diff --git a/kalman/graphics/figure2.py b/kalman/graphics/figure2.py index 897c0cd..8d84cae 100644 --- a/kalman/graphics/figure2.py +++ b/kalman/graphics/figure2.py @@ -72,7 +72,7 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): if bnd_c['id'] == bnd_set['id']: ids.append(bnd_c['id']) current_val.append(bnd_set['value'][0]) - labels.append('R_' + str(bnd_c['id'])) + labels.append('$R_' + str(bnd_c['id'])) elif 'dirichlet' in bnd_c['type']: current_val.append(inputfile['boundary_conditions'][1]['parameters']['U']) @@ -105,13 +105,17 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): for i in range(dim): - axes.plot(t, theta[:, i] + 1.5*i, '-', color=col_,label=legends_) + + true_level = np.log(true_values[ids[i]]/current_val[i])/np.log(2) + rec_value = np.round(2**theta[-1, i]*current_val[i],1) + cur_key = ids[i] + + axes.plot(t, theta[:, i] + 1.5*i, '-', color=col_,label=legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$') axes.fill_between(t, theta[:, i] + 1.5*i - np.sqrt(P[:, i, i]), theta[:, i] + 1.5*i + np.sqrt(P[:, i, i]), alpha=0.3, color=col_) - true_level = np.log(true_values[ids[i]]/current_val[i])/np.log(2) axes.plot(t,1.5*i + t*0 + true_level , color=col_,ls='--') col_ = next(col) legends_=next(legends) diff --git a/kalman/input_files/aorta.yaml b/kalman/input_files/aorta.yaml index 8181195..8badcf1 100755 --- a/kalman/input_files/aorta.yaml +++ b/kalman/input_files/aorta.yaml @@ -4,9 +4,10 @@ mesh: './meshes/coaortaH1.h5' fluid: density: 1.2 dynamic_viscosity: 0.035 + stokes: False io: - write_path: 'results/aorta_master' + write_path: 'results/aorta' restart: path: '' # './projects/nse_coa3d/results/test_restart2/' time: 0 @@ -25,38 +26,40 @@ boundary_conditions: type: 'dirichlet' value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (ThTh)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10)) - - U*sin(DOLFIN_PI*(t-Tc)/Th)*(t>Tc)*(t<= Tc + Th) - + (t<=2*Tc)*(t>Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-Tc)/Th)*exp(-(t-Tc)*10)) - - U*sin(DOLFIN_PI*(t-2*Tc)/Th)*(t>2*Tc)*(t<= 2*Tc + Th) - + (t<=3*Tc)*(t>2*Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-2*Tc)/Th)*exp(-(t-2*Tc)*10)) - - U*sin(DOLFIN_PI*(t-3*Tc)/Th)*(t>3*Tc)*(t<= 3*Tc + Th) - + (t<=4*Tc)*(t>3*Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-3*Tc)/Th)*exp(-(t-3*Tc)*10)) - - U*sin(DOLFIN_PI*(t-4*Tc)/Th)*(t>4*Tc)*(t<= 4*Tc + Th) - + (t<=5*Tc)*(t>4*Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-4*Tc)/Th)*exp(-(t-4*Tc)*10)) '] - parameters: - U: 100 #100 - Th: 0.35 - Tc: 0.8 - t: 0 - - - id: 3 - type: 'windkessel' - value: [10,0,0] - #value: [10,0.0008,2400] # [R_p,C,R_d] SEPARAR - #p0: [80,1333.223874] - p0: [0,1333.223874] - - - id: 4 - type: 'windkessel' - value: [60,0,0] - #value: [60,0.00034,4200] - #p0: [80,1333.223874] - p0: [0,1333.223874] - - - id: 5 - type: 'windkessel' - value: [220,0,0] - #value: [220,0.00034,11000] - #p0: [80,1333.223874] - p0: [0,1333.223874] - - - id: 6 - type: 'windkessel' - value: [160,0,0] - #value: [160,0.00034,7800] - #p0: [80,1333.223874] - p0: [0,1333.223874] - -timemarching: - velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep - - monolithic: - timescheme: 'gmp' # generalized midpoint, steady FIXME TODO - theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged) - nonlinear: - method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes - maxit: 20 - init_steps: 30 - use_aitken: 1 # 0: False, 1: Picard only, 2: all - report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!) - atol: 1.e-6 # note: dot required!! - rtol: 1.e-16 - stol: 0.0 - - fractionalstep: - scheme: 'CT' # CT, IPCS - coupled_velocity: False # False faster, True needed if robin_bc implicit - robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit - transpiration_bc_projection: 'robin' # robin, dirichlet - flux_report_normalize_boundary: 1 - - T: 0.8 # end time - dt: 0.002 - write_dt: 0.04 - checkpoint_dt: 0.04 # <= 0: only last; else value + last - report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux - -# solver setup -fem: - velocity_space: p1 # p1 p1b/p1+ p2 - pressure_space: p1 # p1 p0/dg0 dg1 - - strain_symmetric: False - convection_skew_symmetric: True # aka Temam term - stabilization: - forced_normal: - enabled: False - boundaries: [6] - gamma: 10 - backflow_boundaries: [3,4,5,6] - streamline_diffusion: - enabled: False - parameter: 'standard' # standard, shakib, codina, klr - length_scale: 'metric' # average, max, metric - parameter_element_constant: True - Cinv: ~ - monolithic: - infsup: 'pspg' # pspg, pressure-stabilization - graddiv: False - consistent: False - pressure_stab_constant: 1. - - fix_pressure: False - fix_pressure_point: [0., 0. , 0.] - -linear_solver: - method: 'lu' - -estimation: - boundary_conditions: - #- - # id: 3 - # type: 'windkessel' - # initial_stddev: 1 - - - id: 4 - type: 'windkessel' - initial_stddev: 1 - #- - # id: 5 - # type: 'windkessel' - # initial_stddev: 1 - #- - # id: 6 - # type: 'windkessel' - # initial_stddev: 1 - #- - # id: 2 - # type: 'dirichlet' - # parameters: 'U' - # initial_stddev: 1 - - measurements: - - - mesh: './meshes/coaortaH3_leo2.0.h5' - #mesh: './meshes/coaortaH1.h5' - fe_degree: 1 - #xdmf_file: 'measurements/aorta_C/Perturbation/Ks12V50/u_all.xdmf' - #file_root: 'measurements/aorta_C/Perturbation/Ks12V50/u{i}.h5' - xdmf_file: 'measurements/aorta_s100/u_all.xdmf' - file_root: 'measurements/aorta_s100/u{i}.h5' - indices: 0 # indices of checkpoints to be processed. 0 == all - velocity_direction: ~ - noise_stddev: 15 # standard deviation of Gaussian noise - - roukf: - particles: 'simplex' # unique or simplex - observation_operator: 'postprocessing' #state or postprocessing - reparameterize: True - ODV_functional: - enable: False - VENC: 172 # 241,172 diff --git a/presentations/press_course1/images/catheter_curve.png b/presentations/press_course1/images/catheter_curve.png new file mode 100755 index 0000000..0cacd79 Binary files /dev/null and b/presentations/press_course1/images/catheter_curve.png differ diff --git a/presentations/press_course1/press.tex b/presentations/press_course1/press.tex index 1c14d84..785e997 100755 --- a/presentations/press_course1/press.tex +++ b/presentations/press_course1/press.tex @@ -25,10 +25,9 @@ \usepackage{amssymb,graphicx,enumerate} \usepackage{subcaption} \usepackage{hyperref} - \usepackage[normalem]{ulem} % for strike out command \sout - - +\usepackage{tikz} +\usetikzlibrary{arrows,shapes,positioning} @@ -98,7 +97,7 @@ -\title[]{4D flow MRI in cardiovascular diseases} +\title[]{4D flow MRI in the diagnosis of cardiovascular diseases} %\author[Jeremías Garay Labra] %{Jeremías Garay Labra} \institute[University of Groningen] @@ -118,13 +117,40 @@ University of Groningen\\[0.5cm] % \onslide<1-> +\begin{frame} +\begin{figure}[!hbtp] + \includegraphics[height=0.5\textwidth]{images/aorta_healthy.jpg} + \end{figure} +\end{frame} + + \begin{frame} \begin{figure}[!hbtp] - \includegraphics[height=0.6\textwidth]{images/aortic_stenosis.png} + \includegraphics[height=0.6\textwidth]{images/aortic_stenosis_1.png} \end{figure} \end{frame} +\begin{frame} +\begin{figure}[!hbtp] + \includegraphics[height=0.6\textwidth]{images/aortic_stenosis_2.png} + \end{figure} +\end{frame} + + +\begin{frame} +\begin{figure}[!hbtp] + \includegraphics[height=0.6\textwidth]{images/aortic_stenosis_3.png} + \end{figure} +\end{frame} + +\begin{frame} +\begin{figure}[!hbtp] + \includegraphics[height=0.6\textwidth]{images/aortic_stenosis_4.png} + \end{figure} +\end{frame} + + \begin{frame} @@ -145,10 +171,6 @@ University of Groningen\\[0.5cm] \end{frame} - - - - \begin{frame} \begin{figure}[!hbtp] \begin{center} @@ -161,6 +183,31 @@ University of Groningen\\[0.5cm] +\begin{frame} +\begin{figure} +\centering +\tikzstyle{block} = [rectangle, draw, fill=blue!25,text width=15em, text centered, rounded corners, minimum height=15em, line width=1pt ] +\tikzstyle{block2} = [rectangle, draw, fill=blue!25,text width=4em, text centered, rounded corners, minimum height=2em, line width=1pt ] + +\tikzstyle{line} = [draw, -latex', line width=1pt] +\tikzstyle{alert} = [text=red, fill=red!25, draw=red] + +\begin{tikzpicture}[node distance = 2cm, auto] + % Place nodes + \node [block2] (mri) {velocity data \\ $\vec{u}$ }; + \node [block, right of=mri, node distance=4.5cm] (NS) {Navier-Stokes equations \\[0.3cm] + $$\rho \frac{\partial \vec{u}}{\partial t} + \rho \vec{u} \cdot \nabla \vec{u} + \mu \Delta \vec{u} + \nabla p =0 $$ $$ \nabla \cdot \vec{u} = 0$$}; + \node [block2,alert, right of=NS, node distance=4.5cm] (press) {pressure \\ $p$ }; + % Draw edges + \path [line] (mri) -> (NS); + \path [line] (NS) -- (press); +\end{tikzpicture} +\end{figure} +\end{frame} + + + + \begin{frame} \begin{figure}[!hbtp] @@ -172,6 +219,23 @@ University of Groningen\\[0.5cm] \end{frame} +\begin{frame} +\begin{figure}[!hbtp] + \begin{center} + \includegraphics[height=0.6\textwidth]{images/p2.png} + \caption{\footnotesize reconstructed pressure using NS equations} + \end{center} + \end{figure} +\end{frame} + + + + +\begin{frame} +\begin{center} +\huge{Conclusions} +\end{center} +\end{frame} @@ -180,6 +244,31 @@ University of Groningen\\[0.5cm] + +\begin{frame} +\begin{figure}[!hbtp] + \begin{center} + \includegraphics[height=0.5\textwidth]{images/catheter_curve.png} + \caption{\footnotesize Two different methods for pressure reconstruction (STE, PPE) against actual catheter data in two patients} + \end{center} + \end{figure} +\end{frame} + +\begin{frame} +\title{Conclusion} +\begin{itemize} +\item \onslide<1-> New approach for addressing cardiovascular diagnosis is presented \\[0.3cm] +\item \onslide<2-> Consists in imagining the velocity of blood flows (4D flow)\\[0.3cm] +\item \onslide<3-> Main limitations so far: +\begin{itemize} +\item \onslide<4-> Difficulties in obtaining the special type of data needed +\item \onslide<5-> Practical resolutions are far from the desired ones +\end{itemize} +\end{itemize} +\end{frame} + + + \begin{frame} \begin{center} \huge{Thank you for your time!}