docs formatting

docs/source/generated/backreferences/osipi.aif_parker.examples

@@ -11,6 +11,70 @@ Examples using ``osipi.aif_parker``
 
     <div class="sphx-glr-thumbnails">
 
+.. thumbnail-parent-div-open
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Simulating a Parker AIF with different settings.">
+
+.. only:: html
+
+  .. image:: /generated/examples/aif/images/thumb/sphx_glr_plot_aif_parker_thumb.png
+    :alt:
+
+  :ref:`sphx_glr_generated_examples_aif_plot_aif_parker.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">The Parker AIF - a play with variables</div>
+    </div>
+
+
+.. only:: not html
+
+ * :ref:`sphx_glr_generated_examples_aif_plot_aif_parker.py`
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Dummy script to illustrate structure of examples folder">
+
+.. only:: html
+
+  .. image:: /generated/examples/aif/images/thumb/sphx_glr_plot_dummy_thumb.png
+    :alt:
+
+  :ref:`sphx_glr_generated_examples_aif_plot_dummy.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">A dummy script</div>
+    </div>
+
+
+.. only:: not html
+
+ * :ref:`sphx_glr_generated_examples_aif_plot_dummy.py`
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Simulating tissue concentrations from Tofts model with different settings.">
+
+.. only:: html
+
+  .. image:: /generated/examples/tissue/images/thumb/sphx_glr_plot_tofts_thumb.png
+    :alt:
+
+  :ref:`sphx_glr_generated_examples_tissue_plot_tofts.py`
+
+.. raw:: html
+
+      <div class="sphx-glr-thumbnail-title">The Tofts model</div>
+    </div>
+
+
+.. only:: not html
+
+ * :ref:`sphx_glr_generated_examples_tissue_plot_tofts.py`
 
 .. raw:: html
 
@@ -33,6 +97,8 @@ Examples using ``osipi.aif_parker``
 
  * :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
 
+.. thumbnail-parent-div-close
+
 .. raw:: html
 
     </div>

docs/source/generated/backreferences/osipi.extended_tofts.examples

@@ -11,6 +11,7 @@ Examples using ``osipi.extended_tofts``
 
     <div class="sphx-glr-thumbnails">
 
+.. thumbnail-parent-div-open
 
 .. raw:: html
 
@@ -33,6 +34,8 @@ Examples using ``osipi.extended_tofts``
 
  * :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
 
+.. thumbnail-parent-div-close
+
 .. raw:: html
 
     </div>

docs/source/generated/backreferences/osipi.tofts.examples

@@ -11,6 +11,7 @@ Examples using ``osipi.tofts``
 
     <div class="sphx-glr-thumbnails">
 
+.. thumbnail-parent-div-open
 
 .. raw:: html
 
@@ -33,6 +34,8 @@ Examples using ``osipi.tofts``
 
  * :ref:`sphx_glr_generated_examples_tissue_plot_tofts.py`
 
+.. thumbnail-parent-div-close
+
 .. raw:: html
 
     </div>

docs/source/generated/examples/aif/index.rst

@@ -8,16 +8,15 @@ Arterial Input Functions
 
 
 
-
-
 .. raw:: html
 
     <div class="sphx-glr-thumbnails">
 
+.. thumbnail-parent-div-open
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Simulating a Parker AIF with different settings. ">
+    <div class="sphx-glr-thumbcontainer" tooltip="Simulating a Parker AIF with different settings.">
 
 .. only:: html
 
@@ -34,7 +33,7 @@ Arterial Input Functions
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Dummy script to illustrate structure of examples folder ">
+    <div class="sphx-glr-thumbcontainer" tooltip="Dummy script to illustrate structure of examples folder">
 
