Cardiac tutorial

[aranas]

this PR is a work in progress on the tutorial showcasing how autoemulate can be embedded into an end-to-end cardiac modelling pipeline including sensitivity analysis.

This tutorial still requires some improvements

• add explanations to every step
• add plot that showcases value of autoemulate in the context of sensitivity analysis more specifically

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autoemulate/autoemulate/simulations/flow_functions.py

Line 136 in 0f1382d

fig, ax = plt.subplots(ncols=2, figsize = (10, 5))

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[blackfmt] _{reported by reviewdog 🐶}

autoemulate/autoemulate/simulations/flow_functions.py

Lines 138 to 149 in 0f1382d

	ax[0].plot(self.res.t, self.res.y[2*i,:] , 'r', alpha=0.1 + (1.-i/self.ncomp) *0.9)
	ax[1].plot(self.res.t, self.res.y[2*i+1,:] , 'r', alpha=0.1 + (1.-i/self.ncomp) *0.9)
	ax[0].set_title('Pressure')
	ax[1].set_title('Flow rate')
	ax[0].set_xlabel('Time (s)')
	ax[1].set_xlabel('Time (s)')
	ax[0].set_ylabel('mmHg')
	ax[1].set_ylabel('$ml\cdot s^{-1}$')
	return (fig, ax)

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

	class FlowProblem:
	class FlowProblem:

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

	self,
	T=1.0,
	td=0.2,
	amp=900.0,
	dt=0.001,
	self,
	T=1.0,
	td=0.2,
	amp=900.0,
	dt=0.001,

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

	ncomp = 10,
	C = 38.,
	R = 0.06,
	L = 0.0017,
	R_o = 0.025,
	p_o = 10.,
	) -> None :
	'''
	ncomp=10,
	C=38.0,
	R=0.06,
	L=0.0017,
	R_o=0.025,
	p_o=10.0,
	) -> None:
	"""

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

	'''
	assert td < T, f'td should be smaller than T but {td} >= {T}.'
	self._td = td
	self._T = T
	"""
	assert td < T, f"td should be smaller than T but {td} >= {T}."
	self._td = td
	self._T = T

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

	out[i,0] = (Q_in(t%self.T) - y_temp[i,1]) / Cn
	if i < self.ncomp-1:
	out[i,1] = (-y_temp[i+1, 0] + y_temp[i, 0] - Rn * y_temp[i, 1]) / Ln
	out[i, 0] = (Q_in(t % self.T) - y_temp[i, 1]) / Cn
	if i < self.ncomp - 1:
	out[i, 1] = (-y_temp[i + 1, 0] + y_temp[i, 0] - Rn * y_temp[i, 1]) / Ln

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

	out[i,1] = (-self.p_o + y_temp[i, 0] - (Rn + self.R_o) * y_temp[i, 1]) / Ln
	out[i, 1] = (
	-self.p_o + y_temp[i, 0] - (Rn + self.R_o) * y_temp[i, 1]
	) / Ln

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

	dfdt_fd_spec = lambda t, y : self.dfdt_fd(t=t, y=y, Q_in=self.Q_mi_lambda)
	dfdt_fd_spec = lambda t, y: self.dfdt_fd(t=t, y=y, Q_in=self.Q_mi_lambda)

[github-actions]

[blackfmt] _{reported by reviewdog 🐶}

Suggested change

	dfdt_fd_spec,
	[0.0, self.T * self.ncycles],
	y0 = np.zeros(self.ncomp*2),
	method='BDF',
	max_step=self.dt
	)
	self.res.y = self.res.y[:,self.res.t >= self.T*(self.ncycles-1)]
	self.res.t = self.res.t[self.res.t >= self.T*(self.ncycles-1)]
	dfdt_fd_spec,
	[0.0, self.T * self.ncycles],
	y0=np.zeros(self.ncomp * 2),
	method="BDF",
	max_step=self.dt,
	)
	self.res.y = self.res.y[:, self.res.t >= self.T * (self.ncycles - 1)]
	self.res.t = self.res.t[self.res.t >= self.T * (self.ncycles - 1)]

[github-actions]

Coverage report

This PR does not seem to contain any modification to coverable code.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.54%. Comparing base (2f1d439) to head (c2700e5).
Report is 46 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #233      +/-   ##
==========================================
+ Coverage   91.14%   91.54%   +0.40%     
==========================================
  Files          45       51       +6     
  Lines        2393     2816     +423     
==========================================
+ Hits         2181     2578     +397     
- Misses        212      238      +26     

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[aranas]

@MaxBalmus I managed to transfer our original commits into the autoemulate repo, I think it makes more sense to work here directly, so that Martin can chip in where appropriate.
for example, I have now transferred Max's custom flow functions into the simulations file, but I realized that the other files contain functions, not classes @mastoffel, is this something we should adapt for consistency?

[mastoffel]

@MaxBalmus I managed to transfer our original commits into the autoemulate repo, I think it makes more sense to work here directly, so that Martin can chip in where appropriate. for example, I have now transferred Max's custom flow functions into the simulations file, but I realized that the other files contain functions, not classes @mastoffel, is this something we should adapt for consistency?

@MaxBalmus @aranas: This is great! It would be best to make the simulation a function to be consistent with the other simulations eventually, but this isn't urgent. Let me know when I should have a look at it!