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Feature added: Get WSI at mpp #7574

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Commits on Mar 22, 2024

  1. Added function get_img_at_mpp to class OpenSlideWSIReader of module w…

    …si_reader.py
    Nikolas Schmitz committed Mar 22, 2024
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  2. Added get_img_at_mpp to class CuCIMWSIReader

    Nikolas Schmitz committed Mar 22, 2024
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Commits on Mar 24, 2024

  1. Added function get_img_at_mpp to class TifffileWSIReader; changed res…

    …izing function to Image.resize, cucim.skimage.transform.resize
    Nikolas Schmitz committed Mar 24, 2024
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  2. Small changes

    Nikolas Schmitz committed Mar 24, 2024
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  3. Small changes

    Nikolas Schmitz committed Mar 24, 2024
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Commits on Mar 27, 2024

  1. Stein's Unbiased Risk Estimator (SURE) loss and Conjugate Gradient (P…

    …roject-MONAI#7308)
    
    ### Description
    
    Based on the discussion topic
    [here](Project-MONAI#7161 (comment)),
    we implemented the Conjugate-Gradient algorithm for linear operator
    inversion, and Stein's Unbiased Risk Estimator (SURE) [1] loss for
    ground-truth-date free diffusion process guidance that is proposed in
    [2] and illustrated in the algorithm below:
    
    <img width="650" alt="Screenshot 2023-12-10 at 10 19 25 PM"
    src="https://github.com/Project-MONAI/MONAI/assets/8581162/97069466-cbaf-44e0-b7a7-ae9deb8fd7f2">
    
    The Conjugate-Gradient (CG) algorithm is used to solve for the inversion
    of the linear operator in Line-4 in the algorithm above, where the
    linear operator is too large to store explicitly as a matrix (such as
    FFT/IFFT of an image) and invert directly. Instead, we can solve for the
    linear inversion iteratively as in CG.
    
    The SURE loss is applied for Line-6 above. This is a differentiable loss
    function that can be used to train/giude an operator (e.g. neural
    network), where the pseudo ground truth is available but the reference
    ground truth is not. For example, in the MRI reconstruction, the pseudo
    ground truth is the zero-filled reconstruction and the reference ground
    truth is the fully sampled reconstruction. The reference ground truth is
    not available due to the lack of fully sampled.
    
    **Reference**
    [1] Stein, C.M.: Estimation of the mean of a multivariate normal
    distribution. Annals of Statistics 1981 [[paper
    link](https://projecteuclid.org/journals/annals-of-statistics/volume-9/issue-6/Estimation-of-the-Mean-of-a-Multivariate-Normal-Distribution/10.1214/aos/1176345632.full)]
    [2] B. Ozturkler et al. SMRD: SURE-based Robust MRI Reconstruction with
    Diffusion Models. MICCAI 2023
    [[paper link](https://arxiv.org/pdf/2310.01799.pdf)]
    
    ### Types of changes
    <!--- Put an `x` in all the boxes that apply, and remove the not
    applicable items -->
    - [x] 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).
    - [x] New tests added to cover the changes.
    - [x] Integration tests passed locally by running `./runtests.sh -f -u
    --net --coverage`.
    - [x] Quick tests passed locally by running `./runtests.sh --quick
    --unittests --disttests`.
    - [x] In-line docstrings updated.
    - [x] Documentation updated, tested `make html` command in the `docs/`
    folder.
    
    ---------
    
    Signed-off-by: chaoliu <chaoliu@nvidia.com>
    Signed-off-by: cxlcl <chaoliucxl@gmail.com>
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    Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
    Signed-off-by: Nikolas Schmitz <nikolas.schmitz@rwth-aachen.de>
    4 people authored and NikolasSchmitz committed Mar 27, 2024
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  2. Renamed function to get_wsi_at_mpp

    Signed-off-by: Nikolas Schmitz <nikolas.schmitz@rwth-aachen.de>
    Nikolas Schmitz authored and NikolasSchmitz committed Mar 27, 2024
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks

    for more information, see https://pre-commit.ci
    
    Signed-off-by: Nikolas Schmitz <nikolas.schmitz@rwth-aachen.de>
    pre-commit-ci[bot] authored and NikolasSchmitz committed Mar 27, 2024
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  4. Reformatted wsi_reader.py

