random.normal op for output data type tf.float32 on CPU.
        • tf.random.uniform op for output data type tf.float32 on CPU.
        • tf.random.categorical op for output data type tf.int64 on CPU.
    • tensorflow.experimental.tensorrt:

      • conversion_params is now deprecated inside TrtGraphConverterV2 in favor of direct arguments: max_workspace_size_bytes, precision_mode, minimum_segment_size, maximum_cached_engines, use_calibration and

    ... (truncated)

    Commits
    • 33ed2b1 Merge pull request #56102 from tensorflow/mihaimaruseac-patch-1
    • e1ec480 Fix build due to importlib-metadata/setuptools
    • 63f211c Merge pull request #56033 from tensorflow-jenkins/relnotes-2.6.4-6677
    • 22b8fe4 Update RELEASE.md
    • ec30684 Merge pull request #56070 from tensorflow/mm-cp-adafb45c781-on-r2.6
    • 38774ed Merge pull request #56060 from yongtang:curl-7.83.1
    • 9ef1604 Merge pull request #56036 from tensorflow-jenkins/version-numbers-2.6.4-9925
    • a6526a3 Update version numbers to 2.6.4
    • cb1a481 Update RELEASE.md
    • 4da550f Insert release notes place-fill
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • Bump pillow from 6.0.0 to 9.0.1

    Bump pillow from 6.0.0 to 9.0.1

    Bumps pillow from 6.0.0 to 9.0.1.

    Release notes

    Sourced from pillow's releases.

    9.0.1

    https://pillow.readthedocs.io/en/stable/releasenotes/9.0.1.html

    Changes

    • In show_file, use os.remove to remove temporary images. CVE-2022-24303 #6010 [@​radarhere, @​hugovk]
    • Restrict builtins within lambdas for ImageMath.eval. CVE-2022-22817 #6009 [radarhere]

    9.0.0

    https://pillow.readthedocs.io/en/stable/releasenotes/9.0.0.html

    Changes

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    9.0.1 (2022-02-03)

    • In show_file, use os.remove to remove temporary images. CVE-2022-24303 #6010 [radarhere, hugovk]

    • Restrict builtins within lambdas for ImageMath.eval. CVE-2022-22817 #6009 [radarhere]

    9.0.0 (2022-01-02)

    • Restrict builtins for ImageMath.eval(). CVE-2022-22817 #5923 [radarhere]

    • Ensure JpegImagePlugin stops at the end of a truncated file #5921 [radarhere]

    • Fixed ImagePath.Path array handling. CVE-2022-22815, CVE-2022-22816 #5920 [radarhere]

    • Remove consecutive duplicate tiles that only differ by their offset #5919 [radarhere]

    • Improved I;16 operations on big endian #5901 [radarhere]

    • Limit quantized palette to number of colors #5879 [radarhere]

    • Fixed palette index for zeroed color in FASTOCTREE quantize #5869 [radarhere]

    • When saving RGBA to GIF, make use of first transparent palette entry #5859 [radarhere]

    • Pass SAMPLEFORMAT to libtiff #5848 [radarhere]

    • Added rounding when converting P and PA #5824 [radarhere]

    • Improved putdata() documentation and data handling #5910 [radarhere]

    • Exclude carriage return in PDF regex to help prevent ReDoS #5912 [hugovk]

    • Fixed freeing pointer in ImageDraw.Outline.transform #5909 [radarhere]

    ... (truncated)

    Commits
    • 6deac9e 9.0.1 version bump
    • c04d812 Update CHANGES.rst [ci skip]
    • 4fabec3 Added release notes for 9.0.1
    • 02affaa Added delay after opening image with xdg-open
    • ca0b585 Updated formatting
    • 427221e In show_file, use os.remove to remove temporary images
    • c930be0 Restrict builtins within lambdas for ImageMath.eval
    • 75b69dd Dont need to pin for GHA
    • cd938a7 Autolink CWE numbers with sphinx-issues
    • 2e9c461 Add CVE IDs
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    dependencies 
    opened by dependabot[bot] 1
  • Bump tensorflow from 1.12.2 to 2.5.3

    Bump tensorflow from 1.12.2 to 2.5.3

    Bumps tensorflow from 1.12.2 to 2.5.3.

    Release notes

    Sourced from tensorflow's releases.

    TensorFlow 2.5.3

    Release 2.5.3

    Note: This is the last release in the 2.5 series.

