SimVascular · menon-karthik · Nov 7, 2023 · Nov 7, 2023 · Nov 7, 2023
diff --git a/docs/Doxyfile b/docs/Doxyfile
@@ -189,7 +189,7 @@ ENUM_VALUES_PER_LINE   = 1
 TREEVIEW_WIDTH         = 250
 EXT_LINKS_IN_WINDOW    = NO
 FORMULA_FONTSIZE       = 10
-USE_MATHJAX            = YES
+USE_MATHJAX            = NO
 MATHJAX_FORMAT         = HTML-CSS
 MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
 MATHJAX_EXTENSIONS     = 

diff --git a/docs/pages/developer_guide.md b/docs/pages/developer_guide.md
@@ -88,7 +88,6 @@ If you want to cite a piece literature in your documentation, add
 a respective BibTeX citation to `docs/cpp/references.bib` and use `\cite name_of_citation` to
 cite the document.
 
-
 ### Drawing circuits
 As the elements of the svZeroDSolver are often represented
 in the form of electrical circuits, we use [CircuiTikZ](https://ctan.org/pkg/circuitikz?lang=en)
@@ -101,18 +100,6 @@ To start a CircuitTikZ drawing use the following command:
 \end{circuitikz}
 \f]
 ```
-We currently use MathJax, which only supports [a couple of LaTeX packages](https://docs.mathjax.org/en/latest/input/tex/extensions/index.html). In our `Doxyfile`, this is set as `USE_MATHJAX = YES`. The equations look nicer than without MathJax. Unfortunately, CircuiTikZ is currently not supported by MathJax. Thus, we store all current schematics already compiled in `docs/png`.
-
-If you are adding new schematics, you can follow these steps:
-1. Set `USE_MATHJAX = NO` in `docs/Doxyfile`
-2. Locally build Doxygen (see next section)
-3. Copy `png` output from `docs/build/latex` to `docs/png`
-4. Include image with `\image html FILENAME_dark.png` in `.h`/`.cpp` Doxygen
-5. Set `USE_MATHJAX = YES` in `docs/Doxyfile`
-6. Locally build Doxygen again
-7. Check if LaTeX and schematic look nice
-8. Commit your changes and new `png`
-
 
 ### Build
 The documentation is automatically built in the GitHub CI/CD and published

diff --git a/docs/png/blood_vessel.png b/docs/png/blood_vessel.png
diff --git a/docs/png/blood_vessel_dark.png b/docs/png/blood_vessel_dark.png
diff --git a/docs/png/blood_vessel_junction.png b/docs/png/blood_vessel_junction.png
diff --git a/docs/png/blood_vessel_junction_dark.png b/docs/png/blood_vessel_junction_dark.png
diff --git a/docs/png/blood_vessel_junction_individual.png b/docs/png/blood_vessel_junction_individual.png
diff --git a/docs/png/blood_vessel_junction_individual_dark.png b/docs/png/blood_vessel_junction_individual_dark.png
diff --git a/docs/png/closed_loop_coronary_b_c.png b/docs/png/closed_loop_coronary_b_c.png
diff --git a/docs/png/closed_loop_coronary_b_c_dark.png b/docs/png/closed_loop_coronary_b_c_dark.png
diff --git a/docs/png/closed_loop_r_c_r_b_c.png b/docs/png/closed_loop_r_c_r_b_c.png
diff --git a/docs/png/closed_loop_r_c_r_b_c_dark.png b/docs/png/closed_loop_r_c_r_b_c_dark.png
diff --git a/docs/png/flow_reference_b_c.png b/docs/png/flow_reference_b_c.png
diff --git a/docs/png/flow_reference_b_c_dark.png b/docs/png/flow_reference_b_c_dark.png
diff --git a/docs/png/junction.png b/docs/png/junction.png
diff --git a/docs/png/junction_dark.png b/docs/png/junction_dark.png
diff --git a/docs/png/open_loop_coronary_b_c.png b/docs/png/open_loop_coronary_b_c.png
diff --git a/docs/png/open_loop_coronary_b_c_dark.png b/docs/png/open_loop_coronary_b_c_dark.png
diff --git a/docs/png/pressure_reference_b_c.png b/docs/png/pressure_reference_b_c.png
diff --git a/docs/png/pressure_reference_b_c_dark.png b/docs/png/pressure_reference_b_c_dark.png
diff --git a/docs/png/resistance_b_c.png b/docs/png/resistance_b_c.png
diff --git a/docs/png/resistance_b_c_dark.png b/docs/png/resistance_b_c_dark.png
diff --git a/docs/png/resistive_junction.png b/docs/png/resistive_junction.png
diff --git a/docs/png/resistive_junction_dark.png b/docs/png/resistive_junction_dark.png
diff --git a/docs/png/windkessel_b_c.png b/docs/png/windkessel_b_c.png
diff --git a/docs/png/windkessel_b_c_dark.png b/docs/png/windkessel_b_c_dark.png
diff --git a/src/model/BloodVessel.h b/src/model/BloodVessel.h
@@ -44,7 +44,19 @@
  *
  * Models the mechanical behavior of a bloodvessel with optional stenosis.
