Fiber tissue sim example

ft-example/.gitignore

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+combined.zip

ft-example/ft-example.py

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+#!/usr/bin/env python3
+#
+# FiberTissueSimulation example
+#
+import sys
+import myokit
+
+debug = 'debug' in sys.argv
+
+# Load models
+mf = myokit.load_model('stewart-2009.mmt')
+mt = myokit.load_model('tentusscher-2006-lhopital.mmt')
+
+# Create a protocol
+p = myokit.pacing.blocktrain(period=1000, duration=2)
+
+# Set up a simulation
+s = myokit.FiberTissueSimulation(
+    mf,
+    mt,
+    p,
+    ncells_fiber=(32, 2),
+    ncells_tissue=(32, 32),
+    nx_paced=5,
+    g_fiber=(3, 1),
+    g_tissue=(3, 1),
+    g_fiber_tissue=3,
+)
+s.set_step_size(0.0005)
+
+# Debugging? Then log all variables
+if debug:
+    logf = logt = myokit.LOG_STATE + myokit.LOG_BOUND
+else:
+    logf = ['engine.time', 'membrane.V', 'calcium.Ca_i']
+    logt = ['engine.time', 'membrane.V', 'calcium.Cai']
+
+# Run (using a progress printer to see how far we got)
+pr = myokit.ProgressPrinter()
+df, dt = s.run(50, logf=logf, logt=logt, log_interval=0.5, progress=pr)
+if debug:
+    print('Sim OK!')
+    sys.exit(1)
+
+# Convert the dictionary logs to structured 2d arrays
+bf = df.block2d()
+bt = dt.block2d()
+
+# Create a combined data block
+# First define a map that indicates equivalent variables. Format:
+# new_name : (modelf name, modelt name, padding value)
+varmap = {
+    'V' : ('membrane.V', 'membrane.V', -100),
+    'Cai': ('calcium.Ca_i', 'calcium.Cai', 0),
+}
+b = myokit.DataBlock2d.combine(bf, bt, map2d=varmap, pos1=(0, 15))
+
+# Store the data block
+fname = 'combined.zip'
+print(f'Storing in {fname}')
+b.save(fname)
+
+print('Done!')
+print('View with: python3 -m myokit block combined.zip')
+