    This releases introduces several vulnerability fixes:

    • Fixes a floating point division by 0 when executing convolution operators (CVE-2022-21725)
    • Fixes a heap OOB read in shape inference for ReverseSequence (CVE-2022-21728)
    • Fixes a heap OOB access in Dequantize (CVE-2022-21726)
    • Fixes an integer overflow in shape inference for Dequantize (CVE-2022-21727)
    • Fixes a heap OOB access in FractionalAvgPoolGrad (CVE-2022-21730)
    • Fixes an overflow and divide by zero in UnravelIndex (CVE-2022-21729)
    • Fixes a type confusion in shape inference for ConcatV2 (CVE-2022-21731)
    • Fixes an OOM in ThreadPoolHandle (CVE-2022-21732)
    • Fixes an OOM due to integer overflow in StringNGrams (CVE-2022-21733)
    • Fixes more issues caused by incomplete validation in boosted trees code (CVE-2021-41208)
    • Fixes an integer overflows in most sparse component-wise ops (CVE-2022-23567)
    • Fixes an integer overflows in AddManySparseToTensorsMap (CVE-2022-23568)
    • Fixes a number of CHECK-failures in MapStage (CVE-2022-21734)
    • Fixes a division by zero in FractionalMaxPool (CVE-2022-21735)
    • Fixes a number of CHECK-fails when building invalid/overflowing tensor shapes (CVE-2022-23569)
    • Fixes an undefined behavior in SparseTensorSliceDataset (CVE-2022-21736)
    • Fixes an assertion failure based denial of service via faulty bin count operations (CVE-2022-21737)
    • Fixes a reference binding to null pointer in QuantizedMaxPool (CVE-2022-21739)
    • Fixes an integer overflow leading to crash in SparseCountSparseOutput (CVE-2022-21738)
    • Fixes a heap overflow in SparseCountSparseOutput (CVE-2022-21740)
    • Fixes an FPE in BiasAndClamp in TFLite (CVE-2022-23557)
    • Fixes an FPE in depthwise convolutions in TFLite (CVE-2022-21741)
    • Fixes an integer overflow in TFLite array creation (CVE-2022-23558)
    • Fixes an integer overflow in TFLite (CVE-2022-23559)
    • Fixes a dangerous OOB write in TFLite (CVE-2022-23561)
    • Fixes a vulnerability leading to read and write outside of bounds in TFLite (CVE-2022-23560)
    • Fixes a set of vulnerabilities caused by using insecure temporary files (CVE-2022-23563)
    • Fixes an integer overflow in Range resulting in undefined behavior and OOM (CVE-2022-23562)
    • Fixes a vulnerability where missing validation causes tf.sparse.split to crash when axis is a tuple (CVE-2021-41206)
    • Fixes a CHECK-fail when decoding resource handles from proto (CVE-2022-23564)
    • Fixes a CHECK-fail with repeated AttrDef (CVE-2022-23565)
    • Fixes a heap OOB write in Grappler (CVE-2022-23566)
    • Fixes a CHECK-fail when decoding invalid tensors from proto (CVE-2022-23571)
    • Fixes an unitialized variable access in AssignOp (CVE-2022-23573)
    • Fixes an integer overflow in OpLevelCostEstimator::CalculateTensorSize (CVE-2022-23575)
    • Fixes an integer overflow in OpLevelCostEstimator::CalculateOutputSize (CVE-2022-23576)
    • Fixes a null dereference in GetInitOp (CVE-2022-23577)
    • Fixes a memory leak when a graph node is invalid (CVE-2022-23578)
    • Fixes an abort caused by allocating a vector that is too large (CVE-2022-23580)
    • Fixes multiple CHECK-failures during Grappler's IsSimplifiableReshape (CVE-2022-23581)
    • Fixes multiple CHECK-failures during Grappler's SafeToRemoveIdentity (CVE-2022-23579)
    • Fixes multiple CHECK-failures in TensorByteSize (CVE-2022-23582)
    • Fixes multiple CHECK-failures in binary ops due to type confusion (CVE-2022-23583)

    ... (truncated)

    Changelog

    Sourced from tensorflow's changelog.