  *
- * \image html blood_vessel_dark.png
+ * \f[
+ * \begin{circuitikz} \draw
+ * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+ * \draw (1,0) node[anchor=south]{$P_{in}$}
+ * to [R, l=$R$, *-] (3,0)
+ * to [R, l=$S$, -] (5,0)
+ * (5,0) to [L, l=$L$, -*] (7,0)
+ * node[anchor=south]{$P_{out}$}
+ * (5,0) to [C, l=$C$, -] (5,-1.5)
+ * node[ground]{};
+ * \draw [-latex] (7.2,0) -- (8,0) node[right] {$Q_{out}$};
+ * \end{circuitikz}
+ * \f]
  *
  * ### Governing equations
  *
@@ -129,19 +141,6 @@
  * * `3` Stenosis coefficient
  *
  */
-//  * \f[
-//  * \begin{circuitikz} \draw
-//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
-//  * \draw (1,0) node[anchor=south]{$P_{in}$}
-//  * to [R, l=$R$, *-] (3,0)
-//  * to [R, l=$S$, -] (5,0)
-//  * (5,0) to [L, l=$L$, -*] (7,0)
-//  * node[anchor=south]{$P_{out}$}
-//  * (5,0) to [C, l=$C$, -] (5,-1.5)
-//  * node[ground]{};
-//  * \draw [-latex] (7.2,0) -- (8,0) node[right] {$Q_{out}$};
-//  * \end{circuitikz}
-//  * \f]
 class BloodVessel : public Block {
  public:
   /**

diff --git a/src/model/BloodVesselJunction.h b/src/model/BloodVesselJunction.h
@@ -45,11 +45,36 @@
  * Models a junction with one inlet and arbitrary outlets using
  * modified blood vessel elements between each inlet and outlet pair.
  *
- * \image html blood_vessel_junction_dark.png
+ * \f[
+ * \begin{circuitikz}
+ * \draw node[left] {$Q_\text{in}$} [-latex] (0,0) -- (0.8,0);
+ * \draw (1,0.1) node[anchor=south]{$P_\text{in}$};
+ * \draw (1,0) to [short, *-] (2.5,0.75);
+ * \draw (1,0) to [short, *-] (2.5,-0.75);
+ * \draw (2.5,0.75) node[anchor=south]{} to [generic, l_=$BV_{1}$, -*]
+ * (4.5,0.75); \draw (2.4,0.75) node[anchor=south]{}; \draw (4.6,0.75)
+ * node[anchor=south] {$P_{out,1}$}; \draw (2.5,-0.75) node[anchor=south]{}
+ to
+ * [generic, l^=$BV_{2}$, -*] (4.5,-0.75); \draw (2.4,-0.75)
+ * node[anchor=north]{}; \draw (4.6,-0.75) node[anchor=north]
+ * {$P_{out,2}$}; \draw [-latex] (4.7,0.75) -- (5.5,0.75) node[right]
+ * {$Q_{out,1}$}; \draw [-latex] (4.7,-0.75) -- (5.5,-0.75) node[right]
+ * {$Q_{out,2}$}; \end{circuitikz}
+ * \f]
  *
  * Each blood vessel is modelled as:
  *
- * \image html blood_vessel_junction_individual_dark.png
+ * \f[
+ * \begin{circuitikz} \draw
+ * node[left] {$Q_\text{in}$} [-latex] (0,0) -- (0.8,0);
+ * \draw (1,0) node[anchor=south]{$P_\text{in}$}
+ * to [R, l=$R$, *-] (3,0)
+ * to [R, l=$S$, -] (5,0)
+ * (5,0) to [L, l=$L$, -*] (7,0)
+ * node[anchor=south]{$P_\text{out}$};
+ * \draw [-latex] (7.2,0) -- (8,0) node[right] {$Q_\text{out}$};
+ * \end{circuitikz}
+ * \f]
  *
  * ### Governing equations
  *
@@ -117,34 +142,6 @@
  * * `i+2*num_outlets` Stenosis coefficient for inner blood vessel `i`
  *
  */
-//  * \f[
-//  * \begin{circuitikz}
-//  * \draw node[left] {$Q_\text{in}$} [-latex] (0,0) -- (0.8,0);
-//  * \draw (1,0.1) node[anchor=south]{$P_\text{in}$};
