From c5d8c5da33b6feb278cbba540ee7fb4cfed16a91 Mon Sep 17 00:00:00 2001 From: ncullen93 Date: Wed, 10 Apr 2024 17:52:47 +0200 Subject: [PATCH] update structure --- README.md | 32 +++++++++++++++++-- book/02-01.ipynb | 23 +++++++++++++ book/02-02.ipynb | 23 +++++++++++++ book/02-03.ipynb | 23 +++++++++++++ book/02-04.ipynb | 23 +++++++++++++ book/03-01.ipynb | 23 +++++++++++++ book/03-02.ipynb | 23 +++++++++++++ book/03-03.ipynb | 23 +++++++++++++ book/03-04.ipynb | 23 +++++++++++++ book/04-01.ipynb | 23 +++++++++++++ book/04-02.ipynb | 23 +++++++++++++ book/04-03.ipynb | 23 +++++++++++++ ...-operating-on-images.ipynb => 05-01.ipynb} | 0 book/05-02.ipynb | 23 +++++++++++++ book/05-03.ipynb | 23 +++++++++++++ book/06-01.ipynb | 23 +++++++++++++ book/06-02.ipynb | 23 +++++++++++++ book/06-03.ipynb | 23 +++++++++++++ book/07-01.ipynb | 23 +++++++++++++ book/07-02.ipynb | 23 +++++++++++++ book/07-03.ipynb | 23 +++++++++++++ book/08-01.ipynb | 23 +++++++++++++ book/_toc.yml | 23 +++++++++---- 23 files changed, 507 insertions(+), 8 deletions(-) create mode 100644 book/02-01.ipynb create mode 100644 book/02-02.ipynb create mode 100644 book/02-03.ipynb create mode 100644 book/02-04.ipynb create mode 100644 book/03-01.ipynb create mode 100644 book/03-02.ipynb create mode 100644 book/03-03.ipynb create mode 100644 book/03-04.ipynb create mode 100644 book/04-01.ipynb create mode 100644 book/04-02.ipynb create mode 100644 book/04-03.ipynb rename book/{01-04-operating-on-images.ipynb => 05-01.ipynb} (100%) create mode 100644 book/05-02.ipynb create mode 100644 book/05-03.ipynb create mode 100644 book/06-01.ipynb create mode 100644 book/06-02.ipynb create mode 100644 book/06-03.ipynb create mode 100644 book/07-01.ipynb create mode 100644 book/07-02.ipynb create mode 100644 book/07-03.ipynb create mode 100644 book/08-01.ipynb diff --git a/README.md b/README.md index 846d0d5..c123712 100644 --- a/README.md +++ b/README.md @@ -9,11 +9,39 @@ A final published draft is expected in early 2025. By going through this book, you will learn how to tackle any medical imaging AI problem in Python. That includes building regression, classification, or image-to-image models for any type of medical imaging processing task. It is split up into the following sections that operate more-or-less independently in case you want to sharpen your skills in one particular area: - Handling medical images + - Installing libraries + - Reading and writing + - Visualization + - Applying operations + - Basic processing - Loading imaging datasets -- Creating batches of images + - Using datasets + - Loading from file + - Loading from the cloud + - Processing transforms +- Generating image batches + - Using dataloaders + - Types of inputs + - Augmentation transforms + - Using samplers +- Creating models + - Using architectures + - Pre-trained models + - Custom models - Training models + - Local GPU training + - Cloud-based training + - Training on nitrain.dev - Explaining model results -- Sharing and deploying models + - About explainers + - Occlusion algorithms + - Visualizing results +- Sharing models + - Registering models + - Writing model cards + - Advice for publications +- Appendix + - References ## About the author diff --git a/book/02-01.ipynb b/book/02-01.ipynb new file mode 100644 index 0000000..02fced8 --- /dev/null +++ b/book/02-01.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Using datasets" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/02-02.ipynb b/book/02-02.ipynb new file mode 100644 index 0000000..7006ca9 --- /dev/null +++ b/book/02-02.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Loading from file" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/02-03.ipynb b/book/02-03.ipynb new file mode 100644 index 0000000..add7a01 --- /dev/null +++ b/book/02-03.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Loading from the cloud" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/02-04.ipynb b/book/02-04.ipynb new file mode 100644 index 0000000..5c11fc0 --- /dev/null +++ b/book/02-04.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Processing transforms" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/03-01.ipynb b/book/03-01.ipynb new file mode 100644 index 0000000..7c6f0ed --- /dev/null +++ b/book/03-01.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Using dataloaders" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/03-02.ipynb b/book/03-02.ipynb new file mode 100644 index 0000000..5e5a58e --- /dev/null +++ b/book/03-02.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Types of inputs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/03-03.ipynb b/book/03-03.ipynb new file mode 100644 index 0000000..9c0f4f7 --- /dev/null +++ b/book/03-03.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Augmentation transforms" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/03-04.ipynb b/book/03-04.ipynb new file mode 100644 index 0000000..2028866 --- /dev/null +++ b/book/03-04.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Using samplers" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/04-01.ipynb b/book/04-01.ipynb new file mode 100644 index 0000000..86028eb --- /dev/null +++ b/book/04-01.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Using architectures" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/04-02.ipynb b/book/04-02.ipynb new file mode 100644 index 0000000..2a1676d --- /dev/null +++ b/book/04-02.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Pre-trained models" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/04-03.ipynb b/book/04-03.ipynb new file mode 100644 index 0000000..3f59596 --- /dev/null +++ b/book/04-03.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Custom models" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/01-04-operating-on-images.ipynb b/book/05-01.ipynb similarity index 100% rename from book/01-04-operating-on-images.ipynb rename to book/05-01.ipynb diff --git a/book/05-02.ipynb b/book/05-02.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/05-02.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/05-03.ipynb b/book/05-03.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/05-03.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/06-01.ipynb b/book/06-01.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/06-01.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/06-02.ipynb b/book/06-02.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/06-02.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/06-03.ipynb b/book/06-03.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/06-03.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/07-01.ipynb b/book/07-01.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/07-01.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/07-02.ipynb b/book/07-02.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/07-02.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/07-03.ipynb b/book/07-03.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/07-03.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/08-01.ipynb b/book/08-01.ipynb new file mode 100644 index 0000000..39f61f2 --- /dev/null +++ b/book/08-01.ipynb @@ -0,0 +1,23 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Applying operations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/book/_toc.yml b/book/_toc.yml index f9dde12..270f9e7 100644 --- a/book/_toc.yml +++ b/book/_toc.yml @@ -12,17 +12,28 @@ parts: - file: 01-04-operating-on-images - caption: 2. Loading imaging datasets chapters: - - file: markdown - - caption: 3. Creating batches of images + - file: 02-01 + - file: 02-02 + - file: 02-03 + - file: 02-04 + - caption: 3. Generating image batches chapters: - - file: markdown-notebooks - - caption: 4. Training models + - file: 03-01 + - file: 03-02 + - file: 03-03 + - file: 03-04 + - caption: 4. Creating models + chapters: + - file: 04-01 + - file: 04-02 + - file: 04-03 + - caption: 5. Training models chapters: - file: markdown-copy - - caption: 5. Explaining model results + - caption: 6. Explaining model results chapters: - file: markdown-copy2 - - caption: 6. Sharing and deploying models + - caption: 6. Sharing models chapters: - file: markdown-copy3 - caption: Appendix