    Release 2.5.3

    This releases introduces several vulnerability fixes:

    • Fixes a floating point division by 0 when executing convolution operators (CVE-2022-21725)
    • Fixes a heap OOB read in shape inference for ReverseSequence (CVE-2022-21728)
    • Fixes a heap OOB access in Dequantize (CVE-2022-21726)
    • Fixes an integer overflow in shape inference for Dequantize (CVE-2022-21727)
    • Fixes a heap OOB access in FractionalAvgPoolGrad (CVE-2022-21730)
    • Fixes an overflow and divide by zero in UnravelIndex (CVE-2022-21729)
    • Fixes a type confusion in shape inference for ConcatV2 (CVE-2022-21731)
    • Fixes an OOM in ThreadPoolHandle (CVE-2022-21732)
    • Fixes an OOM due to integer overflow in StringNGrams (CVE-2022-21733)
    • Fixes more issues caused by incomplete validation in boosted trees code (CVE-2021-41208)
    • Fixes an integer overflows in most sparse component-wise ops (CVE-2022-23567)
    • Fixes an integer overflows in AddManySparseToTensorsMap (CVE-2022-23568)
    • Fixes a number of CHECK-failures in MapStage (CVE-2022-21734)
    • Fixes a division by zero in FractionalMaxPool (CVE-2022-21735)
    • Fixes a number of CHECK-fails when building invalid/overflowing tensor shapes (CVE-2022-23569)
    • Fixes an undefined behavior in SparseTensorSliceDataset (CVE-2022-21736)
    • Fixes an assertion failure based denial of service via faulty bin count operations (CVE-2022-21737)
    • Fixes a reference binding to null pointer in QuantizedMaxPool (CVE-2022-21739)
    • Fixes an integer overflow leading to crash in SparseCountSparseOutput (CVE-2022-21738)
    • Fixes a heap overflow in SparseCountSparseOutput (CVE-2022-21740)
    • Fixes an FPE in BiasAndClamp in TFLite (CVE-2022-23557)
    • Fixes an FPE in depthwise convolutions in TFLite (CVE-2022-21741)

    ... (truncated)

    Commits
    • 959e9b2 Merge pull request #54213 from tensorflow/fix-sanity-on-r2.5
    • d05fcbc Fix sanity build
    • f2526a0 Merge pull request #54205 from tensorflow/disable-flaky-tests-on-r2.5
    • a5f94df Disable flaky test
    • 7babe52 Merge pull request #54201 from tensorflow/cherrypick-510ae18200d0a4fad797c0bf...
    • 0e5d378 Set Env Variable to override Setuptools new behavior
    • fdd4195 Merge pull request #54176 from tensorflow-jenkins/relnotes-2.5.3-6805
    • 4083165 Update RELEASE.md
    • a2bb7f1 Merge pull request #54185 from tensorflow/cherrypick-d437dec4d549fc30f9b85c75...
    • 5777ea3 Update third_party/icu/workspace.bzl
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • Bump pillow from 6.0.0 to 9.0.0

    Bump pillow from 6.0.0 to 9.0.0

    Bumps pillow from 6.0.0 to 9.0.0.

    Release notes

    Sourced from pillow's releases.

    9.0.0

    https://pillow.readthedocs.io/en/stable/releasenotes/9.0.0.html

    Changes

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    9.0.0 (2022-01-02)

    • Restrict builtins for ImageMath.eval(). CVE-2022-22817 #5923 [radarhere]

    • Ensure JpegImagePlugin stops at the end of a truncated file #5921 [radarhere]

    • Fixed ImagePath.Path array handling. CVE-2022-22815, CVE-2022-22816 #5920 [radarhere]

    • Remove consecutive duplicate tiles that only differ by their offset #5919 [radarhere]

    • Improved I;16 operations on big endian #5901 [radarhere]

    • Limit quantized palette to number of colors #5879 [radarhere]

    • Fixed palette index for zeroed color in FASTOCTREE quantize #5869 [radarhere]

    • When saving RGBA to GIF, make use of first transparent palette entry #5859 [radarhere]

    • Pass SAMPLEFORMAT to libtiff #5848 [radarhere]

    • Added rounding when converting P and PA #5824 [radarhere]

    • Improved putdata() documentation and data handling #5910 [radarhere]

    • Exclude carriage return in PDF regex to help prevent ReDoS #5912 [hugovk]

    • Fixed freeing pointer in ImageDraw.Outline.transform #5909 [radarhere]

    • Added ImageShow support for xdg-open #5897 [m-shinder, radarhere]

    • Support 16-bit grayscale ImageQt conversion #5856 [cmbruns, radarhere]

    • Convert subsequent GIF frames to RGB or RGBA #5857 [radarhere]

    ... (truncated)

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    dependencies 
    opened by dependabot[bot] 1
  • Bump pillow from 6.0.0 to 8.3.2

    Bump pillow from 6.0.0 to 8.3.2

    Bumps pillow from 6.0.0 to 8.3.2.

