Merge pull request #4 from LucyKershaw/LEK_development

Added extended Tofts
OSIPI · Feb 19, 2024 · 5804f63 · 5804f63
2 parents 316f928 + 7cd756f
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
diff --git a/.github/workflows/pytest-actions.yaml b/.github/workflows/pytest-actions.yaml
diff --git a/.gitignore b/.gitignore
diff --git a/.idea/.gitignore b/.idea/.gitignore
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/modules.xml b/.idea/modules.xml
diff --git a/.idea/other.xml b/.idea/other.xml
diff --git a/.idea/pypi.iml b/.idea/pypi.iml
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/docs/.DS_Store b/docs/.DS_Store
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/examples/.DS_Store b/docs/examples/.DS_Store
diff --git a/docs/examples/README.rst b/docs/examples/README.rst
diff --git a/docs/examples/aif/README.rst b/docs/examples/aif/README.rst
diff --git a/docs/examples/aif/plot_aif_parker.py b/docs/examples/aif/plot_aif_parker.py
diff --git a/docs/examples/aif/plot_dummy.py b/docs/examples/aif/plot_dummy.py
diff --git a/docs/examples/tissue/README.rst b/docs/examples/tissue/README.rst
diff --git a/docs/examples/tissue/plot_extended_tofts.py b/docs/examples/tissue/plot_extended_tofts.py
@@ -0,0 +1,53 @@
+"""
+====================
+The Extended Tofts model
+====================
+
+Simulating tissue concentrations from extended Tofts model with different settings.
+"""
+
+# %%
+# Import necessary packages
+import numpy as np
+import matplotlib.pyplot as plt
+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/examples/tissue/plot_tofts.py b/docs/examples/tissue/plot_tofts.py
diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/source/.DS_Store b/docs/source/.DS_Store
diff --git a/docs/source/_static/osipi.png b/docs/source/_static/osipi.png
diff --git a/docs/source/_templates/autosummary.rst b/docs/source/_templates/autosummary.rst
diff --git a/docs/source/about/index.rst b/docs/source/about/index.rst
diff --git a/docs/source/conf.py b/docs/source/conf.py
diff --git a/docs/source/developers_guide/index.rst b/docs/source/developers_guide/index.rst
diff --git a/docs/source/generated/.DS_Store b/docs/source/generated/.DS_Store
diff --git a/docs/source/generated/api/osipi.aif_georgiou.rst b/docs/source/generated/api/osipi.aif_georgiou.rst
diff --git a/docs/source/generated/api/osipi.aif_parker.rst b/docs/source/generated/api/osipi.aif_parker.rst
diff --git a/docs/source/generated/api/osipi.aif_weinmann.rst b/docs/source/generated/api/osipi.aif_weinmann.rst
diff --git a/docs/source/generated/api/osipi.extended_tofts.rst b/docs/source/generated/api/osipi.extended_tofts.rst
diff --git a/docs/source/generated/api/osipi.tofts.rst b/docs/source/generated/api/osipi.tofts.rst
diff --git a/docs/source/generated/backreferences/osipi.aif_georgiou.examples b/docs/source/generated/backreferences/osipi.aif_georgiou.examples
diff --git a/docs/source/generated/backreferences/osipi.aif_parker.examples b/docs/source/generated/backreferences/osipi.aif_parker.examples
@@ -14,66 +14,24 @@ Examples using ``osipi.aif_parker``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="Simulating a Parker AIF with different settings. ">
+    <div class="sphx-glr-thumbcontainer" tooltip="Simulating tissue concentrations from extended Tofts model with different settings.">
 
 .. only:: html
 
-  .. image:: /generated/examples/aif/images/thumb/sphx_glr_plot_aif_parker_thumb.png
+  .. image:: /generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png
     :alt:
 
-  :ref:`sphx_glr_generated_examples_aif_plot_aif_parker.py`
+  :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
 
 .. raw:: html
 
-      <div class="sphx-glr-thumbnail-title">The Parker AIF - a play with variables</div>
+      <div class="sphx-glr-thumbnail-title">The Extended Tofts model</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`
+ * :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
 
