diff --git a/README.md b/README.md index 081713363..4a3cd65b4 100644 --- a/README.md +++ b/README.md @@ -58,9 +58,6 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)). Code quality - - Code maintainability - pre-commit diff --git a/docs/source/README.rst b/docs/source/README.rst index ac1c0db2a..12e966587 100644 --- a/docs/source/README.rst +++ b/docs/source/README.rst @@ -4,7 +4,7 @@ TorchIO |PyPI-downloads| |PyPI-version| |Conda-version| |Google-Colab-notebook| |Docs-status| |Tests-status| |Ruff| -|Coverage-codecov| |Code-Quality| |Code-Maintainability| |pre-commit| +|Coverage-codecov| |Code-Quality| |pre-commit| |YouTube| @@ -22,7 +22,7 @@ or `k-space motion artifacts `_. TorchIO is part of the official `PyTorch Ecosystem `_, and was featured at -the `PyTorch Ecosystem Day 2021 `_ and +the `PyTorch Ecosystem Day 2021 `_ and the `PyTorch Developer Day 2021 `_. Many groups have used TorchIO for their research. @@ -109,10 +109,6 @@ If you found a bug or have a feature request, please open an issue: :target: https://github.com/TorchIO-project/torchio#contributors :alt: All contributors -.. |Code-Maintainability| image:: https://api.codeclimate.com/v1/badges/518673e49a472dd5714d/maintainability - :target: https://codeclimate.com/github/TorchIO-project/torchio - :alt: Maintainability - .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white :target: https://github.com/pre-commit/pre-commit :alt: pre-commit diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst index ffec8c6e4..64fe6c9a2 100644 --- a/docs/source/quickstart.rst +++ b/docs/source/quickstart.rst @@ -7,13 +7,8 @@ Installation The Python package is hosted on the `Python Package Index (PyPI) `_. -To install the latest PyTorch version before installing TorchIO, it is -recommended to use `light-the-torch `_:: - - $ pip install light-the-torch && ltt install torch - The latest published version of TorchIO can be installed using Pip Installs -Packages (``pip``):: +Packages (PIP):: $ pip install torchio @@ -25,12 +20,15 @@ If you would like to install Matplotlib to use the plotting features, use:: $ pip install torchio[plot] +You can also install TorchIO with Conda:: + + $ conda install -c conda-forge torchio If you are on Windows and have `trouble installing TorchIO `_, try `installing PyTorch `_ with -`conda `_ before pip-installing -TorchIO. +`conda `_ +before pip-installing TorchIO. Hello, World! ------------- @@ -50,6 +48,7 @@ in parallel:: t1=tio.ScalarImage('subject_a.nii.gz'), label=tio.LabelMap('subject_a.nii'), diagnosis='positive', + age=36, ) # Image files can be in any format supported by SimpleITK or NiBabel, including DICOM @@ -57,6 +56,7 @@ in parallel:: t1=tio.ScalarImage('subject_b_dicom_folder'), label=tio.LabelMap('subject_b_seg.nrrd'), diagnosis='negative', + age=24, ) # Images may also be created using PyTorch tensors or NumPy arrays @@ -65,9 +65,14 @@ in parallel:: t1=tio.ScalarImage(tensor=tensor_4d), label=tio.LabelMap(tensor=(tensor_4d > 0.5)), diagnosis='negative', + age=19, ) - subjects_list = [subject_a, subject_b, subject_c] + subjects_list = [ + subject_a, + subject_b, + subject_c, + ] # Let's use one preprocessing transform and one augmentation transform # This transform will be applied only to scalar images: diff --git a/src/torchio/transforms/augmentation/intensity/random_spike.py b/src/torchio/transforms/augmentation/intensity/random_spike.py index c20e1fcb7..8b63aea8c 100644 --- a/src/torchio/transforms/augmentation/intensity/random_spike.py +++ b/src/torchio/transforms/augmentation/intensity/random_spike.py @@ -15,7 +15,7 @@ class RandomSpike(RandomTransform, IntensityTransform, FourierTransform): r"""Add random MRI spike artifacts. Also known as `Herringbone artifact - `_, + `_, crisscross artifact or corduroy artifact, it creates stripes in different directions in image space due to spikes in k-space.