    Release notes

    Sourced from pillow's releases.

    8.3.2

    https://pillow.readthedocs.io/en/stable/releasenotes/8.3.2.html

    Security

    • CVE-2021-23437 Raise ValueError if color specifier is too long [hugovk, radarhere]

    • Fix 6-byte OOB read in FliDecode [wiredfool]

    Python 3.10 wheels

    • Add support for Python 3.10 #5569, #5570 [hugovk, radarhere]

    Fixed regressions

    • Ensure TIFF RowsPerStrip is multiple of 8 for JPEG compression #5588 [kmilos, radarhere]

    • Updates for ImagePalette channel order #5599 [radarhere]

    • Hide FriBiDi shim symbols to avoid conflict with real FriBiDi library #5651 [nulano]

    8.3.1

    https://pillow.readthedocs.io/en/stable/releasenotes/8.3.1.html

    Changes

    8.3.0

    https://pillow.readthedocs.io/en/stable/releasenotes/8.3.0.html

    Changes

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    8.3.2 (2021-09-02)

    • CVE-2021-23437 Raise ValueError if color specifier is too long [hugovk, radarhere]

    • Fix 6-byte OOB read in FliDecode [wiredfool]

    • Add support for Python 3.10 #5569, #5570 [hugovk, radarhere]

    • Ensure TIFF RowsPerStrip is multiple of 8 for JPEG compression #5588 [kmilos, radarhere]

    • Updates for ImagePalette channel order #5599 [radarhere]

    • Hide FriBiDi shim symbols to avoid conflict with real FriBiDi library #5651 [nulano]

    8.3.1 (2021-07-06)

    • Catch OSError when checking if fp is sys.stdout #5585 [radarhere]

    • Handle removing orientation from alternate types of EXIF data #5584 [radarhere]

    • Make Image.array take optional dtype argument #5572 [t-vi, radarhere]

    8.3.0 (2021-07-01)

    • Use snprintf instead of sprintf. CVE-2021-34552 #5567 [radarhere]

    • Limit TIFF strip size when saving with LibTIFF #5514 [kmilos]

    • Allow ICNS save on all operating systems #4526 [baletu, radarhere, newpanjing, hugovk]

    • De-zigzag JPEG's DQT when loading; deprecate convert_dict_qtables #4989 [gofr, radarhere]

    • Replaced xml.etree.ElementTree #5565 [radarhere]

    ... (truncated)

    Commits
    • 8013f13 8.3.2 version bump
    • 23c7ca8 Update CHANGES.rst
    • 8450366 Update release notes
    • a0afe89 Update test case
    • 9e08eb8 Raise ValueError if color specifier is too long
    • bd5cf7d FLI tests for Oss-fuzz crash.
    • 94a0cf1 Fix 6-byte OOB read in FliDecode
    • cece64f Add 8.3.2 (2021-09-02) [CI skip]
    • e422386 Add release notes for Pillow 8.3.2
    • 08dcbb8 Pillow 8.3.2 supports Python 3.10 [ci skip]
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    dependencies 
    opened by dependabot[bot] 1
  • Bump tensorflow from 1.12.2 to 2.5.1

    Bump tensorflow from 1.12.2 to 2.5.1

    Bumps tensorflow from 1.12.2 to 2.5.1.

    Release notes

    Sourced from tensorflow's releases.

