Merge pull request #61 from zivy/moveToModernNotebooks

Move to modern notebooks

Author: zivy

.github/workflows/main.yml

@@ -45,7 +45,7 @@ jobs:
       matrix:
         # using macos-15-intel, last available intel architecture. macos-latest is arm64 architecture.
         os: [ubuntu-latest, windows-latest, macos-latest, macos-15-intel]
-        inputs: ["00_ or 01_ or 02_ or 03_ or 04_ or 05_", "06_ or 07_ or 08_ or 09_ or 10_"]
+        inputs: ["00_ or 01_ or 03_ or 04_ or 05_", "06_ or 07_ or 08_ or 09_ or 10_"]
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v6

00_setup.ipynb

@@ -13,16 +13,19 @@
     "\n",
     "For additional details see the [Jupyter project documentation](https://jupyter.org/documentation) on Jupyter Notebook or JupyterLab.\n",
     "\n",
-    "## Convenience\n",
+    "## Convenience (notebook v7.x)\n",
     "By default the contents of the Jupyter notebooks do not occupy the full browser window width. To take advantage of the full window width you can either configure each notebook independently by adding the following into a code cell:\n",
+    "\n",
     "```\n",
-    "from IPython.core.display import display, HTML\n",
-    "display(HTML(\"<style>.container { width:100% !important; }</style>\"))\n",
+    "from IPython.display import display, HTML\n",
+    "display(HTML(\"<style>:root { --jp-notebook-max-width: 100% !important; }</style>\"))\n",
     "```\n",
     "Or apply this configuration to all notebooks by adding the following to\n",
     "the custom.css jupyter configuration file:\n",
     "```\n",
-    ".container { width:100% !important; }\n",
+    ":root {\n",
+    "    --jp-notebook-max-width: 100% !important;\n",
+    "}\n",
     "```\n",
     "On OSX/Linux this file is found in `~/.jupyter/custom/custom.css` on windows it is\n",
     "found in `C:\\Users\\[your_user_name]\\.jupyter\\custom\\custom.css`.\n",
@@ -120,7 +123,9 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true
+   },
    "source": [
     "<a href=\"01_spatial_transformations.ipynb\"><h2 align=right>Next &raquo;</h2></a>"
    ]
@@ -142,9 +147,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

01_spatial_transformations.ipynb

@@ -296,6 +296,7 @@
     "    plt.xlim(xlim)\n",
     "    plt.ylim(ylim)\n",
     "    plt.legend(loc=(0.25, 1.01))\n",
+    "    plt.show()\n",
     "\n",
     "\n",
     "# 2D square centered on (0,0)\n",
@@ -667,7 +668,7 @@
     "original_transformed = np.array(bspline.TransformPoint(pnt))\n",
     "secondary_transformed = np.array(displacement_field_transform.TransformPoint(pnt))\n",
     "print(\"Original transformation result: {0}\".format(original_transformed))\n",
-    "print(\"Deformaiton field transformation result: {0}\".format(secondary_transformed))\n",
+    "print(\"Deformation field transformation result: {0}\".format(secondary_transformed))\n",
     "print(\n",
     "    \"Difference between transformed points is: {0}\".format(\n",
     "        np.linalg.norm(original_transformed - secondary_transformed)\n",
@@ -863,7 +864,9 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true
+   },
    "source": [
     "<a href=\"02_images_and_resampling.ipynb\"><h2 align=right>Next &raquo;</h2></a>"
    ]
@@ -885,9 +888,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

02_images_and_resampling.ipynb

@@ -135,7 +135,10 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "Or, creation from file."
@@ -309,7 +312,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Comparative operators (>, >=, <, <=, ==) are also supported, returning binary images."
+    "Comparative operators (>, >=, <, <=, ==) are also supported, returning binary images with pixel type of sitkUInt8."
    ]
   },
   {
@@ -552,7 +555,10 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "Write the volume as a series of JPEGs. The WriteImage function receives a volume and a list of images names and writes the volume according to the z axis. For a displayable result we need to rescale the image intensities (default is [0,255]) since the JPEG format requires a cast to the UInt8 pixel type."
@@ -820,9 +826,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

03_trust_but_verify.ipynb

@@ -70,11 +70,10 @@
     "import tempfile\n",
     "import pickle\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib ipympl\n",
     "import matplotlib.pyplot as plt\n",
     "import ipywidgets as widgets\n",
     "\n",
-    "\n",
     "# utility method that either downloads data from the Girder repository or\n",
     "# if already downloaded returns the file name for reading from disk (cached data)\n",
     "from downloaddata import fetch_data as fdata\n",
@@ -498,6 +497,7 @@
     "        )\n",
     "        self.fig.tight_layout()\n",
     "        self.update_display()\n",
+    "        plt.show()\n",
     "\n",
     "    def create_ui(self):\n",
     "        # Create the active GUI components. Height and width are specified in 'em' units. This is\n",
@@ -677,9 +677,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "with open(faux_image_volume_file_name, \"rb\") as fp:\n",
@@ -734,9 +732,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "with open(faux_series_volume_file_name, \"rb\") as fp:\n",
@@ -764,7 +760,9 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true
+   },
    "source": [
     "<a href=\"04_data_augmentation.ipynb\"><h2 align=right>Next &raquo;</h2></a>"
    ]
@@ -786,7 +784,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,

04_data_augmentation.ipynb

@@ -29,7 +29,7 @@
     "import numpy as np\n",
     "import os\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib ipympl\n",
     "import gui\n",
     "\n",
     "from downloaddata import fetch_data as fdata\n",
@@ -386,7 +386,10 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "## What about flipping\n",
@@ -884,9 +887,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

05_basic_registration.ipynb

@@ -130,7 +130,7 @@
     "import SimpleITK as sitk\n",
     "from downloaddata import fetch_data as fdata\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib ipympl\n",
     "import gui\n",
     "import registration_gui as rgui\n",
     "\n",
@@ -445,7 +445,10 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "## Initialization\n",
@@ -757,9 +760,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

06_advanced_registration.ipynb

@@ -687,7 +687,11 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jp-MarkdownHeadingCollapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "<a href=\"07_registration_application.ipynb\"><h2 align=right>Next &raquo;</h2></a>"
@@ -710,9 +714,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

07_registration_application.ipynb

@@ -45,7 +45,7 @@
     "import os.path\n",
     "import copy\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib ipympl\n",
     "import gui\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
@@ -115,9 +115,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# The ROI we specify is in a region that is expected to have uniform intensities.\n",
@@ -473,9 +471,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "metric_sampling_percentage = 0.2\n",
@@ -684,9 +680,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

08_segmentation_and_shape_analysis.ipynb

@@ -23,7 +23,7 @@
     "import SimpleITK as sitk\n",
     "import pandas as pd\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib ipympl\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "import gui\n",
@@ -432,9 +432,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "bacteria_labels = shape_stats.GetLabels()\n",
@@ -505,9 +503,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }