diff --git a/.gitignore b/.gitignore
index cd03b8d..2ac6e53 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,5 @@ tests/__pycache__
.coverage
junit
docs/build
+docs/source/generated
+docs/source/sg_execution_times.rst
diff --git a/docs/source/generated/.DS_Store b/docs/source/generated/.DS_Store
deleted file mode 100644
index 6e4d486..0000000
Binary files a/docs/source/generated/.DS_Store and /dev/null differ
diff --git a/docs/source/generated/api/osipi.aif_georgiou.rst b/docs/source/generated/api/osipi.aif_georgiou.rst
deleted file mode 100755
index 598737f..0000000
--- a/docs/source/generated/api/osipi.aif_georgiou.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-osipi.aif\_georgiou
-===================
-
-
-.. currentmodule:: osipi
-
-
-
-.. autofunction:: aif_georgiou
-
-
-
-
-
-
-.. minigallery:: osipi.aif_georgiou
- :add-heading:
diff --git a/docs/source/generated/api/osipi.aif_parker.rst b/docs/source/generated/api/osipi.aif_parker.rst
deleted file mode 100755
index f910623..0000000
--- a/docs/source/generated/api/osipi.aif_parker.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-osipi.aif\_parker
-=================
-
-
-.. currentmodule:: osipi
-
-
-
-.. autofunction:: aif_parker
-
-
-
-
-
-
-.. minigallery:: osipi.aif_parker
- :add-heading:
diff --git a/docs/source/generated/api/osipi.aif_weinmann.rst b/docs/source/generated/api/osipi.aif_weinmann.rst
deleted file mode 100755
index 14f68bd..0000000
--- a/docs/source/generated/api/osipi.aif_weinmann.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-osipi.aif\_weinmann
-===================
-
-
-.. currentmodule:: osipi
-
-
-
-.. autofunction:: aif_weinmann
-
-
-
-
-
-
-.. minigallery:: osipi.aif_weinmann
- :add-heading:
diff --git a/docs/source/generated/api/osipi.extended_tofts.rst b/docs/source/generated/api/osipi.extended_tofts.rst
deleted file mode 100755
index 5a9d3c5..0000000
--- a/docs/source/generated/api/osipi.extended_tofts.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-osipi.extended\_tofts
-=====================
-
-
-.. currentmodule:: osipi
-
-
-
-.. autofunction:: extended_tofts
-
-
-
-
-
-
-.. minigallery:: osipi.extended_tofts
- :add-heading:
diff --git a/docs/source/generated/api/osipi.tofts.rst b/docs/source/generated/api/osipi.tofts.rst
deleted file mode 100755
index 48f8f3c..0000000
--- a/docs/source/generated/api/osipi.tofts.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-osipi.tofts
-===========
-
-
-.. currentmodule:: osipi
-
-
-
-.. autofunction:: tofts
-
-
-
-
-
-
-.. minigallery:: osipi.tofts
- :add-heading:
diff --git a/docs/source/generated/backreferences/osipi.aif_georgiou.examples b/docs/source/generated/backreferences/osipi.aif_georgiou.examples
deleted file mode 100755
index e69de29..0000000
diff --git a/docs/source/generated/backreferences/osipi.aif_parker.examples b/docs/source/generated/backreferences/osipi.aif_parker.examples
deleted file mode 100755
index 19ff462..0000000
--- a/docs/source/generated/backreferences/osipi.aif_parker.examples
+++ /dev/null
@@ -1,104 +0,0 @@
-
-
-Examples using ``osipi.aif_parker``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-.. start-sphx-glr-thumbnails
-
-
-.. raw:: html
-
-
-
-.. thumbnail-parent-div-open
-
-.. raw:: html
-
-
-
-.. 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
-
-
The Parker AIF - a play with variables
-
-
-
-.. only:: not html
-
- * :ref:`sphx_glr_generated_examples_aif_plot_aif_parker.py`
-
-.. raw:: html
-
-
-
-.. 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
-
-
A dummy script
-
-
-
-.. only:: not html
-
- * :ref:`sphx_glr_generated_examples_aif_plot_dummy.py`
-
-.. raw:: html
-
-
-
-.. 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
-
-
The Tofts model
-
-
-
-.. only:: not html
-
- * :ref:`sphx_glr_generated_examples_tissue_plot_tofts.py`
-
-.. raw:: html
-
-
-
-.. only:: html
-
- .. image:: /generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png
- :alt:
-
- :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
-
-.. raw:: html
-
-
The Extended Tofts model
-
-
-
-.. only:: not html
-
- * :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
-
-.. thumbnail-parent-div-close
-
-.. raw:: html
-
-
diff --git a/docs/source/generated/backreferences/osipi.aif_weinmann.examples b/docs/source/generated/backreferences/osipi.aif_weinmann.examples
deleted file mode 100755
index e69de29..0000000
diff --git a/docs/source/generated/backreferences/osipi.extended_tofts.examples b/docs/source/generated/backreferences/osipi.extended_tofts.examples
deleted file mode 100755
index 945a7bb..0000000
--- a/docs/source/generated/backreferences/osipi.extended_tofts.examples
+++ /dev/null
@@ -1,41 +0,0 @@
-
-
-Examples using ``osipi.extended_tofts``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-.. start-sphx-glr-thumbnails
-
-
-.. raw:: html
-
-
-
-.. thumbnail-parent-div-open
-
-.. raw:: html
-
-
-
-.. only:: html
-
- .. image:: /generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png
- :alt:
-
- :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
-
-.. raw:: html
-
-
The Extended Tofts model
-
-
-
-.. only:: not html
-
- * :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
-
-.. thumbnail-parent-div-close
-
-.. raw:: html
-
-
diff --git a/docs/source/generated/backreferences/osipi.tofts.examples b/docs/source/generated/backreferences/osipi.tofts.examples
deleted file mode 100755
index 78bbfe4..0000000
--- a/docs/source/generated/backreferences/osipi.tofts.examples
+++ /dev/null
@@ -1,41 +0,0 @@
-
-
-Examples using ``osipi.tofts``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-.. start-sphx-glr-thumbnails
-
-
-.. raw:: html
-
-
-
-.. thumbnail-parent-div-open
-
-.. raw:: html
-
-
-