    TensorFlow 2.5.1

    Release 2.5.1

    This release introduces several vulnerability fixes:

    • Fixes a heap out of bounds access in sparse reduction operations (CVE-2021-37635)
    • Fixes a floating point exception in SparseDenseCwiseDiv (CVE-2021-37636)
    • Fixes a null pointer dereference in CompressElement (CVE-2021-37637)
    • Fixes a null pointer dereference in RaggedTensorToTensor (CVE-2021-37638)
    • Fixes a null pointer dereference and a heap OOB read arising from operations restoring tensors (CVE-2021-37639)
    • Fixes an integer division by 0 in sparse reshaping (CVE-2021-37640)
    • Fixes a division by 0 in ResourceScatterDiv (CVE-2021-37642)
    • Fixes a heap OOB in RaggedGather (CVE-2021-37641)
    • Fixes a std::abort raised from TensorListReserve (CVE-2021-37644)
    • Fixes a null pointer dereference in MatrixDiagPartOp (CVE-2021-37643)
    • Fixes an integer overflow due to conversion to unsigned (CVE-2021-37645)
    • Fixes a bad allocation error in StringNGrams caused by integer conversion (CVE-2021-37646)
    • Fixes a null pointer dereference in SparseTensorSliceDataset (CVE-2021-37647)
    • Fixes an incorrect validation of SaveV2 inputs (CVE-2021-37648)
    • Fixes a null pointer dereference in UncompressElement (CVE-2021-37649)
    • Fixes a segfault and a heap buffer overflow in {Experimental,}DatasetToTFRecord (CVE-2021-37650)
    • Fixes a heap buffer overflow in FractionalAvgPoolGrad (CVE-2021-37651)
    • Fixes a use after free in boosted trees creation (CVE-2021-37652)
    • Fixes a division by 0 in ResourceGather (CVE-2021-37653)
    • Fixes a heap OOB and a CHECK fail in ResourceGather (CVE-2021-37654)
    • Fixes a heap OOB in ResourceScatterUpdate (CVE-2021-37655)
    • Fixes an undefined behavior arising from reference binding to nullptr in RaggedTensorToSparse (CVE-2021-37656)
    • Fixes an undefined behavior arising from reference binding to nullptr in MatrixDiagV* ops (CVE-2021-37657)
    • Fixes an undefined behavior arising from reference binding to nullptr in MatrixSetDiagV* ops (CVE-2021-37658)
    • Fixes an undefined behavior arising from reference binding to nullptr and heap OOB in binary cwise ops (CVE-2021-37659)
    • Fixes a division by 0 in inplace operations (CVE-2021-37660)
    • Fixes a crash caused by integer conversion to unsigned (CVE-2021-37661)
    • Fixes an undefined behavior arising from reference binding to nullptr in boosted trees (CVE-2021-37662)
    • Fixes a heap OOB in boosted trees (CVE-2021-37664)
    • Fixes vulnerabilities arising from incomplete validation in QuantizeV2 (CVE-2021-37663)
    • Fixes vulnerabilities arising from incomplete validation in MKL requantization (CVE-2021-37665)
    • Fixes an undefined behavior arising from reference binding to nullptr in RaggedTensorToVariant (CVE-2021-37666)
    • Fixes an undefined behavior arising from reference binding to nullptr in unicode encoding (CVE-2021-37667)
    • Fixes an FPE in tf.raw_ops.UnravelIndex (CVE-2021-37668)
    • Fixes a crash in NMS ops caused by integer conversion to unsigned (CVE-2021-37669)
    • Fixes a heap OOB in UpperBound and LowerBound (CVE-2021-37670)
    • Fixes an undefined behavior arising from reference binding to nullptr in map operations (CVE-2021-37671)
    • Fixes a heap OOB in SdcaOptimizerV2 (CVE-2021-37672)
    • Fixes a CHECK-fail in MapStage (CVE-2021-37673)
    • Fixes a vulnerability arising from incomplete validation in MaxPoolGrad (CVE-2021-37674)
    • Fixes an undefined behavior arising from reference binding to nullptr in shape inference (CVE-2021-37676)
    • Fixes a division by 0 in most convolution operators (CVE-2021-37675)
    • Fixes vulnerabilities arising from missing validation in shape inference for Dequantize (CVE-2021-37677)
    • Fixes an arbitrary code execution due to YAML deserialization (CVE-2021-37678)
    • Fixes a heap OOB in nested tf.map_fn with RaggedTensors (CVE-2021-37679)

    ... (truncated)

    Changelog

    Sourced from tensorflow's changelog.