 .. raw:: html
 

diff --git a/docs/source/generated/backreferences/osipi.aif_weinmann.examples b/docs/source/generated/backreferences/osipi.aif_weinmann.examples
diff --git a/docs/source/generated/backreferences/osipi.extended_tofts.examples b/docs/source/generated/backreferences/osipi.extended_tofts.examples
@@ -0,0 +1,39 @@
+
+
+Examples using ``osipi.extended_tofts``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+
+.. start-sphx-glr-thumbnails
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbnails">
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Simulating tissue concentrations from extended Tofts model with different settings.">
+
+.. 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
+
+      <div class="sphx-glr-thumbnail-title">The Extended Tofts model</div>
+    </div>
+
+
+.. only:: not html
+
+ * :ref:`sphx_glr_generated_examples_tissue_plot_extended_tofts.py`
+
+.. raw:: html
+
+    </div>
+
diff --git a/docs/source/generated/backreferences/osipi.tofts.examples b/docs/source/generated/backreferences/osipi.tofts.examples
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
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
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
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
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
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
diff --git a/docs/source/generated/examples/aif/index.rst b/docs/source/generated/examples/aif/index.rst
diff --git a/docs/source/generated/examples/aif/plot_aif_parker.ipynb b/docs/source/generated/examples/aif/plot_aif_parker.ipynb
diff --git a/docs/source/generated/examples/aif/plot_aif_parker.py b/docs/source/generated/examples/aif/plot_aif_parker.py
diff --git a/docs/source/generated/examples/aif/plot_aif_parker.py.md5 b/docs/source/generated/examples/aif/plot_aif_parker.py.md5
diff --git a/docs/source/generated/examples/aif/plot_aif_parker.rst b/docs/source/generated/examples/aif/plot_aif_parker.rst
diff --git a/docs/source/generated/examples/aif/plot_aif_parker_codeobj.pickle b/docs/source/generated/examples/aif/plot_aif_parker_codeobj.pickle
diff --git a/docs/source/generated/examples/aif/plot_dummy.ipynb b/docs/source/generated/examples/aif/plot_dummy.ipynb
diff --git a/docs/source/generated/examples/aif/plot_dummy.py b/docs/source/generated/examples/aif/plot_dummy.py
diff --git a/docs/source/generated/examples/aif/plot_dummy.py.md5 b/docs/source/generated/examples/aif/plot_dummy.py.md5
diff --git a/docs/source/generated/examples/aif/plot_dummy.rst b/docs/source/generated/examples/aif/plot_dummy.rst
diff --git a/docs/source/generated/examples/aif/plot_dummy_codeobj.pickle b/docs/source/generated/examples/aif/plot_dummy_codeobj.pickle
diff --git a/docs/source/generated/examples/aif/sg_execution_times.rst b/docs/source/generated/examples/aif/sg_execution_times.rst
diff --git a/docs/source/generated/examples/index.rst b/docs/source/generated/examples/index.rst
@@ -100,6 +100,23 @@ Tissue concentrations
     </div>
 
 
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Simulating tissue concentrations from extended Tofts model with different settings.">
+
+.. 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
+
+      <div class="sphx-glr-thumbnail-title">The Extended Tofts model</div>
+    </div>
+
+
 .. raw:: html
 
     </div>

diff --git a/docs/source/generated/examples/sg_execution_times.rst b/docs/source/generated/examples/sg_execution_times.rst
@@ -0,0 +1,37 @@
+
+: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
+
+    <style scoped>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
+    <link href="https://cdn.datatables.net/1.13.6/css/dataTables.bootstrap5.min.css" rel="stylesheet" />
+    </style>
+    <script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/dataTables.bootstrap5.min.js"></script>
+    <script type="text/javascript" class="init">
+    $(document).ready( function () {
+        $('table.sg-datatable').DataTable({order: [[1, 'desc']]});
+    } );
+    </script>
+
+  .. 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
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
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
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
diff --git a/...e/generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png b/...e/generated/examples/tissue/images/thumb/sphx_glr_plot_extended_tofts_thumb.png
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
diff --git a/docs/source/generated/examples/tissue/index.rst b/docs/source/generated/examples/tissue/index.rst
@@ -32,6 +32,23 @@ Tissue concentrations
     </div>
 
 
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Simulating tissue concentrations from extended Tofts model with different settings.">
+
+.. 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
+
+      <div class="sphx-glr-thumbnail-title">The Extended Tofts model</div>
+    </div>
+
+
 .. raw:: html
 
     </div>
@@ -41,4 +58,5 @@ Tissue concentrations
    :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
@@ -0,0 +1,104 @@
+{
+  "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": "markdown",
+      "metadata": {},
+      "source": [
+        "Import necessary packages\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "import numpy as np\nimport matplotlib.pyplot as plt\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 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 of 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 volume 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": "3.11.2"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}