-.. 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
-
-
The Tofts model
-
-
-
-.. only:: not html
-
- * :ref:`sphx_glr_generated_examples_tissue_plot_tofts.py`
-
-.. thumbnail-parent-div-close
-
-.. raw:: html
-
-
diff --git a/docs/source/generated/examples/aif/images/sphx_glr_plot_aif_parker_001.png b/docs/source/generated/examples/aif/images/sphx_glr_plot_aif_parker_001.png
deleted file mode 100755
index b08ebc8..0000000
Binary files a/docs/source/generated/examples/aif/images/sphx_glr_plot_aif_parker_001.png and /dev/null differ
diff --git a/docs/source/generated/examples/aif/images/sphx_glr_plot_aif_parker_002.png b/docs/source/generated/examples/aif/images/sphx_glr_plot_aif_parker_002.png
deleted file mode 100755
index 326d195..0000000
Binary files a/docs/source/generated/examples/aif/images/sphx_glr_plot_aif_parker_002.png and /dev/null differ
diff --git a/docs/source/generated/examples/aif/images/sphx_glr_plot_dummy_001.png b/docs/source/generated/examples/aif/images/sphx_glr_plot_dummy_001.png
deleted file mode 100755
index b08ebc8..0000000
Binary files a/docs/source/generated/examples/aif/images/sphx_glr_plot_dummy_001.png and /dev/null differ
diff --git a/docs/source/generated/examples/aif/images/sphx_glr_plot_dummy_002.png b/docs/source/generated/examples/aif/images/sphx_glr_plot_dummy_002.png
deleted file mode 100755
index 326d195..0000000
Binary files a/docs/source/generated/examples/aif/images/sphx_glr_plot_dummy_002.png and /dev/null differ
diff --git a/docs/source/generated/examples/aif/images/thumb/sphx_glr_plot_aif_parker_thumb.png b/docs/source/generated/examples/aif/images/thumb/sphx_glr_plot_aif_parker_thumb.png
deleted file mode 100755
index 22d8ed5..0000000
Binary files a/docs/source/generated/examples/aif/images/thumb/sphx_glr_plot_aif_parker_thumb.png and /dev/null differ
diff --git a/docs/source/generated/examples/aif/images/thumb/sphx_glr_plot_dummy_thumb.png b/docs/source/generated/examples/aif/images/thumb/sphx_glr_plot_dummy_thumb.png
deleted file mode 100755
index 22d8ed5..0000000
Binary files a/docs/source/generated/examples/aif/images/thumb/sphx_glr_plot_dummy_thumb.png and /dev/null differ
diff --git a/docs/source/generated/examples/aif/index.rst b/docs/source/generated/examples/aif/index.rst
deleted file mode 100755
index c83c965..0000000
--- a/docs/source/generated/examples/aif/index.rst
+++ /dev/null
@@ -1,62 +0,0 @@
-
-
-.. _sphx_glr_generated_examples_aif:
-
-************************
-Arterial Input Functions
-************************
-
-
-
-.. raw:: html
-
-
-
-.. thumbnail-parent-div-open
-
-.. raw:: html
-
-
-
-.. 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
-
-
The Parker AIF - a play with variables
-
-
-
-.. raw:: html
-
-
-
-.. 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
-
-
A dummy script
-
-
-
-.. thumbnail-parent-div-close
-
-.. raw:: html
-
-
-
-
-.. toctree::
- :hidden:
-
- /generated/examples/aif/plot_aif_parker
- /generated/examples/aif/plot_dummy
diff --git a/docs/source/generated/examples/aif/plot_aif_parker.ipynb b/docs/source/generated/examples/aif/plot_aif_parker.ipynb
deleted file mode 100755
index 3276336..0000000
--- a/docs/source/generated/examples/aif/plot_aif_parker.ipynb
+++ /dev/null
@@ -1,97 +0,0 @@
-{
- "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"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
diff --git a/docs/source/generated/examples/aif/plot_aif_parker.py b/docs/source/generated/examples/aif/plot_aif_parker.py
deleted file mode 100755
index 374cbce..0000000
--- a/docs/source/generated/examples/aif/plot_aif_parker.py
+++ /dev/null
@@ -1,52 +0,0 @@
-"""
-======================================
-The Parker AIF - a play with variables
-======================================
-
-Simulating a Parker AIF with different settings.
-
-"""
-
-import matplotlib.pyplot as plt
-
-# %%
-# Import necessary packages
-import numpy as np
-import osipi
-
-# %%
-# Generate synthetic AIF with default settings and plot the result.
-
-# 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.
-t = np.arange(0, 6 * 60, 0.5)
-
-# Create an AIF with default settings
-ca = osipi.aif_parker(t)
-
-# Plot the AIF over the full range
-plt.plot(t, ca, "r-")
-plt.plot(t, 0 * t, "k-")
-plt.xlabel("Time (sec)")
-plt.ylabel("Plasma concentration (mM)")
-plt.show()
-
-# %%
-# The bolus arrival time (BAT) defaults to 0s. What happens if we
-# change it? Let's try, by changing it in steps of 30s:
-
-ca = osipi.aif_parker(t, BAT=0)
-plt.plot(t, ca, "b-", label="BAT = 0s")
-ca = osipi.aif_parker(t, BAT=30)
-plt.plot(t, ca, "r-", label="BAT = 30s")
-ca = osipi.aif_parker(t, BAT=60)
-plt.plot(t, ca, "g-", label="BAT = 60s")
-ca = osipi.aif_parker(t, BAT=90)
-plt.plot(t, ca, "m-", label="BAT = 90s")
-plt.xlabel("Time (sec)")
-plt.ylabel("Plasma concentration (mM)")
-plt.legend()
-plt.show()
-
-# Choose the last image as a thumbnail for the gallery
-# sphinx_gallery_thumbnail_number = -1
diff --git a/docs/source/generated/examples/aif/plot_aif_parker.py.md5 b/docs/source/generated/examples/aif/plot_aif_parker.py.md5
deleted file mode 100755
index 3b68fca..0000000
--- a/docs/source/generated/examples/aif/plot_aif_parker.py.md5
+++ /dev/null
@@ -1 +0,0 @@
-e93d51ea52bd242140d5fb616a34364e
diff --git a/docs/source/generated/examples/aif/plot_aif_parker.rst b/docs/source/generated/examples/aif/plot_aif_parker.rst
deleted file mode 100755
index f5df0a9..0000000
--- a/docs/source/generated/examples/aif/plot_aif_parker.rst
+++ /dev/null
@@ -1,156 +0,0 @@
-
-.. DO NOT EDIT.
-.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
-.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "generated\examples\aif\plot_aif_parker.py"
-.. LINE NUMBERS ARE GIVEN BELOW.