    Release 2.5.1

    This release introduces several vulnerability fixes:

    • Fixes a heap out of bounds access in sparse reduction operations (CVE-2021-37635)
    • Fixes a floating point exception in SparseDenseCwiseDiv (CVE-2021-37636)
    • Fixes a null pointer dereference in CompressElement (CVE-2021-37637)
    • Fixes a null pointer dereference in RaggedTensorToTensor (CVE-2021-37638)
    • Fixes a null pointer dereference and a heap OOB read arising from operations restoring tensors (CVE-2021-37639)
    • Fixes an integer division by 0 in sparse reshaping (CVE-2021-37640)
    • Fixes a division by 0 in ResourceScatterDiv (CVE-2021-37642)
    • Fixes a heap OOB in RaggedGather (CVE-2021-37641)
    • Fixes a std::abort raised from TensorListReserve (CVE-2021-37644)
    • Fixes a null pointer dereference in MatrixDiagPartOp (CVE-2021-37643)
    • Fixes an integer overflow due to conversion to unsigned (CVE-2021-37645)
    • Fixes a bad allocation error in StringNGrams caused by integer conversion (CVE-2021-37646)
    • Fixes a null pointer dereference in SparseTensorSliceDataset (CVE-2021-37647)
    • Fixes an incorrect validation of SaveV2 inputs (CVE-2021-37648)
    • Fixes a null pointer dereference in UncompressElement (CVE-2021-37649)
    • Fixes a segfault and a heap buffer overflow in {Experimental,}DatasetToTFRecord (CVE-2021-37650)
    • Fixes a heap buffer overflow in FractionalAvgPoolGrad (CVE-2021-37651)
    • Fixes a use after free in boosted trees creation (CVE-2021-37652)
    • Fixes a division by 0 in ResourceGather (CVE-2021-37653)
    • Fixes a heap OOB and a CHECK fail in ResourceGather (CVE-2021-37654)
    • Fixes a heap OOB in ResourceScatterUpdate (CVE-2021-37655)
    • Fixes an undefined behavior arising from reference binding to nullptr in RaggedTensorToSparse

    ... (truncated)

    Commits
    • 8222c1c Merge pull request #51381 from tensorflow/mm-fix-r2.5-build
    • d584260 Disable broken/flaky test
    • f6c6ce3 Merge pull request #51367 from tensorflow-jenkins/version-numbers-2.5.1-17468
    • 3ca7812 Update version numbers to 2.5.1
    • 4fdf683 Merge pull request #51361 from tensorflow/mm-update-relnotes-on-r2.5
    • 05fc01a Put CVE numbers for fixes in parentheses
    • bee1dc4 Update release notes for the new patch release
    • 47beb4c Merge pull request #50597 from kruglov-dmitry/v2.5.0-sync-abseil-cmake-bazel
    • 6f39597 Merge pull request #49383 from ashahab/abin-load-segfault-r2.5
    • 0539b34 Merge pull request #48979 from liufengdb/r2.5-cherrypick
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    dependencies 
    opened by dependabot[bot] 1
  • Bump pillow from 6.0.0 to 8.2.0

    Bump pillow from 6.0.0 to 8.2.0

    Bumps pillow from 6.0.0 to 8.2.0.

    Release notes

    Sourced from pillow's releases.

    8.2.0

    https://pillow.readthedocs.io/en/stable/releasenotes/8.2.0.html

    Changes

    Dependencies

    Deprecations

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    8.2.0 (2021-04-01)

    • Added getxmp() method #5144 [UrielMaD, radarhere]

    • Add ImageShow support for GraphicsMagick #5349 [latosha-maltba, radarhere]

    • Do not load transparent pixels from subsequent GIF frames #5333 [zewt, radarhere]

    • Use LZW encoding when saving GIF images #5291 [raygard]

    • Set all transparent colors to be equal in quantize() #5282 [radarhere]

    • Allow PixelAccess to use Python int when parsing x and y #5206 [radarhere]

    • Removed Image._MODEINFO #5316 [radarhere]

    • Add preserve_tone option to autocontrast #5350 [elejke, radarhere]

    • Fixed linear_gradient and radial_gradient I and F modes #5274 [radarhere]

    • Add support for reading TIFFs with PlanarConfiguration=2 #5364 [kkopachev, wiredfool, nulano]

    • Deprecated categories #5351 [radarhere]

    • Do not premultiply alpha when resizing with Image.NEAREST resampling #5304 [nulano]

    • Dynamically link FriBiDi instead of Raqm #5062 [nulano]

    • Allow fewer PNG palette entries than the bit depth maximum when saving #5330 [radarhere]

    • Use duration from info dictionary when saving WebP #5338 [radarhere]

    • Stop flattening EXIF IFD into getexif() #4947 [radarhere, kkopachev]