    Signed-off-by: Nikolas Schmitz <nikolas.schmitz@rwth-aachen.de>
    NikolasSchmitz committed Mar 27, 2024
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  5. auto updates (Project-MONAI#7577)

    Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
    
    Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
    Signed-off-by: Nikolas Schmitz <nikolas.schmitz@rwth-aachen.de>
    monai-bot authored and NikolasSchmitz committed Mar 27, 2024
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  6. Fixed return type

    Signed-off-by: Nikolas Schmitz <nikolas.schmitz@rwth-aachen.de>
    NikolasSchmitz committed Mar 27, 2024
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  7. Small fixes

    Signed-off-by: Nikolas Schmitz <nikolas.schmitz@rwth-aachen.de>
    NikolasSchmitz committed Mar 27, 2024
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  8. Remove nested error propagation on ConfigComponent instantiate (Pro…

    …ject-MONAI#7569)
    
    Fixes Project-MONAI#7451
    
    ### Description
    Reduces the length of error messages and error messages being propagated
    twice. This helps debug better when long `ConfigComponent`s are being
    instantiated. Refer to issue Project-MONAI#7451 for more details
    
    ### Types of changes
    <!--- Put an `x` in all the boxes that apply, and remove the not
    applicable items -->
    - [x] 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`.
    - [x] Quick tests passed locally by running `./runtests.sh --quick
    --unittests --disttests`.
    - [ ] In-line docstrings updated.
    - [ ] Documentation updated, tested `make html` command in the `docs/`
    folder.
    
    Signed-off-by: Suraj Pai <b.pai@maastrichtuniversity.nl>
    Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
    2 people authored and NikolasSchmitz committed Mar 27, 2024
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  9. 2872 implementation of mixup, cutmix and cutout (Project-MONAI#7198)

    Fixes Project-MONAI#2872 
    
    ### Description
    
    Implementation of mixup, cutmix and cutout as described in the original
    papers.
    Current implementation support both, the dictionary-based batches and
    tuples of tensors.
    
    ### Types of changes
    <!--- Put an `x` in all the boxes that apply, and remove the not
    applicable items -->
    - [x] 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).
    - [x] New tests added to cover the changes.
    - [ ] Integration tests passed locally by running `./runtests.sh -f -u
    --net --coverage`.
    - [x] Quick tests passed locally by running `./runtests.sh --quick
    --unittests --disttests`.
    - [x] In-line docstrings updated.
    - [x] Documentation updated, tested `make html` command in the `docs/`
    folder.
    
    ---------
    
    Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>
    Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
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Commits on Apr 9, 2024

  1. Merge branch 'dev' into 4980-get-wsi-at-mpp

    Signed-off-by: Dr. Behrooz Hashemian <3968947+drbeh@users.noreply.github.com>
    drbeh authored Apr 9, 2024
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Commits on Jul 31, 2024

  1. Updated function get_wsi_at_mpp; added function _resize_to_mpp_res to…

    … reduce redundancy; for get_mpp of TiffFileWSIReader: added check to prevent division by zero error.
    NikolasSchmitz committed Jul 31, 2024
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Commits on Aug 2, 2024

  1. Merge branch 'dev' into 4980-get-wsi-at-mpp

    Signed-off-by: Nikolas Schmitz <144900452+NikolasSchmitz@users.noreply.github.com>
    NikolasSchmitz authored Aug 2, 2024
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Commits on Aug 4, 2024

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Commits on Aug 7, 2024

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Commits on Aug 11, 2024

  1. Added a function _compute_mpp_tolerances which checks the mpp toleran…

    …ces to BaseWSIReader; Edited docstrings
    NikolasSchmitz committed Aug 11, 2024
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Commits on Aug 14, 2024

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Commits on Aug 27, 2024

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Commits on Sep 10, 2024

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Commits on Sep 16, 2024

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Commits on Sep 21, 2024

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