-//  * \draw (1,0) to [short, *-] (2.5,0.75);
-//  * \draw (1,0) to [short, *-] (2.5,-0.75);
-//  * \draw (2.5,0.75) node[anchor=south]{} to [generic, l_=$BV_{1}$, -*]
-//  * (4.5,0.75); \draw (2.4,0.75) node[anchor=south]{}; \draw (4.6,0.75)
-//  * node[anchor=south] {$P_{out,1}$}; \draw (2.5,-0.75) node[anchor=south]{}
-//  to
-//  * [generic, l^=$BV_{2}$, -*] (4.5,-0.75); \draw (2.4,-0.75)
-//  * node[anchor=north]{}; \draw (4.6,-0.75) node[anchor=north]
-//  * {$P_{out,2}$}; \draw [-latex] (4.7,0.75) -- (5.5,0.75) node[right]
-//  * {$Q_{out,1}$}; \draw [-latex] (4.7,-0.75) -- (5.5,-0.75) node[right]
-//  * {$Q_{out,2}$}; \end{circuitikz}
-//  * \f]
-//
-//  * \f[
-//  * \begin{circuitikz} \draw
-//  * node[left] {$Q_\text{in}$} [-latex] (0,0) -- (0.8,0);
-//  * \draw (1,0) node[anchor=south]{$P_\text{in}$}
-//  * to [R, l=$R$, *-] (3,0)
-//  * to [R, l=$S$, -] (5,0)
-//  * (5,0) to [L, l=$L$, -*] (7,0)
-//  * node[anchor=south]{$P_\text{out}$};
-//  * \draw [-latex] (7.2,0) -- (8,0) node[right] {$Q_\text{out}$};
-//  * \end{circuitikz}
-//  * \f]
 class BloodVesselJunction : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/ClosedLoopCoronaryBC.h b/src/model/ClosedLoopCoronaryBC.h
@@ -44,7 +44,21 @@ enum class Side { LEFT, RIGHT, NONE };
  * @brief Closed loop coronary boundary condition (connected to other blocks on
  * both sides).
  *
- * \image html closed_loop_coronary_b_c_dark.png
+ * \f[
+ * \begin{circuitikz} \draw
+ * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+ * \draw (1,0) node[anchor=south]{$P_{in}$}
+ * to [R, l=$R_a$, *-] (3,0)
+ * to [R, l=$R_{am}$, -] (5,0)
+ * to [R, l=$R_v$, *-*] (7,0)
+ * node[anchor=south]{$P_{out}$}
+ * (5,0) to [C, l=$C_{im} \;V_{im}$, -*] (5,-1.5)
+ * node[left]{$P_{im}$}
+ * (3,0) to [C, l=$C_a$, -*] (3,-1.5)
+ * node[left]{$P_a$};
+ * \draw [-latex] (7.2,0) -- (8.0,0) node[right] {$Q_{out}$};
+ * \end{circuitikz}
+ * \f]
  *
  * ### Governing equations
  *
@@ -102,21 +116,6 @@ enum class Side { LEFT, RIGHT, NONE };
  * * `4` Cim
  *
  */
-//  * \f[
-//  * \begin{circuitikz} \draw
-//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
-//  * \draw (1,0) node[anchor=south]{$P_{in}$}
-//  * to [R, l=$R_a$, *-] (3,0)
-//  * to [R, l=$R_{am}$, -] (5,0)
-//  * to [R, l=$R_v$, *-*] (7,0)
-//  * node[anchor=south]{$P_{out}$}
-//  * (5,0) to [C, l=$C_{im} \;V_{im}$, -*] (5,-1.5)
-//  * node[left]{$P_{im}$}
-//  * (3,0) to [C, l=$C_a$, -*] (3,-1.5)
-//  * node[left]{$P_a$};
-//  * \draw [-latex] (7.2,0) -- (8.0,0) node[right] {$Q_{out}$};
-//  * \end{circuitikz}
-//  * \f]
 class ClosedLoopCoronaryBC : public Block {
  public:
   explicit ClosedLoopCoronaryBC(int id, const std::vector<int> &param_ids,

diff --git a/src/model/ClosedLoopRCRBC.h b/src/model/ClosedLoopRCRBC.h
@@ -43,7 +43,18 @@
  * Models the mechanical behavior of a Windkessel boundary condition that is
  * connected to other blocks on both sides.