-
-.. only:: html
-
- .. note::
- :class: sphx-glr-download-link-note
-
- :ref:`Go to the end `
- to download the full example code.
-
-.. rst-class:: sphx-glr-example-title
-
-.. _sphx_glr_generated_examples_aif_plot_aif_parker.py:
-
-
-======================================
-The Parker AIF - a play with variables
-======================================
-
-Simulating a Parker AIF with different settings.
-
-.. GENERATED FROM PYTHON SOURCE LINES 9-12
-
-.. code-block:: Python
-
-
- import matplotlib.pyplot as plt
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 13-14
-
-Import necessary packages
-
-.. GENERATED FROM PYTHON SOURCE LINES 14-17
-
-.. code-block:: Python
-
- import numpy as np
- import osipi
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 18-19
-
-Generate synthetic AIF with default settings and plot the result.
-
-.. GENERATED FROM PYTHON SOURCE LINES 19-34
-
-.. code-block:: Python
-
-
- # 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.
- t = np.arange(0, 6 * 60, 0.5)
-
- # Create an AIF with default settings
- ca = osipi.aif_parker(t)
-
- # Plot the AIF over the full range
- plt.plot(t, ca, "r-")
- plt.plot(t, 0 * t, "k-")
- plt.xlabel("Time (sec)")
- plt.ylabel("Plasma concentration (mM)")
- plt.show()
-
-
-
-
-.. image-sg:: /generated/examples/aif/images/sphx_glr_plot_aif_parker_001.png
- :alt: plot aif parker
- :srcset: /generated/examples/aif/images/sphx_glr_plot_aif_parker_001.png
- :class: sphx-glr-single-img
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 35-37
-
-The bolus arrival time (BAT) defaults to 0s. What happens if we
-change it? Let's try, by changing it in steps of 30s:
-
-.. GENERATED FROM PYTHON SOURCE LINES 37-53
-
-.. code-block:: Python
-
-
- ca = osipi.aif_parker(t, BAT=0)
- plt.plot(t, ca, "b-", label="BAT = 0s")
- ca = osipi.aif_parker(t, BAT=30)
- plt.plot(t, ca, "r-", label="BAT = 30s")
- ca = osipi.aif_parker(t, BAT=60)
- plt.plot(t, ca, "g-", label="BAT = 60s")
- ca = osipi.aif_parker(t, BAT=90)
- plt.plot(t, ca, "m-", label="BAT = 90s")
- plt.xlabel("Time (sec)")
- plt.ylabel("Plasma concentration (mM)")
- plt.legend()
- plt.show()
-
- # Choose the last image as a thumbnail for the gallery
- # sphinx_gallery_thumbnail_number = -1
-
-
-
-.. image-sg:: /generated/examples/aif/images/sphx_glr_plot_aif_parker_002.png
- :alt: plot aif parker
- :srcset: /generated/examples/aif/images/sphx_glr_plot_aif_parker_002.png
- :class: sphx-glr-single-img
-
-
-
-
-
-
-.. rst-class:: sphx-glr-timing
-
- **Total running time of the script:** (0 minutes 0.183 seconds)
-
-
-.. _sphx_glr_download_generated_examples_aif_plot_aif_parker.py:
-
-.. only:: html
-
- .. container:: sphx-glr-footer sphx-glr-footer-example
-
- .. container:: sphx-glr-download sphx-glr-download-jupyter
-
- :download:`Download Jupyter notebook: plot_aif_parker.ipynb `
-
- .. container:: sphx-glr-download sphx-glr-download-python
-
- :download:`Download Python source code: plot_aif_parker.py `
-
-
-.. only:: html
-
- .. rst-class:: sphx-glr-signature
-
- `Gallery generated by Sphinx-Gallery `_
diff --git a/docs/source/generated/examples/aif/plot_aif_parker_codeobj.pickle b/docs/source/generated/examples/aif/plot_aif_parker_codeobj.pickle
deleted file mode 100755
index 51b6d51..0000000
Binary files a/docs/source/generated/examples/aif/plot_aif_parker_codeobj.pickle and /dev/null differ
diff --git a/docs/source/generated/examples/aif/plot_dummy.ipynb b/docs/source/generated/examples/aif/plot_dummy.ipynb
deleted file mode 100755
index 2565681..0000000
--- a/docs/source/generated/examples/aif/plot_dummy.ipynb
+++ /dev/null
@@ -1,97 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "\n# A dummy script\n\nDummy script to illustrate structure of examples folder\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 30s. 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"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
diff --git a/docs/source/generated/examples/aif/plot_dummy.py b/docs/source/generated/examples/aif/plot_dummy.py
deleted file mode 100755
index 13cbac2..0000000
--- a/docs/source/generated/examples/aif/plot_dummy.py
+++ /dev/null
@@ -1,51 +0,0 @@
-"""
-==============
-A dummy script
-==============
-
-Dummy script to illustrate structure of examples folder
-"""
-
-import matplotlib.pyplot as plt
-
-# %%
-# Import necessary packages
-import numpy as np
-import osipi
-
-# %%
-# Generate synthetic AIF with default settings and plot the result.
-
-# 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.
-t = np.arange(0, 6 * 60, 0.5)
-
-# Create an AIF with default settings
-ca = osipi.aif_parker(t)
-
-# Plot the AIF over the full range
-plt.plot(t, ca, "r-")
-plt.plot(t, 0 * t, "k-")
-plt.xlabel("Time (sec)")
-plt.ylabel("Plasma concentration (mM)")
-plt.show()
-
-# %%
-# The bolus arrival time (BAT) defaults to 30s. What happens if we
-# change it? Let's try, by changing it in steps of 30s:
-
-ca = osipi.aif_parker(t, BAT=0)
-plt.plot(t, ca, "b-", label="BAT = 0s")
-ca = osipi.aif_parker(t, BAT=30)
-plt.plot(t, ca, "r-", label="BAT = 30s")
-ca = osipi.aif_parker(t, BAT=60)
-plt.plot(t, ca, "g-", label="BAT = 60s")
-ca = osipi.aif_parker(t, BAT=90)
-plt.plot(t, ca, "m-", label="BAT = 90s")
-plt.xlabel("Time (sec)")
-plt.ylabel("Plasma concentration (mM)")
-plt.legend()
-plt.show()
-
-# Choose the last image as a thumbnail for the gallery
-# sphinx_gallery_thumbnail_number = -1
diff --git a/docs/source/generated/examples/aif/plot_dummy.py.md5 b/docs/source/generated/examples/aif/plot_dummy.py.md5
deleted file mode 100755
index 481354c..0000000
--- a/docs/source/generated/examples/aif/plot_dummy.py.md5
+++ /dev/null
@@ -1 +0,0 @@
-80d36b7d06c5985854776b4c11214ab1
diff --git a/docs/source/generated/examples/aif/plot_dummy.rst b/docs/source/generated/examples/aif/plot_dummy.rst
deleted file mode 100755
index 06dee68..0000000
--- a/docs/source/generated/examples/aif/plot_dummy.rst
+++ /dev/null
@@ -1,156 +0,0 @@
-
-.. DO NOT EDIT.