    ... (truncated)

    Commits
    • e0e353c 8.2.0 version bump
    • ee635be Merge pull request #5377 from hugovk/security-and-release-notes
    • 694c84f Fix typo [ci skip]
    • 8febdad Review, typos and lint
    • fea4196 Reorder, roughly alphabetic
    • 496245a Fix BLP DOS -- CVE-2021-28678
    • 22e9bee Fix DOS in PSDImagePlugin -- CVE-2021-28675
    • ba65f0b Fix Memory DOS in ImageFont
    • bb6c11f Fix FLI DOS -- CVE-2021-28676
    • 5a5e6db Fix EPS DOS on _open -- CVE-2021-28677
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    dependencies 
    opened by dependabot[bot] 1
  • Bump pillow from 6.0.0 to 8.1.1

    Bump pillow from 6.0.0 to 8.1.1

    Bumps pillow from 6.0.0 to 8.1.1.

    Release notes

    Sourced from pillow's releases.

    8.1.1

    https://pillow.readthedocs.io/en/stable/releasenotes/8.1.1.html

    8.1.0

    https://pillow.readthedocs.io/en/stable/releasenotes/8.1.0.html

    Changes

    Dependencies

    Deprecations

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    8.1.1 (2021-03-01)

    • Use more specific regex chars to prevent ReDoS. CVE-2021-25292 [hugovk]

    • Fix OOB Read in TiffDecode.c, and check the tile validity before reading. CVE-2021-25291 [wiredfool]

    • Fix negative size read in TiffDecode.c. CVE-2021-25290 [wiredfool]

    • Fix OOB read in SgiRleDecode.c. CVE-2021-25293 [wiredfool]

    • Incorrect error code checking in TiffDecode.c. CVE-2021-25289 [wiredfool]

    • PyModule_AddObject fix for Python 3.10 #5194 [radarhere]

    8.1.0 (2021-01-02)

    • Fix TIFF OOB Write error. CVE-2020-35654 #5175 [wiredfool]

    • Fix for Read Overflow in PCX Decoding. CVE-2020-35653 #5174 [wiredfool, radarhere]

    • Fix for SGI Decode buffer overrun. CVE-2020-35655 #5173 [wiredfool, radarhere]

    • Fix OOB Read when saving GIF of xsize=1 #5149 [wiredfool]

    • Makefile updates #5159 [wiredfool, radarhere]

    • Add support for PySide6 #5161 [hugovk]

    • Use disposal settings from previous frame in APNG #5126 [radarhere]

    • Added exception explaining that repr_png saves to PNG #5139 [radarhere]

    • Use previous disposal method in GIF load_end #5125 [radarhere]

    ... (truncated)

    Commits
    • 741d874 8.1.1 version bump
    • 179cd1c Added 8.1.1 release notes to index
    • 7d29665 Update CHANGES.rst [ci skip]
    • d25036f Credits
    • 973a4c3 Release notes for 8.1.1
    • 521dab9 Use more specific regex chars to prevent ReDoS
    • 8b8076b Fix for CVE-2021-25291
    • e25be1e Fix negative size read in TiffDecode.c
    • f891baa Fix OOB read in SgiRleDecode.c
    • cbfdde7 Incorrect error code checking in TiffDecode.c
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    dependencies 
    opened by dependabot[bot] 1
  • Bump pillow from 6.0.0 to 9.3.0

    Bump pillow from 6.0.0 to 9.3.0

    Bumps pillow from 6.0.0 to 9.3.0.

    Release notes

    Sourced from pillow's releases.

    9.3.0

    https://pillow.readthedocs.io/en/stable/releasenotes/9.3.0.html

    Changes

    ... (truncated)

    Changelog

    Sourced from pillow's changelog.

