diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..4f546d5 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git*,.codespellrc +check-hidden = true +ignore-regex = ^\s*"image/\S+": ".* +# ignore-words-list = diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..c59e047 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,25 @@ +# Codespell configuration is within .codespellrc +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: read + +jobs: + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Annotate locations with typos + uses: codespell-project/codespell-problem-matcher@v1 + - name: Codespell + uses: codespell-project/actions-codespell@v2 diff --git a/README.md b/README.md index 1963491..6976502 100644 --- a/README.md +++ b/README.md @@ -81,7 +81,7 @@ training/derivatives/sub-verse000/ 5. (VerSe'20) https://s3.bonescreen.de/public/VerSe-complete/dataset-verse20validation.zip 6. (VerSe'20) https://s3.bonescreen.de/public/VerSe-complete/dataset-verse20test.zip -### OSF Reporsitories: +### OSF Repositories: 1. VerSe'19: https://osf.io/nqjyw/ 2. VerSe'20: https://osf.io/t98fz/ @@ -99,7 +99,7 @@ We provide helper code and guiding notebooks. * Data reading, standardising, and writing: [Data utilities](https://github.com/anjany/verse/blob/main/utils/data_utilities.py) * Evaluation (as employed in the 2020 challenge): [Evaluation utilities](https://github.com/anjany/verse/blob/main/utils/eval_utilities.py) -* Notebooks: [Data preperation](https://github.com/anjany/verse/blob/main/utils/prepare_data.ipynb), [Evaluation](https://github.com/anjany/verse/blob/main/utils/evaluate.ipynb) +* Notebooks: [Data preparation](https://github.com/anjany/verse/blob/main/utils/prepare_data.ipynb), [Evaluation](https://github.com/anjany/verse/blob/main/utils/evaluate.ipynb) ## Contact For queries and issues not fit for a github issue, please email [Anjany Sekuboyina](mailto:anjany.sekuboyina@tum.de) or [Jan Kirschke](mailto:jan.kirschke@tum.de) . diff --git a/utils/eval_utilities.py b/utils/eval_utilities.py index ed448bb..723899c 100644 --- a/utils/eval_utilities.py +++ b/utils/eval_utilities.py @@ -83,8 +83,8 @@ def get_hits(cent_list_gt, cent_list_pred, max_vert_idx): Successful identification defined as the correct label being closest and < 20mm away. hit_list: array-like - A 1-d array of lenght max_vert_idx. Contains nan (if vertebra is absent in GT), - 1 (if vertebra is succesfully identified), and 0 (if failed to identify) + A 1-d array of length max_vert_idx. Contains nan (if vertebra is absent in GT), + 1 (if vertebra is successfully identified), and 0 (if failed to identify) Notes ----- diff --git a/utils/evaluate.ipynb b/utils/evaluate.ipynb index 2cb67fd..f2cfdd9 100644 --- a/utils/evaluate.ipynb +++ b/utils/evaluate.ipynb @@ -13,7 +13,7 @@ "Please look at the data_utilities notebook for data-preperation! \n", "\n", "**Note**: We do not provide scripts for Hausdorff distance and localisation distance.\n", - " Eventhough they were used for the benchamrking process, these were not used for VerSe'20. \n", + " Even though they were used for the benchmarking process, these were not used for VerSe'20. \n", " This is because of their invalidity when evaluating 'missed vertebrae'. " ] }, @@ -155,7 +155,7 @@ "verts_in_gt = np.argwhere(~np.isnan(true_ctd_arr[:, 0])).reshape(-1) + 1 # list of vertebrae present in annotation\n", "\n", "print('id.rate:{:.2f}\\n'.format(num_hits/len(verts_in_gt)))\n", - "print('Hits:\\n', hit_list) # nan : vertebrae is absent. 1 : successful identifcation. 0 : failed identification\n" + "print('Hits:\\n', hit_list) # nan : vertebrae is absent. 1 : successful identification. 0 : failed identification\n" ] }, {