-.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
-.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "generated\examples\aif\plot_dummy.py"
-.. LINE NUMBERS ARE GIVEN BELOW.
-
-.. only:: html
-
- .. note::
- :class: sphx-glr-download-link-note
-
- :ref:`Go to the end `
- to download the full example code.
-
-.. rst-class:: sphx-glr-example-title
-
-.. _sphx_glr_generated_examples_aif_plot_dummy.py:
-
-
-==============
-A dummy script
-==============
-
-Dummy script to illustrate structure of examples folder
-
-.. GENERATED FROM PYTHON SOURCE LINES 8-11
-
-.. code-block:: Python
-
-
- import matplotlib.pyplot as plt
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 12-13
-
-Import necessary packages
-
-.. GENERATED FROM PYTHON SOURCE LINES 13-16
-
-.. code-block:: Python
-
- import numpy as np
- import osipi
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 17-18
-
-Generate synthetic AIF with default settings and plot the result.
-
-.. GENERATED FROM PYTHON SOURCE LINES 18-33
-
-.. code-block:: Python
-
-
- # 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.
- t = np.arange(0, 6 * 60, 0.5)
-
- # Create an AIF with default settings
- ca = osipi.aif_parker(t)
-
- # Plot the AIF over the full range
- plt.plot(t, ca, "r-")
- plt.plot(t, 0 * t, "k-")
- plt.xlabel("Time (sec)")
- plt.ylabel("Plasma concentration (mM)")
- plt.show()
-
-
-
-
-.. image-sg:: /generated/examples/aif/images/sphx_glr_plot_dummy_001.png
- :alt: plot dummy
- :srcset: /generated/examples/aif/images/sphx_glr_plot_dummy_001.png
- :class: sphx-glr-single-img
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 34-36
-
-The bolus arrival time (BAT) defaults to 30s. What happens if we
-change it? Let's try, by changing it in steps of 30s:
-
-.. GENERATED FROM PYTHON SOURCE LINES 36-52
-
-.. code-block:: Python
-
-
- ca = osipi.aif_parker(t, BAT=0)
- plt.plot(t, ca, "b-", label="BAT = 0s")
- ca = osipi.aif_parker(t, BAT=30)
- plt.plot(t, ca, "r-", label="BAT = 30s")
- ca = osipi.aif_parker(t, BAT=60)
- plt.plot(t, ca, "g-", label="BAT = 60s")
- ca = osipi.aif_parker(t, BAT=90)
- plt.plot(t, ca, "m-", label="BAT = 90s")
- plt.xlabel("Time (sec)")
- plt.ylabel("Plasma concentration (mM)")
- plt.legend()
- plt.show()
-
- # Choose the last image as a thumbnail for the gallery
- # sphinx_gallery_thumbnail_number = -1
-
-
-
-.. image-sg:: /generated/examples/aif/images/sphx_glr_plot_dummy_002.png
- :alt: plot dummy
- :srcset: /generated/examples/aif/images/sphx_glr_plot_dummy_002.png
- :class: sphx-glr-single-img
-
-
-
-
-
-
-.. rst-class:: sphx-glr-timing
-
- **Total running time of the script:** (0 minutes 0.118 seconds)
-
-
-.. _sphx_glr_download_generated_examples_aif_plot_dummy.py:
-
-.. only:: html
-
- .. container:: sphx-glr-footer sphx-glr-footer-example
-
- .. container:: sphx-glr-download sphx-glr-download-jupyter
-
- :download:`Download Jupyter notebook: plot_dummy.ipynb `
-
- .. container:: sphx-glr-download sphx-glr-download-python
-
- :download:`Download Python source code: plot_dummy.py `
-
-
-.. only:: html
-
- .. rst-class:: sphx-glr-signature
-
- `Gallery generated by Sphinx-Gallery `_
diff --git a/docs/source/generated/examples/aif/plot_dummy_codeobj.pickle b/docs/source/generated/examples/aif/plot_dummy_codeobj.pickle
deleted file mode 100755
index 51b6d51..0000000
Binary files a/docs/source/generated/examples/aif/plot_dummy_codeobj.pickle and /dev/null differ
diff --git a/docs/source/generated/examples/aif/sg_execution_times.rst b/docs/source/generated/examples/aif/sg_execution_times.rst
deleted file mode 100755
index 9b8a507..0000000
--- a/docs/source/generated/examples/aif/sg_execution_times.rst
+++ /dev/null
@@ -1,40 +0,0 @@
-
-:orphan:
-
-.. _sphx_glr_generated_examples_aif_sg_execution_times:
-
-
-Computation times
-=================
-**00:00.301** total execution time for 2 files **from generated\examples\aif**:
-
-.. container::
-
- .. raw:: html
-
-
-
-
-
-
-
- .. list-table::
- :header-rows: 1
- :class: table table-striped sg-datatable
-
- * - Example
- - Time
- - Mem (MB)
- * - :ref:`sphx_glr_generated_examples_aif_plot_aif_parker.py` (``plot_aif_parker.py``)
- - 00:00.183
- - 0.0
- * - :ref:`sphx_glr_generated_examples_aif_plot_dummy.py` (``plot_dummy.py``)
- - 00:00.118
- - 0.0
diff --git a/docs/source/generated/examples/index.rst b/docs/source/generated/examples/index.rst
deleted file mode 100755
index 1f44f23..0000000
--- a/docs/source/generated/examples/index.rst
+++ /dev/null
@@ -1,142 +0,0 @@
-:orphan:
-
-########
-Examples
-########
-
-Illustrating common use cases of osipi.