 .. only:: html
 
@@ -49,6 +48,8 @@ Arterial Input Functions
     </div>
 
 
+.. thumbnail-parent-div-close
+
 .. raw:: html
 
     </div>

docs/source/generated/examples/aif/plot_aif_parker.ipynb

@@ -1,113 +1,97 @@
 {
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "\n# The Parker AIF - a play with variables\n\nSimulating a Parker AIF with different settings. \n"
-   ]
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# The Parker AIF - a play with variables\n\nSimulating a Parker AIF with different settings.\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "import matplotlib.pyplot as plt"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Import necessary packages\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "import numpy as np\nimport osipi"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Generate synthetic AIF with default settings and plot the result.\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "# Define time points in units of seconds - in this case we use a time\n# resolution of 0.5 sec and a total duration of 6 minutes.\nt = np.arange(0, 6 * 60, 0.5)\n\n# Create an AIF with default settings\nca = osipi.aif_parker(t)\n\n# Plot the AIF over the full range\nplt.plot(t, ca, \"r-\")\nplt.plot(t, 0 * t, \"k-\")\nplt.xlabel(\"Time (sec)\")\nplt.ylabel(\"Plasma concentration (mM)\")\nplt.show()"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "The bolus arrival time (BAT) defaults to 0s. What happens if we\nchange it? Let's try, by changing it in steps of 30s:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "ca = osipi.aif_parker(t, BAT=0)\nplt.plot(t, ca, \"b-\", label=\"BAT = 0s\")\nca = osipi.aif_parker(t, BAT=30)\nplt.plot(t, ca, \"r-\", label=\"BAT = 30s\")\nca = osipi.aif_parker(t, BAT=60)\nplt.plot(t, ca, \"g-\", label=\"BAT = 60s\")\nca = osipi.aif_parker(t, BAT=90)\nplt.plot(t, ca, \"m-\", label=\"BAT = 90s\")\nplt.xlabel(\"Time (sec)\")\nplt.ylabel(\"Plasma concentration (mM)\")\nplt.legend()\nplt.show()\n\n# Choose the last image as a thumbnail for the gallery\n# sphinx_gallery_thumbnail_number = -1"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "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": "3.10.8"
+    }
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Import necessary packages\n\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import osipi"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Generate synthetic AIF with default settings and plot the result.\n\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "# Define time points in units of seconds - in this case we use a time resolution of 0.5 sec and a total duration of 6 minutes.\n",
-    "t = np.arange(0, 6 * 60, 0.5)\n",
-    "\n",
-    "# Create an AIF with default settings\n",
-    "ca = osipi.aif_parker(t)\n",
-    "\n",
-    "# Plot the AIF over the full range\n",
-    "plt.plot(t, ca, \"r-\")\n",
-    "plt.plot(t, 0 * t, \"k-\")\n",
-    "plt.xlabel(\"Time (sec)\")\n",
-    "plt.ylabel(\"Plasma concentration (mM)\")\n",
-    "plt.show()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "The bolus arrival time (BAT) defaults to 0s. What happens if we change it? Let's try, by changing it in steps of 30s:\n\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "ca = osipi.aif_parker(t, BAT=0)\n",
-    "plt.plot(t, ca, \"b-\", label=\"BAT = 0s\")\n",
-    "ca = osipi.aif_parker(t, BAT=30)\n",
-    "plt.plot(t, ca, \"r-\", label=\"BAT = 30s\")\n",
-    "ca = osipi.aif_parker(t, BAT=60)\n",
-    "plt.plot(t, ca, \"g-\", label=\"BAT = 60s\")\n",
-    "ca = osipi.aif_parker(t, BAT=90)\n",
-    "plt.plot(t, ca, \"m-\", label=\"BAT = 90s\")\n",
-    "plt.xlabel(\"Time (sec)\")\n",
-    "plt.ylabel(\"Plasma concentration (mM)\")\n",
-    "plt.legend()\n",
-    "plt.show()\n",
-    "\n",
-    "# Choose the last image as a thumbnail for the gallery\n",
-    "# sphinx_gallery_thumbnail_number = -1"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "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": "3.9.16"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 0
+  "nbformat": 4,
+  "nbformat_minor": 0
 }

docs/source/generated/examples/aif/plot_aif_parker.py

@@ -1,7 +1,9 @@
-"""======================================
+"""
+======================================
+The Parker AIF - a play with variables
+======================================
 
-The Parker AIF - a play with variables ======================================  Simulating a Parker
-AIF with different settings.
+Simulating a Parker AIF with different settings.
 
 """
 

docs/source/generated/examples/aif/plot_aif_parker.py.md5

@@ -1 +1 @@
-2ad42a0f8a1b8aa8ec46f9a5f66e86e4
+e93d51ea52bd242140d5fb616a34364e