Updated StoC

Modified code, tests, docs and examples for S to C.

docs/build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: e14b72e891830c1f1d56435aced99033
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_downloads/13d29bba0b7f4883cb92cda379ddc864/plot_dummy.py

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+"""
+==============
+A dummy script
+==============
+
+Dummy script to illustrate structure of examples folder 
+"""
+
+# %%
+# Import necessary packages
+import numpy as np
+import matplotlib.pyplot as plt
+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

docs/build/html/_downloads/6794ff0fe2ebfd1be519862fb198ceb5/plot_aif_parker.py

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+"""
+======================================
+The Parker AIF - a play with variables
+======================================
+
+Simulating a Parker AIF with different settings. 
+"""
+
+# %%
+# Import necessary packages
+import numpy as np
+import matplotlib.pyplot as plt
+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