Merge pull request #4 from mpl-extensions/fix-doc2

feat: add stacked images + add more tests + fix docs

Author: ianhi

.github/workflows/ci.yml

@@ -49,7 +49,7 @@ jobs:
           pip install -e ".[test]"
 
       - name: Test
-        run: pytest -v --color=yes --cov=pymmcore_plus --cov-report=xml
+        run: pytest -v --color=yes --cov=mpl_image_segmenter --cov-report=xml
 
       - name: Coverage
         uses: codecov/codecov-action@v3

.readthedocs.yaml

@@ -0,0 +1,12 @@
+version: 2
+python:
+    version: 3.8
+    install:
+      - method: pip
+        path: .
+        extra_requirements:
+          - doc
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py

docs/_static/images/segment.gif

@@ -42,7 +42,7 @@
             "--no-toc",
             "--templatedir _templates",
             "--separate",
-            "../mpl_image_segmenter/",
+            "../src/mpl_image_segmenter/",
             # excluded modules
             # nothing here for cookiecutter
         ]
@@ -57,21 +57,16 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    "jupyter_sphinx",
     "myst_nb",
+    "sphinx_copybutton",
+    "sphinx.ext.napoleon",
     "numpydoc",
     "sphinx.ext.autodoc",
+    "sphinx.ext.inheritance_diagram",
+    "autoapi.sphinx",
     "sphinx.ext.intersphinx",
-    "sphinx.ext.linkcode",
-    "sphinx.ext.mathjax",
-    "sphinx.ext.napoleon",
-    "sphinx_copybutton",
-    "sphinx_panels",
-    "sphinx_thebe",
-    "sphinx_togglebutton",
 ]
 
-
 # API settings
 autodoc_default_options = {
     "members": True,
@@ -116,10 +111,6 @@
 linkcheck_ignore = []  # type: ignore
 
 execution_timeout = -1
-jupyter_execute_notebooks = "off"
-if "EXECUTE_NB" in os.environ:
-    print("\033[93;1mWill run Jupyter notebooks!\033[0m")
-    jupyter_execute_notebooks = "force"
 
 # Settings for myst-parser
 myst_enable_extensions = [
@@ -156,32 +147,14 @@
 html_css_files = [
     "custom.css",
 ]
-html_sourcelink_suffix = ""
-html_static_path = ["_static"]
-html_theme = "sphinx_book_theme"
-html_theme_options = {
-    "launch_buttons": {
-        "binderhub_url": "https://mybinder.org",
-        "colab_url": "https://colab.research.google.com",
-        "notebook_interface": "jupyterlab",
-        "thebe": True,
-        "thebelab": True,
-    },
-    "path_to_docs": "docs",
-    "repository_branch": "main",
-    "repository_url": "https://github.com/ianhi/mpl-image-segmenter",
-    "use_download_button": True,
-    "use_edit_page_button": True,
-    "use_issues_button": True,
-    "use_repository_button": True,
-}
 html_title = "mpl-image-segmenter"
+html_theme = "furo"
 
 master_doc = "index"
-thebe_config = {
-    "repository_url": html_theme_options["repository_url"],
-    "repository_branch": html_theme_options["repository_branch"],
-}
+# thebe_config = {
+#     "repository_url": html_theme_options["repository_url"],
+#     "repository_branch": html_theme_options["repository_branch"],
+# }
 
 
 # based on pandas/doc/source/conf.py

docs/conf.py

@@ -10,14 +10,14 @@ On moving to it's own package a few changes to API were made.
 The class is now named `ImageSegmenter`
 **mpl-image-segmenter**
 ```python
-from mpl-image-segmenter import ImageSegmenter
+from mpl_image_segmenter import ImageSegmenter
 
 segmenter = ImageSegmenter(img)
 ```
 
 **mpl-interactions**
 ```python
-from mpl-interactions import image_segmenter
+from mpl_interactions import image_segmenter
 segmenter = image_segmenter(img)
 ```
 
@@ -26,6 +26,7 @@ segmenter = image_segmenter(img)
 The `lineprops` argument has been dropped in favor `props` to be consistent with
 Matplotlib 3.7+.
 
+The `color_image` argument was introduced in order to allow for the new behavior of allowing a stack of images.
 
 ## Properties
 
@@ -34,3 +35,6 @@ Matplotlib 3.7+.
 
 
 `segmenter.verts` which was never fully functional has been removed and replaced by `segmenter.get_paths()`
+
+## Stacking
+You can now pass a stack of images, and control which is currently displayed using the `image_index` property.

docs/differences.md

@@ -0,0 +1,96 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "b0664eca-1f81-43ae-8f4a-d514b86a5bf5",
+   "metadata": {},
+   "source": [
+    "# Integration with ipywidgets\n",
+    "\n",
+    "To reduce friction in the labelling workflow you can construct controls for the currently selected class and whether to be in erasing mode using ipywidgets."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f1bab7f9-34df-463e-b6ec-52df6fba5737",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "%matplotlib ipympl"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a5ad14e1-4525-4093-bd7d-449a355784a5",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import ipywidgets as widgets\n",
+    "from mpl_image_segmenter import ImageSegmenter\n",
+    "from mpl_image_segmenter.example_images import gray_image_stack\n",
+    "\n",
+    "\n",
+    "image_stack = gray_image_stack()\n",
+    "\n",
+    "N_classes = 3\n",
+    "\n",
+    "\n",
+    "\n",
+    "segmenter = ImageSegmenter(image_stack, classes=N_classes, mask_alpha=0.76, cmap='gray')\n",
+    "\n",
+    "def set_class(change):\n",
+    "    segmenter.current_class = class_selector.value\n",
+    "\n",
+    "def set_erasing(change):\n",
+    "    segmenter.erasing = erasing_button.value\n",
+    "\n",
+    "def set_img(change):\n",
+    "    segmenter.image_index = change['new']\n",
+    "\n",
+    "class_selector = widgets.Dropdown(options=list(range(1, N_classes + 1)), description=\"class\")\n",
+    "img_slider = widgets.IntSlider(value=0, min=0, max=image_stack.shape[0]-1, description=\"img index\")\n",
+    "erasing_button = widgets.Checkbox(value=False, description=\"Erasing\")\n",
+    "\n",
+    "erasing_button.observe(set_erasing, names=\"value\")\n",
+    "class_selector.observe(set_class, names=\"value\")\n",
+    "img_slider.observe(set_img, names=\"value\")\n",
+    "\n",
+    "display(widgets.VBox([widgets.HBox([erasing_button, class_selector, img_slider]), segmenter.fig.canvas]))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.0"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}