  *
- * \image html closed_loop_r_c_r_b_c_dark.png
+ * \f[
+ * \begin{circuitikz} \draw
+ * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+ * \draw (1,0) node[anchor=south]{$P_{in}$}
+ * to [R, l=$R_p$, *-] (3,0)
+ * to [R, l=$R_d$, *-*] (5,0)
+ * node[anchor=south]{$P_{out}$}
+ * (3,0) to [C, l=$C$, *-] (3,-1.5)
+ * node[ground]{$P_{C}$};
+ * \draw [-latex] (5.2,0) -- (6.0,0) node[right] {$Q_{out}$} ;
+ * \end{circuitikz}
+ * \f]
  *
  * ### Governing equations
  *
@@ -97,18 +108,6 @@
  * * `2` Distal resistance
  *
  */
-//  * \f[
-//  * \begin{circuitikz} \draw
-//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
-//  * \draw (1,0) node[anchor=south]{$P_{in}$}
-//  * to [R, l=$R_p$, *-] (3,0)
-//  * to [R, l=$R_d$, *-*] (5,0)
-//  * node[anchor=south]{$P_{out}$}
-//  * (3,0) to [C, l=$C$, *-] (3,-1.5)
-//  * node[ground]{$P_{C}$};
-//  * \draw [-latex] (5.2,0) -- (6.0,0) node[right] {$Q_{out}$} ;
-//  * \end{circuitikz}
-//  * \f]
 class ClosedLoopRCRBC : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/FlowReferenceBC.h b/src/model/FlowReferenceBC.h
@@ -43,7 +43,13 @@
  *
  * Applies a prescribed flow to a boundary.
  *
- * \image html flow_reference_b_c_dark.png
+ * \f[
+ * \begin{circuitikz} \draw
+ * node[left] {$\hat{Q}$} [-latex] (0,0) -- (0.8,0);
+ * \draw (1,0) node[anchor=south]{$P$} to [short, *-] (1.2,0) ;
+ * \draw [-latex] (1.4,0) -- (2.2,0) node[right] {$Q$};
+ * \end{circuitikz}
+ * \f]
  *
  * ### Governing equations
  *
@@ -72,13 +78,6 @@
  * * `0` Flow
  *
  */
-//  * \f[
-//  * \begin{circuitikz} \draw
-//  * node[left] {$\hat{Q}$} [-latex] (0,0) -- (0.8,0);
-//  * \draw (1,0) node[anchor=south]{$P$} to [short, *-] (1.2,0) ;
-//  * \draw [-latex] (1.4,0) -- (2.2,0) node[right] {$Q$};
-//  * \end{circuitikz}
-//  * \f]
 class FlowReferenceBC : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/Junction.h b/src/model/Junction.h
@@ -43,7 +43,18 @@
  * Models a junction with arbitrary inlets and outlets. Across all inlets and
  * outlets of the junction, mass is conserved and pressure is continuous.
