OSIPI · stadmill · Mar 14, 2024 · Sep 6, 2023 · Sep 20, 2023 · Sep 20, 2023
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/LICENSE b/LICENSE
diff --git a/README.md b/README.md
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
@@ -29,7 +29,7 @@
 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:
+# 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')
@@ -44,21 +44,5 @@
 plt.legend()
 plt.show()
 
-# %%
-# the dose defaults to 0.1- what happens if we change it too?
-
-ca = osipi.aif_parker(t, BAT=0, dose=0.05)
-plt.plot(t, ca, 'b-', label='BAT = 0s, dose = 0.05')
-ca = osipi.aif_parker(t, BAT=30, dose=0.1)
-plt.plot(t, ca, 'r-', label='BAT = 30s, dose = 0.1')
-ca = osipi.aif_parker(t, BAT=60, dose=0.2)
-plt.plot(t, ca, 'g-', label='BAT = 60s, dose = 0.2')
-ca = osipi.aif_parker(t, BAT=90, dose=0.3)
-plt.plot(t, ca, 'm-', label='BAT = 90s, dose = 0.3')
-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/examples/aif/plot_dummy.py b/docs/examples/aif/plot_dummy.py
@@ -44,21 +44,5 @@
 plt.legend()
 plt.show()
 
-# %%
-# the dose defaults to 0.1- what happens if we change it too?
-
-ca = osipi.aif_parker(t, BAT=0, dose=0.05)
-plt.plot(t, ca, 'b-', label='BAT = 0s, dose = 0.05')
-ca = osipi.aif_parker(t, BAT=30, dose=0.1)
-plt.plot(t, ca, 'r-', label='BAT = 30s, dose = 0.1')
-ca = osipi.aif_parker(t, BAT=60, dose=0.2)
-plt.plot(t, ca, 'g-', label='BAT = 60s, dose = 0.2')
-ca = osipi.aif_parker(t, BAT=90, dose=0.3)
-plt.plot(t, ca, 'm-', label='BAT = 90s, dose = 0.3')
-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/examples/tissue/README.rst b/docs/examples/tissue/README.rst
diff --git a/docs/examples/tissue/plot_dummy.py b/docs/examples/tissue/plot_dummy.py
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
@@ -0,0 +1,52 @@
+"""
+====================
+The Tofts model
+====================
+
+Simulating tissue concentrations from 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 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/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
@@ -36,7 +36,7 @@ If you want to edit the documentation of a specific function, then you need to f
 How to contribute tests
 ***********************
 
-Beyond documentation and functionality, solid testing is equally critical for ensuring long-term stability of a package. `osipi` uses a continuous integration model where all tests are run before each push to the central respository. This is important because often changes at one part of the code, even if tested well locally, can have unintended consequences at other parts. The testing prevents that these errors propagate and destablize parts of the package. 
+Beyond documentation and functionality, solid testing is equally critical for ensuring long-term stability of a package. `osipi` uses a continuous integration model where all tests are run before each push to the central repository. This is important because often changes at one part of the code, even if tested well locally, can have unintended consequences at other parts. The testing prevents that these errors propagate and destablize parts of the package.
 
 If you find a bug in any part of the code, this obviously points to a flaw in the code, but it also reveals a gap in the testing. It is critical when this happens that both the code AND the tests are reviewed to ensure that in future a scenario of this type is picked up during testing. 
 
@@ -47,7 +47,7 @@ The tests are defined in the folder `osipi-tests`.
 How to contribute functionality
 *******************************
 
-OSIPI is always happy to recieve new functionality for inclusion in the `osipi` package. This can be code that addresses a gap in the current functionality, or it can be code that improves the performance of a current implementation. Improvements can consist of extending the functionality (e.g. with new optional arguments), user friendliness or consistency, improvement of the accuracy or precision in the results, computation time, or platform independence, or improved documentation or code structure. 
+OSIPI is always happy to receive new functionality for inclusion in the `osipi` package. This can be code that addresses a gap in the current functionality, or it can be code that improves the performance of a current implementation. Improvements can consist of extending the functionality (e.g. with new optional arguments), user friendliness or consistency, improvement of the accuracy or precision in the results, computation time, or platform independence, or improved documentation or code structure.
 
 Contribution of functionality generally proceeds in two steps. In the first step you submit your code to the primary *contributions* repository as explained in its `wiki <https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/wiki/How-to-contribute-code>`_. The task force will catalogue your code in the contributions repository and test it as explained in the `guidance <https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/wiki/The-testing-approach>`_. Afterwards, if it is found to address a gap in `osipi` and/or improve existing functionality, you will be invited to submit a pull request to `osipi` containing your contribution formatted as required by the package. 
 

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
@@ -0,0 +1,18 @@
+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
@@ -0,0 +1,18 @@
+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