-
-
-
-.. raw:: html
-
-
-
-.. thumbnail-parent-div-open
-
-.. thumbnail-parent-div-close
-
-.. raw:: html
-
-
-
-************************
-Arterial Input Functions
-************************
-
-
-
-.. raw:: html
-
-
-
-.. thumbnail-parent-div-open
-
-.. raw:: html
-
-
-
-.. 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
-
-
The Parker AIF - a play with variables
-
-
-
-.. raw:: html
-
-
-
-.. 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
-
-
A dummy script
-
-
-
-.. thumbnail-parent-div-close
-
-.. raw:: html
-
-
-
-*********************
-Tissue concentrations
-*********************
-
-
-
-.. raw:: html
-
-
-
-.. thumbnail-parent-div-open
-
-.. raw:: html
-
-
-
-.. 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
-
-
The Tofts model
-
-
-
-.. raw:: html
-
-
-
-.. only:: html
-
- .. image:: /generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png
- :alt:
-
- :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
-
-.. raw:: html
-
-
The Extended Tofts model
-
-
-
-.. thumbnail-parent-div-close
-
-.. raw:: html
-
-
-
-
-.. toctree::
- :hidden:
- :includehidden:
-
-
- /generated/examples/aif/index.rst
- /generated/examples/tissue/index.rst
-
-
-
-.. only:: html
-
- .. rst-class:: sphx-glr-signature
-
- `Gallery generated by Sphinx-Gallery `_
diff --git a/docs/source/generated/examples/sg_execution_times.rst b/docs/source/generated/examples/sg_execution_times.rst
deleted file mode 100755
index e8da946..0000000
--- a/docs/source/generated/examples/sg_execution_times.rst
+++ /dev/null
@@ -1,37 +0,0 @@
-
-:orphan:
-
-.. _sphx_glr_generated_examples_sg_execution_times:
-
-
-Computation times
-=================
-**00:00.000** total execution time for 0 files **from generated/examples**:
-
-.. container::
-
- .. raw:: html
-
-
-
-
-
-
-
- .. list-table::
- :header-rows: 1
- :class: table table-striped sg-datatable
-
- * - Example
- - Time
- - Mem (MB)
- * - N/A
- - N/A
- - N/A
diff --git a/docs/source/generated/examples/tissue/images/sphx_glr_plot_extended_tofts_001.png b/docs/source/generated/examples/tissue/images/sphx_glr_plot_extended_tofts_001.png
deleted file mode 100755
index d1fd592..0000000
Binary files a/docs/source/generated/examples/tissue/images/sphx_glr_plot_extended_tofts_001.png and /dev/null differ
diff --git a/docs/source/generated/examples/tissue/images/sphx_glr_plot_extended_tofts_002.png b/docs/source/generated/examples/tissue/images/sphx_glr_plot_extended_tofts_002.png
deleted file mode 100755
index 579b30a..0000000
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diff --git a/docs/source/generated/examples/tissue/images/sphx_glr_plot_tofts_001.png b/docs/source/generated/examples/tissue/images/sphx_glr_plot_tofts_001.png
deleted file mode 100755
index 7ef6265..0000000
Binary files a/docs/source/generated/examples/tissue/images/sphx_glr_plot_tofts_001.png and /dev/null differ
diff --git a/docs/source/generated/examples/tissue/images/sphx_glr_plot_tofts_002.png b/docs/source/generated/examples/tissue/images/sphx_glr_plot_tofts_002.png
deleted file mode 100755
index 0276780..0000000
Binary files a/docs/source/generated/examples/tissue/images/sphx_glr_plot_tofts_002.png and /dev/null differ
diff --git a/docs/source/generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png b/docs/source/generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png
deleted file mode 100755
index 13e5769..0000000
Binary files a/docs/source/generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png and /dev/null differ
diff --git a/docs/source/generated/examples/tissue/images/thumb/sphx_glr_plot_tofts_thumb.png b/docs/source/generated/examples/tissue/images/thumb/sphx_glr_plot_tofts_thumb.png
deleted file mode 100755
index bd0ec5f..0000000
Binary files a/docs/source/generated/examples/tissue/images/thumb/sphx_glr_plot_tofts_thumb.png and /dev/null differ
diff --git a/docs/source/generated/examples/tissue/index.rst b/docs/source/generated/examples/tissue/index.rst
deleted file mode 100755
index f2e344d..0000000
--- a/docs/source/generated/examples/tissue/index.rst
+++ /dev/null
@@ -1,62 +0,0 @@
-
-
-.. _sphx_glr_generated_examples_tissue:
-
-*********************
-Tissue concentrations
-*********************
-
-
-
-.. raw:: html
-
-
-
-.. thumbnail-parent-div-open
-
-.. raw:: html
-
-
-
-.. 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
-
-
The Tofts model
-
-
-
-.. raw:: html
-
-
-
-.. only:: html
-
- .. image:: /generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png
- :alt:
-
- :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
-
-.. raw:: html
-
-
The Extended Tofts model
-
-
-
-.. thumbnail-parent-div-close
-
-.. raw:: html
-
-
-
-
-.. toctree::
- :hidden:
-
- /generated/examples/tissue/plot_tofts
- /generated/examples/tissue/plot_extended_tofts
diff --git a/docs/source/generated/examples/tissue/plot_extended_tofts.ipynb b/docs/source/generated/examples/tissue/plot_extended_tofts.ipynb
deleted file mode 100755
index b4d9c3c..0000000
--- a/docs/source/generated/examples/tissue/plot_extended_tofts.ipynb
+++ /dev/null
@@ -1,115 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "\n# The Extended Tofts model\n\nSimulating tissue concentrations from extended Tofts model 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 Parker AIF with default settings.\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 1 sec and a total duration of 6 minutes.\nt = np.arange(0, 6 * 60, 1)\n\n# Create an AIF with default settings\nca = osipi.aif_parker(t)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Plot the tissue concentrations for an extracellular volume fraction\nof 0.2 and 3 different plasma volumes of 0.05, 0.2 and 0.6\n\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "Ktrans = 0.2 # in units of 1/min\nve = 0.2 # volume fraction between 0 and 1\nvp = [0.05, 0.2, 0.6] # volume fraction between 0 and 1\nct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0])\nplt.plot(t, ct, \"b-\", label=f\"vp = {vp[0]}\")\nct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[1])\nplt.plot(t, ct, \"g-\", label=f\"vp = {vp[1]}\")\nct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[2])\nplt.plot(t, ct, \"m-\", label=f\"vp = {vp[2]}\")\nplt.xlabel(\"Time (sec)\")\nplt.ylabel(\"Tissue concentration (mM)\")\nplt.legend()\nplt.show()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Comparing different discretization methods for an extracellular\nvolume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05\n\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0]) # Defaults to Convolution\nplt.plot(t, ct, \"b-\", label=\"Convolution\")\nct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0], discretization_method=\"exp\")\nplt.plot(t, ct, \"g-\", label=\"Exponential Convolution\")\nplt.title(f\"Ktrans = {Ktrans} /min\")\nplt.xlabel(\"Time (sec)\")\nplt.ylabel(\"Tissue 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"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
diff --git a/docs/source/generated/examples/tissue/plot_extended_tofts.py b/docs/source/generated/examples/tissue/plot_extended_tofts.py
deleted file mode 100755
index f2df6fb..0000000
--- a/docs/source/generated/examples/tissue/plot_extended_tofts.py
+++ /dev/null
@@ -1,57 +0,0 @@
-"""
-====================
-The Extended Tofts model
-====================
-
-Simulating tissue concentrations from extended Tofts model with different settings.