  *
- * \image html junction_dark.png
+ * \f[
+ * \begin{circuitikz}
+ * \draw node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+ * \draw (1,0) node[anchor=south]{$P_{in}$} to [short, *-*] (3.0,0);
+ * \draw (3,0) node[anchor=south]{} to [short, -*] (4.5,1.0);
+ * \draw (4.3,1.1) node[anchor=south] {$P_{out,1}$};
+ * \draw (3,0) node[anchor=south]{} to [short, -*] (4.5,-1.0);
+ * \draw (4.3,-1.1) node[anchor=north] {$P_{out,2}$};
+ * \draw [-latex] (4.65,1.1) -- (5.25,1.5) node[right] {$Q_{out,1}$};
+ * \draw [-latex] (4.65,-1.1) -- (5.25,-1.5) node[right] {$Q_{out,2}$};
+ * \end{circuitikz}
+ * \f]
  *
  * ### Governing equations
  *
@@ -74,18 +85,6 @@
  * \quad \mathrm{with} \quad i \neq j \f]
  *
  */
-//  * \f[
-//  * \begin{circuitikz}
-//  * \draw node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
-//  * \draw (1,0) node[anchor=south]{$P_{in}$} to [short, *-*] (3.0,0);
-//  * \draw (3,0) node[anchor=south]{} to [short, -*] (4.5,1.0);
-//  * \draw (4.3,1.1) node[anchor=south] {$P_{out,1}$};
-//  * \draw (3,0) node[anchor=south]{} to [short, -*] (4.5,-1.0);
-//  * \draw (4.3,-1.1) node[anchor=north] {$P_{out,2}$};
-//  * \draw [-latex] (4.65,1.1) -- (5.25,1.5) node[right] {$Q_{out,1}$};
-//  * \draw [-latex] (4.65,-1.1) -- (5.25,-1.5) node[right] {$Q_{out,2}$};
-//  * \end{circuitikz}
-//  * \f]
 class Junction : public Block {
  public:
   using Block::Block;

diff --git a/src/model/OpenLoopCoronaryBC.h b/src/model/OpenLoopCoronaryBC.h
@@ -41,7 +41,20 @@
 /**
  * @brief Open loop coronary boundary condition based on \cite kim_coronary.
  *
- * \image html open_loop_coronary_b_c_dark.png
+ * \f[
+ * \begin{circuitikz} \draw
+ * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
+ * \draw (1,0) node[anchor=south]{$P_{in}$}
+ * to [R, l=$R_a$, *-] (3,0)
+ * to [R, l=$R_{am}$, -] (5,0)
+ * to [R, l=$R_v$, *-*] (7,0)
+ * node[anchor=south]{$P_{v}$}
+ * (5,0) to [C, l=$C_{im} \;V_{im}$, -*] (5,-1.5)
+ * node[left]{$P_{im}$}
+ * (3,0) to [C, l=$C_a$, -*] (3,-1.5)
+ * node[left]{$P_a$};
+ * \end{circuitikz}
+ * \f]
  *
  * ### Governing equations
  *
@@ -91,20 +104,6 @@
  * * `6` Pv
  *
  */
-//  * \f[
-//  * \begin{circuitikz} \draw
-//  * node[left] {$Q_{in}$} [-latex] (0,0) -- (0.8,0);
-//  * \draw (1,0) node[anchor=south]{$P_{in}$}
-//  * to [R, l=$R_a$, *-] (3,0)
-//  * to [R, l=$R_{am}$, -] (5,0)
-//  * to [R, l=$R_v$, *-*] (7,0)
-//  * node[anchor=south]{$P_{v}$}
-//  * (5,0) to [C, l=$C_{im} \;V_{im}$, -*] (5,-1.5)
-//  * node[left]{$P_{im}$}
-//  * (3,0) to [C, l=$C_a$, -*] (3,-1.5)
-//  * node[left]{$P_a$};
-//  * \end{circuitikz}
-//  * \f]
 class OpenLoopCoronaryBC : public Block {
  public:
   // Inherit constructors

diff --git a/src/model/PressureReferenceBC.h b/src/model/PressureReferenceBC.h
@@ -43,7 +43,14 @@
  *
  * Applies a predefined pressure at a boundary.
  *
- * \image html pressure_reference_b_c_dark.png
+ * \f[
+ * \begin{circuitikz}
+ * \draw (1,0) node[anchor=south]{$P$} to [short, *-] (1.2,0) ;
+ * \draw [-latex] (1.4,0) -- (2.2,0) node[right] {$Q$};
+ * \draw (1,0) to [short, l=, *-] (1,-1)
+ * node[ground]{$\hat{P}$};
+ * \end{circuitikz}
+ * \f]
  *
  * ### Governing equations
  *
@@ -72,14 +79,6 @@
  * * `0` Pressure
  *
  */
-//  * \f[
-//  * \begin{circuitikz}
-//  * \draw (1,0) node[anchor=south]{$P$} to [short, *-] (1.2,0) ;
-//  * \draw [-latex] (1.4,0) -- (2.2,0) node[right] {$Q$};
-//  * \draw (1,0) to [short, l=, *-] (1,-1)
-//  * node[ground]{$\hat{P}$};
-//  * \end{circuitikz}
-//  * \f]
 class PressureReferenceBC : public Block {
  public:
   // Inherit constructors