diff --git a/.github/workflows/auto-test-dependencies_timed.yml b/.github/workflows/auto-test-dependencies_timed.yml index 61acd87b..6fc6640a 100644 --- a/.github/workflows/auto-test-dependencies_timed.yml +++ b/.github/workflows/auto-test-dependencies_timed.yml @@ -3,7 +3,7 @@ # Automated tests are run at 6:30 UTC on the first and fifteenth day of each month. -name: Run automated tests on multiple platforms to detect dependency issues +name: build-check on: workflow_dispatch: diff --git a/NEWS.md b/NEWS.md index 27074d61..a99a6a76 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# Version 2.2.4 + +## Fixes + +- Masks can now be plotted in images without causing an error when using `matplotlib` version 3.9.0 or later. + # Version 2.2.3 ## Minor changes @@ -7,7 +13,7 @@ - MIRP now checks whether there are potential problems between the frames of reference of image and mask files. -# Fixes +## Fixes - Fixed an error that occurs when attempting to create a deep copy `ImageITKFile` objects. diff --git a/README.md b/README.md index d0d90904..449f2015 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,35 @@ +![GitHub License](https://img.shields.io/github/license/oncoray/mirp) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mirp) +[![PyPI - Version](https://img.shields.io/pypi/v/mirp)](https://pypi.org/project/mirp/) +![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/oncoray/mirp/auto-test-dependencies_timed.yml) +[![JOSS](https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577/status.svg)](https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577) + # Medical Image Radiomics Processor -Medical Image Radiomics Processor (MIRP) is a python package for medical image analysis that is compliant with the -reference standards of the Image Biomarker Standardisation Initiative (IBSI). MIRP focuses on radiomics applications -and supports computation of features for conventional radiomics and image processing for deep-learning applications. +MIRP is a python package for quantitative analysis of medical images. It focuses on processing images for integration +with radiomics workflows. These workflows either use quantitative features computed using MIRP, or directly use MIRP +to process images as input for neural networks and other deep learning models. + +MIRP offers the following main functionality: + +- [Extract and collect metadata](https://oncoray.github.io/mirp/image_metadata.html) from medical images. +- [Find and collect labels or names](https://oncoray.github.io/mirp/mask_labels.html) of regions of interest from image + segmentations. +- [Compute quantitative features](https://oncoray.github.io/mirp/quantitative_image_analysis.html) from regions of interest in medical images. +- [Process images for deep learning](https://oncoray.github.io/mirp/deep_learning.html). + +## Tutorials + +We currently offer the following tutorials: + +- [Computing quantitative features from MR images](https://oncoray.github.io/mirp/tutorial_compute_radiomics_features_mr.html) +- [Applying filters to images](https://oncoray.github.io/mirp/tutorial_apply_image_filter.html) -## Documentation and tutorials +## Documentation -Documentation and tutorials can be found here: https://oncoray.github.io/mirp/ +Documentation can be found here: https://oncoray.github.io/mirp/ ## Supported Python and OS diff --git a/docs/.buildinfo b/docs/.buildinfo index 92258720..72a9ef27 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: b7d3c05f6bec86800f0a1510ac564b73 +config: 92a05a2b300f0adee19d846b9e8f30a1 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_images/tutorial_apply_image_filter_13_0.png b/docs/_images/tutorial_apply_image_filter_14_0.png similarity index 100% rename from docs/_images/tutorial_apply_image_filter_13_0.png rename to docs/_images/tutorial_apply_image_filter_14_0.png diff --git a/docs/_images/tutorial_apply_image_filter_15_0.png b/docs/_images/tutorial_apply_image_filter_16_0.png similarity index 100% rename from docs/_images/tutorial_apply_image_filter_15_0.png rename to docs/_images/tutorial_apply_image_filter_16_0.png diff --git a/docs/_images/tutorial_apply_image_filter_17_0.png b/docs/_images/tutorial_apply_image_filter_18_0.png similarity index 100% rename from docs/_images/tutorial_apply_image_filter_17_0.png rename to docs/_images/tutorial_apply_image_filter_18_0.png diff --git a/docs/_images/tutorial_apply_image_filter_19_0.png b/docs/_images/tutorial_apply_image_filter_20_0.png similarity index 100% rename from docs/_images/tutorial_apply_image_filter_19_0.png rename to docs/_images/tutorial_apply_image_filter_20_0.png diff --git a/docs/_images/tutorial_apply_image_filter_21_0.png b/docs/_images/tutorial_apply_image_filter_22_0.png similarity index 100% rename from docs/_images/tutorial_apply_image_filter_21_0.png rename to docs/_images/tutorial_apply_image_filter_22_0.png diff --git a/docs/_images/tutorial_apply_image_filter_23_0.png b/docs/_images/tutorial_apply_image_filter_24_0.png similarity index 100% rename from docs/_images/tutorial_apply_image_filter_23_0.png rename to docs/_images/tutorial_apply_image_filter_24_0.png diff --git a/docs/_images/tutorial_apply_image_filter_25_0.png b/docs/_images/tutorial_apply_image_filter_26_0.png similarity index 100% rename from docs/_images/tutorial_apply_image_filter_25_0.png rename to docs/_images/tutorial_apply_image_filter_26_0.png diff --git a/docs/_images/tutorial_apply_image_filter_7_0.png b/docs/_images/tutorial_apply_image_filter_8_0.png similarity index 100% rename from docs/_images/tutorial_apply_image_filter_7_0.png rename to docs/_images/tutorial_apply_image_filter_8_0.png diff --git a/docs/_images/tutorial_compute_radiomics_features_mr_7_0.png b/docs/_images/tutorial_compute_radiomics_features_mr_7_0.png deleted file mode 100644 index ac067068..00000000 Binary files a/docs/_images/tutorial_compute_radiomics_features_mr_7_0.png and /dev/null differ diff --git a/docs/_images/tutorial_compute_radiomics_features_mr_8_0.png b/docs/_images/tutorial_compute_radiomics_features_mr_8_0.png new file mode 100644 index 00000000..210c438e Binary files /dev/null and b/docs/_images/tutorial_compute_radiomics_features_mr_8_0.png differ diff --git a/docs/_modules/index.html b/docs/_modules/index.html index 173b7822..f32ad8f9 100644 --- a/docs/_modules/index.html +++ b/docs/_modules/index.html @@ -3,8 +3,8 @@ - Overview: module code — mirp 2.2.3 documentation - + Overview: module code — mirp 2.2.4 documentation + @@ -14,7 +14,7 @@ - + @@ -52,7 +52,7 @@
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