-"""
-
-import matplotlib.pyplot as plt
-
-# %%
-# Import necessary packages
-import numpy as np
-import osipi
-
-# %%
-# Generate Parker AIF with default settings.
-
-# Define time points in units of seconds - in this case we use a time
-# resolution of 1 sec and a total duration of 6 minutes.
-t = np.arange(0, 6 * 60, 1)
-
-# Create an AIF with default settings
-ca = osipi.aif_parker(t)
-
-# %%
-# Plot the tissue concentrations for an extracellular volume fraction
-# of 0.2 and 3 different plasma volumes of 0.05, 0.2 and 0.6
-Ktrans = 0.2 # in units of 1/min
-ve = 0.2 # volume fraction between 0 and 1
-vp = [0.05, 0.2, 0.6] # volume fraction between 0 and 1
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0])
-plt.plot(t, ct, "b-", label=f"vp = {vp[0]}")
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[1])
-plt.plot(t, ct, "g-", label=f"vp = {vp[1]}")
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[2])
-plt.plot(t, ct, "m-", label=f"vp = {vp[2]}")
-plt.xlabel("Time (sec)")
-plt.ylabel("Tissue concentration (mM)")
-plt.legend()
-plt.show()
-
-# %%
-# Comparing different discretization methods for an extracellular
-# volume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0]) # Defaults to Convolution
-plt.plot(t, ct, "b-", label="Convolution")
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0], discretization_method="exp")
-plt.plot(t, ct, "g-", label="Exponential Convolution")
-plt.title(f"Ktrans = {Ktrans} /min")
-plt.xlabel("Time (sec)")
-plt.ylabel("Tissue concentration (mM)")
-plt.legend()
-plt.show()
-
-# Choose the last image as a thumbnail for the gallery
-# sphinx_gallery_thumbnail_number = -1
diff --git a/docs/source/generated/examples/tissue/plot_extended_tofts.py.md5 b/docs/source/generated/examples/tissue/plot_extended_tofts.py.md5
deleted file mode 100755
index 1e726a8..0000000
--- a/docs/source/generated/examples/tissue/plot_extended_tofts.py.md5
+++ /dev/null
@@ -1 +0,0 @@
-67f6424a8ea349ea69f2a6e0993d78c7
diff --git a/docs/source/generated/examples/tissue/plot_extended_tofts.rst b/docs/source/generated/examples/tissue/plot_extended_tofts.rst
deleted file mode 100755
index 13d638f..0000000
--- a/docs/source/generated/examples/tissue/plot_extended_tofts.rst
+++ /dev/null
@@ -1,175 +0,0 @@
-
-.. DO NOT EDIT.
-.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
-.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "generated\examples\tissue\plot_extended_tofts.py"
-.. LINE NUMBERS ARE GIVEN BELOW.
-
-.. only:: html
-
- .. note::
- :class: sphx-glr-download-link-note
-
- :ref:`Go to the end `
- to download the full example code.
-
-.. rst-class:: sphx-glr-example-title
-
-.. _sphx_glr_generated_examples_tissue_plot_extended_tofts.py:
-
-
-=========================
-The Extended Tofts model
-=========================
-
-Simulating tissue concentrations from extended Tofts model with different settings.
-
-.. GENERATED FROM PYTHON SOURCE LINES 8-11
-
-.. code-block:: Python
-
-
- import matplotlib.pyplot as plt
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 12-13
-
-Import necessary packages
-
-.. GENERATED FROM PYTHON SOURCE LINES 13-16
-
-.. code-block:: Python
-
- import numpy as np
- import osipi
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 17-18
-
-Generate Parker AIF with default settings.
-
-.. GENERATED FROM PYTHON SOURCE LINES 18-26
-
-.. code-block:: Python
-
-
- # Define time points in units of seconds - in this case we use a time
- # resolution of 1 sec and a total duration of 6 minutes.