    9.3.0 (2022-10-29)

    • Limit SAMPLESPERPIXEL to avoid runtime DOS #6700 [wiredfool]

    • Initialize libtiff buffer when saving #6699 [radarhere]

    • Inline fname2char to fix memory leak #6329 [nulano]

    • Fix memory leaks related to text features #6330 [nulano]

    • Use double quotes for version check on old CPython on Windows #6695 [hugovk]

    • Remove backup implementation of Round for Windows platforms #6693 [cgohlke]

    • Fixed set_variation_by_name offset #6445 [radarhere]

    • Fix malloc in _imagingft.c:font_setvaraxes #6690 [cgohlke]

    • Release Python GIL when converting images using matrix operations #6418 [hmaarrfk]

    • Added ExifTags enums #6630 [radarhere]

    • Do not modify previous frame when calculating delta in PNG #6683 [radarhere]

    • Added support for reading BMP images with RLE4 compression #6674 [npjg, radarhere]

    • Decode JPEG compressed BLP1 data in original mode #6678 [radarhere]

    • Added GPS TIFF tag info #6661 [radarhere]

    • Added conversion between RGB/RGBA/RGBX and LAB #6647 [radarhere]

    • Do not attempt normalization if mode is already normal #6644 [radarhere]

    ... (truncated)

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    dependencies 
    opened by dependabot[bot] 0
  • Bump tensorflow from 1.12.2 to 2.9.3

    Bump tensorflow from 1.12.2 to 2.9.3

    Bumps tensorflow from 1.12.2 to 2.9.3.

    Release notes

    Sourced from tensorflow's releases.

    TensorFlow 2.9.3

    Release 2.9.3

    This release introduces several vulnerability fixes:

    TensorFlow 2.9.2

    Release 2.9.2

    This releases introduces several vulnerability fixes:

    ... (truncated)

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    Release 2.9.3

    This release introduces several vulnerability fixes:

    Release 2.8.4

    This release introduces several vulnerability fixes:

    ... (truncated)

    Commits
    • a5ed5f3 Merge pull request #58584 from tensorflow/vinila21-patch-2
    • 258f9a1 Update py_func.cc
    • cd27cfb Merge pull request #58580 from tensorflow-jenkins/version-numbers-2.9.3-24474
    • 3e75385 Update version numbers to 2.9.3
    • bc72c39 Merge pull request #58482 from tensorflow-jenkins/relnotes-2.9.3-25695
    • 3506c90 Update RELEASE.md
    • 8dcb48e Update RELEASE.md
    • 4f34ec8 Merge pull request #58576 from pak-laura/c2.99f03a9d3bafe902c1e6beb105b2f2417...
    • 6fc67e4 Replace CHECK with returning an InternalError on failing to create python tuple
    • 5dbe90a Merge pull request #58570 from tensorflow/r2.9-7b174a0f2e4
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    dependencies 
    opened by dependabot[bot] 0
  • Bump numpy from 1.16.2 to 1.22.0

    Bump numpy from 1.16.2 to 1.22.0

    Bumps numpy from 1.16.2 to 1.22.0.

    Release notes

    Sourced from numpy's releases.

    v1.22.0

    NumPy 1.22.0 Release Notes

    NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

    • Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.
    • A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.
    • NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.
    • New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.
    • A new configurable allocator for use by downstream projects.

    These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

    The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

    Expired deprecations

    Deprecated numeric style dtype strings have been removed

    Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

    (gh-19539)

    Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

    numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

    (gh-19615)

    ... (truncated)

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    dependencies 
    opened by dependabot[bot] 0
  • After UNet Inference, how to overlay / superimpose the different size predicted masks to the original image size?

    After UNet Inference, how to overlay / superimpose the different size predicted masks to the original image size?

    Let us suppose we have an RGB image of 1024x720 and our Net inputs (and output mask) are of shape 512x512 with N classes.

    So during training and inference, we need to convert our input image and mask to the desired shape of 512x512

    But in real life scenario, when we are using it on Videos, images etc; we can't use the 512x512 image. Instead we need to use the original size. So how could we do this? How are we supposed to map / overlay / superimpose the predicted output mask of shape 512x512 to the input image of shape 1024x720 ?

    opened by deshwalmahesh 0
  • Negative loss value

    Negative loss value

    When I train this model with the default run command python train.py

    I see negative loss values and 0 Dice coefficient value

    loss for step: 622 = [-0.9068316221237183]
    loss for step: 623 = [-0.9329317808151245]
    loss for step: 624 = [-0.9376015663146973]
    Best validation mean DSC: 0.000000
    

    This code is using Torch 1.10 on Nvidia GPU with CUDA 11. Is there something that needs fixing in the code (dataloader etc.)?

    opened by memani1 2
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MIC-DKFZ 1.2k Jan 4, 2023
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Rishabh Anand 2 Oct 13, 2021
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Srijarko Roy 23 Aug 20, 2022
Official and maintained implementation of the paper "OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data" [BMVC 2021].

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