- t = np.arange(0, 6 * 60, 1)
-
- # Create an AIF with default settings
- ca = osipi.aif_parker(t)
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 27-29
-
-Plot the tissue concentrations for an extracellular volume fraction
-of 0.2 and 3 different plasma volumes of 0.05, 0.2 and 0.6
-
-.. GENERATED FROM PYTHON SOURCE LINES 29-43
-
-.. code-block:: Python
-
- Ktrans = 0.2 # in units of 1/min
- ve = 0.2 # volume fraction between 0 and 1
- vp = [0.05, 0.2, 0.6] # volume fraction between 0 and 1
- ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0])
- plt.plot(t, ct, "b-", label=f"vp = {vp[0]}")
- ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[1])
- plt.plot(t, ct, "g-", label=f"vp = {vp[1]}")
- ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[2])
- plt.plot(t, ct, "m-", label=f"vp = {vp[2]}")
- plt.xlabel("Time (sec)")
- plt.ylabel("Tissue concentration (mM)")
- plt.legend()
- plt.show()
-
-
-
-
-.. image-sg:: /generated/examples/tissue/images/sphx_glr_plot_extended_tofts_001.png
- :alt: plot extended tofts
- :srcset: /generated/examples/tissue/images/sphx_glr_plot_extended_tofts_001.png
- :class: sphx-glr-single-img
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 44-46
-
-Comparing different discretization methods for an extracellular
-volume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05
-
-.. GENERATED FROM PYTHON SOURCE LINES 46-58
-
-.. code-block:: Python
-
- ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0]) # Defaults to Convolution
- plt.plot(t, ct, "b-", label="Convolution")
- ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0], discretization_method="exp")
- plt.plot(t, ct, "g-", label="Exponential Convolution")
- plt.title(f"Ktrans = {Ktrans} /min")
- plt.xlabel("Time (sec)")
- plt.ylabel("Tissue concentration (mM)")
- plt.legend()
- plt.show()
-
- # Choose the last image as a thumbnail for the gallery
- # sphinx_gallery_thumbnail_number = -1
-
-
-
-.. image-sg:: /generated/examples/tissue/images/sphx_glr_plot_extended_tofts_002.png
- :alt: Ktrans = 0.2 /min
- :srcset: /generated/examples/tissue/images/sphx_glr_plot_extended_tofts_002.png
- :class: sphx-glr-single-img
-
-
-
-
-
-
-.. rst-class:: sphx-glr-timing
-
- **Total running time of the script:** (0 minutes 0.136 seconds)
-
-
-.. _sphx_glr_download_generated_examples_tissue_plot_extended_tofts.py:
-
-.. only:: html
-
- .. container:: sphx-glr-footer sphx-glr-footer-example
-
- .. container:: sphx-glr-download sphx-glr-download-jupyter
-
- :download:`Download Jupyter notebook: plot_extended_tofts.ipynb `
-
- .. container:: sphx-glr-download sphx-glr-download-python
-
- :download:`Download Python source code: plot_extended_tofts.py `
-
-
-.. only:: html
-
- .. rst-class:: sphx-glr-signature
-
- `Gallery generated by Sphinx-Gallery `_
diff --git a/docs/source/generated/examples/tissue/plot_extended_tofts_codeobj.pickle b/docs/source/generated/examples/tissue/plot_extended_tofts_codeobj.pickle
deleted file mode 100755
index b58f99b..0000000
Binary files a/docs/source/generated/examples/tissue/plot_extended_tofts_codeobj.pickle and /dev/null differ
diff --git a/docs/source/generated/examples/tissue/plot_tofts.ipynb b/docs/source/generated/examples/tissue/plot_tofts.ipynb
deleted file mode 100755
index 1e137aa..0000000
--- a/docs/source/generated/examples/tissue/plot_tofts.ipynb
+++ /dev/null
@@ -1,115 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "\n# The Tofts model\n\nSimulating tissue concentrations from Tofts model 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 Parker AIF with default settings.\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 1 sec and a total duration of 6 minutes.\nt = np.arange(0, 6 * 60, 1)\n\n# Create an AIF with default settings\nca = osipi.aif_parker(t)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Plot the tissue concentrations for an extracellular volume fraction\nof 0.2 and 3 different transfer rate constants of 0.05, 0.2 and 0.6\n/min\n\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "Ktrans = [0.05, 0.2, 0.6] # in units of 1/min\nve = 0.2 # volume fraction between 0 and 1\nct = osipi.tofts(t, ca, Ktrans=Ktrans[0], ve=ve)\nplt.plot(t, ct, \"b-\", label=f\"Ktrans = {Ktrans[0]} /min\")\nct = osipi.tofts(t, ca, Ktrans[1], ve)\nplt.plot(t, ct, \"g-\", label=f\"Ktrans = {Ktrans[1]} /min\")\nct = osipi.tofts(t, ca, Ktrans[2], ve)\nplt.plot(t, ct, \"m-\", label=f\"Ktrans = {Ktrans[2]} /min\")\nplt.xlabel(\"Time (sec)\")\nplt.ylabel(\"Tissue concentration (mM)\")\nplt.legend()\nplt.show()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Comparing different discretization methods for an extracellular\nvolume fraction of 0.2 and Ktrans of 0.2 /min\n\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve) # Defaults to Convolution\nplt.plot(t, ct, \"b-\", label=\"Convolution\")\nct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve, discretization_method=\"exp\")\nplt.plot(t, ct, \"g-\", label=\"Exponential Convolution\")\nplt.title(f\"Ktrans = {Ktrans[1]} /min\")\nplt.xlabel(\"Time (sec)\")\nplt.ylabel(\"Tissue 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"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
diff --git a/docs/source/generated/examples/tissue/plot_tofts.py b/docs/source/generated/examples/tissue/plot_tofts.py
deleted file mode 100755
index d623da9..0000000
--- a/docs/source/generated/examples/tissue/plot_tofts.py
+++ /dev/null
@@ -1,57 +0,0 @@
-"""
-====================
-The Tofts model
-====================
-
-Simulating tissue concentrations from Tofts model with different settings.
-"""
-
-import matplotlib.pyplot as plt
-
-# %%
-# Import necessary packages
-import numpy as np
-import osipi
-
-# %%
-# Generate Parker AIF with default settings.
-
-# Define time points in units of seconds - in this case we use a time
-# resolution of 1 sec and a total duration of 6 minutes.
-t = np.arange(0, 6 * 60, 1)
-
-# Create an AIF with default settings
-ca = osipi.aif_parker(t)
-
-# %%
-# Plot the tissue concentrations for an extracellular volume fraction
-# of 0.2 and 3 different transfer rate constants of 0.05, 0.2 and 0.6
-# /min
-Ktrans = [0.05, 0.2, 0.6] # in units of 1/min
-ve = 0.2 # volume fraction between 0 and 1
-ct = osipi.tofts(t, ca, Ktrans=Ktrans[0], ve=ve)
-plt.plot(t, ct, "b-", label=f"Ktrans = {Ktrans[0]} /min")
-ct = osipi.tofts(t, ca, Ktrans[1], ve)
-plt.plot(t, ct, "g-", label=f"Ktrans = {Ktrans[1]} /min")
-ct = osipi.tofts(t, ca, Ktrans[2], ve)
-plt.plot(t, ct, "m-", label=f"Ktrans = {Ktrans[2]} /min")
-plt.xlabel("Time (sec)")
-plt.ylabel("Tissue concentration (mM)")
-plt.legend()
-plt.show()
-
-# %%
-# Comparing different discretization methods for an extracellular
-# volume fraction of 0.2 and Ktrans of 0.2 /min
-ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve) # Defaults to Convolution
-plt.plot(t, ct, "b-", label="Convolution")
-ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve, discretization_method="exp")
-plt.plot(t, ct, "g-", label="Exponential Convolution")
-plt.title(f"Ktrans = {Ktrans[1]} /min")
-plt.xlabel("Time (sec)")
-plt.ylabel("Tissue concentration (mM)")
-plt.legend()
-plt.show()
-
-# Choose the last image as a thumbnail for the gallery
-# sphinx_gallery_thumbnail_number = -1
diff --git a/docs/source/generated/examples/tissue/plot_tofts.py.md5 b/docs/source/generated/examples/tissue/plot_tofts.py.md5
deleted file mode 100755
index 2ef949a..0000000
--- a/docs/source/generated/examples/tissue/plot_tofts.py.md5
+++ /dev/null
@@ -1 +0,0 @@
-00e98a230054047d6b50baaf857b22b3
diff --git a/docs/source/generated/examples/tissue/plot_tofts.rst b/docs/source/generated/examples/tissue/plot_tofts.rst
deleted file mode 100755
index 2b0b9e0..0000000
--- a/docs/source/generated/examples/tissue/plot_tofts.rst
+++ /dev/null
@@ -1,175 +0,0 @@
-
-.. DO NOT EDIT.
-.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
-.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "generated\examples\tissue\plot_tofts.py"
-.. LINE NUMBERS ARE GIVEN BELOW.
-
-.. only:: html
-
- .. note::
- :class: sphx-glr-download-link-note
-
- :ref:`Go to the end `
- to download the full example code.
-
-.. rst-class:: sphx-glr-example-title
-
-.. _sphx_glr_generated_examples_tissue_plot_tofts.py:
-
-
-====================
-The Tofts model
-====================
-
-Simulating tissue concentrations from Tofts model with different settings.
-
-.. GENERATED FROM PYTHON SOURCE LINES 8-11
-
-.. code-block:: Python
-
-
- import matplotlib.pyplot as plt
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 12-13
-
-Import necessary packages
-
-.. GENERATED FROM PYTHON SOURCE LINES 13-16
-
-.. code-block:: Python
-
- import numpy as np
- import osipi
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 17-18
-
-Generate Parker AIF with default settings.
-
-.. GENERATED FROM PYTHON SOURCE LINES 18-26
-
-.. code-block:: Python
-
-
- # Define time points in units of seconds - in this case we use a time
- # resolution of 1 sec and a total duration of 6 minutes.
- t = np.arange(0, 6 * 60, 1)
-
- # Create an AIF with default settings
- ca = osipi.aif_parker(t)
-
-
-
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 27-30
-
-Plot the tissue concentrations for an extracellular volume fraction
-of 0.2 and 3 different transfer rate constants of 0.05, 0.2 and 0.6
-/min
-
-.. GENERATED FROM PYTHON SOURCE LINES 30-43
-
-.. code-block:: Python
-
- Ktrans = [0.05, 0.2, 0.6] # in units of 1/min
- ve = 0.2 # volume fraction between 0 and 1
- ct = osipi.tofts(t, ca, Ktrans=Ktrans[0], ve=ve)
- plt.plot(t, ct, "b-", label=f"Ktrans = {Ktrans[0]} /min")
- ct = osipi.tofts(t, ca, Ktrans[1], ve)
- plt.plot(t, ct, "g-", label=f"Ktrans = {Ktrans[1]} /min")
- ct = osipi.tofts(t, ca, Ktrans[2], ve)
- plt.plot(t, ct, "m-", label=f"Ktrans = {Ktrans[2]} /min")
- plt.xlabel("Time (sec)")
- plt.ylabel("Tissue concentration (mM)")
- plt.legend()
- plt.show()
-
-
-
-
-.. image-sg:: /generated/examples/tissue/images/sphx_glr_plot_tofts_001.png
- :alt: plot tofts
- :srcset: /generated/examples/tissue/images/sphx_glr_plot_tofts_001.png
- :class: sphx-glr-single-img
-
-
-
-
-
-.. GENERATED FROM PYTHON SOURCE LINES 44-46
-
-Comparing different discretization methods for an extracellular
-volume fraction of 0.2 and Ktrans of 0.2 /min
-
-.. GENERATED FROM PYTHON SOURCE LINES 46-58
-
-.. code-block:: Python
-
- ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve) # Defaults to Convolution
- plt.plot(t, ct, "b-", label="Convolution")
- ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve, discretization_method="exp")
- plt.plot(t, ct, "g-", label="Exponential Convolution")
- plt.title(f"Ktrans = {Ktrans[1]} /min")
- plt.xlabel("Time (sec)")
- plt.ylabel("Tissue concentration (mM)")
- plt.legend()
- plt.show()
-
- # Choose the last image as a thumbnail for the gallery
- # sphinx_gallery_thumbnail_number = -1
-
-
-
-.. image-sg:: /generated/examples/tissue/images/sphx_glr_plot_tofts_002.png
- :alt: Ktrans = 0.2 /min
- :srcset: /generated/examples/tissue/images/sphx_glr_plot_tofts_002.png
- :class: sphx-glr-single-img
-
-
-
-
-
-
-.. rst-class:: sphx-glr-timing
-
- **Total running time of the script:** (0 minutes 0.143 seconds)
-
-
-.. _sphx_glr_download_generated_examples_tissue_plot_tofts.py:
-
-.. only:: html
-
- .. container:: sphx-glr-footer sphx-glr-footer-example
-
- .. container:: sphx-glr-download sphx-glr-download-jupyter
-
- :download:`Download Jupyter notebook: plot_tofts.ipynb `
-
- .. container:: sphx-glr-download sphx-glr-download-python
-
- :download:`Download Python source code: plot_tofts.py `
-
-
-.. only:: html
-
- .. rst-class:: sphx-glr-signature
-
- `Gallery generated by Sphinx-Gallery `_
diff --git a/docs/source/generated/examples/tissue/plot_tofts_codeobj.pickle b/docs/source/generated/examples/tissue/plot_tofts_codeobj.pickle
deleted file mode 100755
index deefd59..0000000
Binary files a/docs/source/generated/examples/tissue/plot_tofts_codeobj.pickle and /dev/null differ
diff --git a/docs/source/generated/examples/tissue/sg_execution_times.rst b/docs/source/generated/examples/tissue/sg_execution_times.rst
deleted file mode 100755
index b41261a..0000000
--- a/docs/source/generated/examples/tissue/sg_execution_times.rst
+++ /dev/null
@@ -1,40 +0,0 @@
-
-:orphan:
-
-.. _sphx_glr_generated_examples_tissue_sg_execution_times:
-
-
-Computation times
-=================
-**00:00.279** total execution time for 2 files **from generated\examples\tissue**:
-
-.. container::
-
- .. raw:: html
-
-
-
-
-
-
-
- .. list-table::
- :header-rows: 1
- :class: table table-striped sg-datatable
-
- * - Example
- - Time
- - Mem (MB)
- * - :ref:`sphx_glr_generated_examples_tissue_plot_tofts.py` (``plot_tofts.py``)
- - 00:00.143
- - 0.0
- * - :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py` (``plot_extended_tofts.py``)
- - 00:00.136
- - 0.0