Commit b3522e89 authored by Chris Cantwell's avatar Chris Cantwell

Fixed images in user guide. Moved images to img subdirectory for consistency.

parent 66db4e4a
......@@ -2,7 +2,6 @@ SET(DEVGUIDESRC ${CMAKE_CURRENT_SOURCE_DIR})
SET(DEVGUIDE ${CMAKE_BINARY_DIR}/docs/developer-guide)
FILE(MAKE_DIRECTORY ${DEVGUIDE}/html)
FILE(GLOB_RECURSE pngfiles "*.png")
FIND_PROGRAM(HTLATEX htlatex)
ADD_CUSTOM_TARGET(developer-guide-html
......@@ -13,11 +12,21 @@ ADD_CUSTOM_TARGET(developer-guide-html
)
# If tex4ht successful, create img dir and copy images across
FILE(GLOB_RECURSE imgfiles "*/img/*.png" "*/img/*.jpg")
ADD_CUSTOM_COMMAND(TARGET developer-guide-html
POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${DEVGUIDE}/html/img)
FOREACH(png ${pngfiles})
FOREACH(img ${imgfiles})
ADD_CUSTOM_COMMAND(TARGET developer-guide-html
POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${png} ${DEVGUIDE}/html/img)
POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${img} ${DEVGUIDE}/html/img)
ENDFOREACH()
FILE(GLOB_RECURSE pdffiles "*/img/*.pdf")
FIND_PROGRAM(CONVERT convert)
FOREACH(pdf ${pdffiles})
GET_FILENAME_COMPONENT(BASENAME ${pdf} NAME_WE)
ADD_CUSTOM_COMMAND(TARGET developer-guide-html
POST_BUILD COMMAND
${CONVERT} ${pdf} ${DEVGUIDE}/html/img/${BASENAME}.png)
ENDFOREACH()
FIND_PROGRAM(PDFLATEX pdflatex)
......
......@@ -12,6 +12,26 @@ ADD_CUSTOM_TARGET(user-guide-html
WORKING_DIRECTORY ${USERGUIDE}/html
)
# If tex4ht successful, create img dir and copy images across
FILE(GLOB_RECURSE imgfiles "*/img/*.png" "*/img/*.jpg")
ADD_CUSTOM_COMMAND(TARGET user-guide-html
POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${USERGUIDE}/html/img)
FOREACH(img ${imgfiles})
ADD_CUSTOM_COMMAND(TARGET user-guide-html
POST_BUILD COMMAND
${CMAKE_COMMAND} -E copy ${img} ${USERGUIDE}/html/img)
ENDFOREACH()
FILE(GLOB_RECURSE pdffiles "*/img/*.pdf")
FIND_PROGRAM(CONVERT convert)
FOREACH(pdf ${pdffiles})
GET_FILENAME_COMPONENT(BASENAME ${pdf} NAME_WE)
ADD_CUSTOM_COMMAND(TARGET user-guide-html
POST_BUILD COMMAND
${CONVERT} ${pdf} ${USERGUIDE}/html/img/${BASENAME}.png)
ENDFOREACH()
FIND_PROGRAM(PDFLATEX pdflatex)
MARK_AS_ADVANCED(PDFLATEX)
FIND_PROGRAM(BIBTEX bibtex)
......
......@@ -370,7 +370,7 @@ Fig.~\ref{f:adrsolver:helmholtz2D}
\begin{figure}
\begin{center}
\includegraphics[width=6cm]{Figures/Helmholtz2D}
\includegraphics[width=6cm]{img/Helmholtz2D}
\caption{Solution of the 2D Helmholtz Problem.}
\label{f:adrsolver:helmholtz2D}
\end{center}
......@@ -429,7 +429,7 @@ The geometry under consideration is a pipe of radius, $R = 0.5$ and length $l =
\begin{figure}[h!]
\begin{center}
\includegraphics[width=6cm]{Figures/pipe}
\includegraphics[width=6cm]{img/pipe}
\caption{Pipe.}
\end{center}
\end{figure}
......@@ -544,7 +544,7 @@ streamwise direction, as shown in Fig.~\ref{f:adrsolver:masstransport}.
\begin{figure}[h!]
\begin{center}
\includegraphics[width=7cm]{Figures/graetz-nusselt}
\includegraphics[width=7cm]{img/graetz-nusselt}
\caption{Concentration gradient at the surface of the pipe.}
\label{f:adrsolver:masstransport}
\end{center}
......
......@@ -65,7 +65,7 @@ of $64$ quadrilateral elements, as shown in Fig.~\ref{f:apesolver:geometry}.
\begin{figure}
\centering
\includegraphics[width=0.5\linewidth]{Figures/APE_Geometry.png}
\includegraphics[width=0.5\linewidth]{img/APE_Geometry.png}
\caption{Geometry used for the example case of modelling propagation of
acoustic waves where $\overline{u}_i = 0, \, \overline{p}=p_{\infty}=10^6, \, \overline{\rho} = \rho_0 = 1.204$}
\label{f:apesolver:geometry}
......@@ -131,9 +131,9 @@ time steps, showing the acoustic propagation.
\begin{figure}
\centering
\includegraphics[width=0.3\linewidth]{Figures/Prop_1.png}
\includegraphics[width=0.3\linewidth]{Figures/Prop_2.png}
\includegraphics[width=0.3\linewidth]{Figures/Prop_3.png}
\includegraphics[width=0.3\linewidth]{img/Prop_1.png}
\includegraphics[width=0.3\linewidth]{img/Prop_2.png}
\includegraphics[width=0.3\linewidth]{img/Prop_3.png}
\caption{}
\label{f:apesolver:results}
\end{figure}
......@@ -146,7 +146,7 @@ predicted by literature \cite{DoFf83}.
\begin{figure}
\centering
\includegraphics[width=0.7\linewidth]{Figures/prog_4.png}
\includegraphics[width=0.7\linewidth]{img/prog_4.png}
\caption{}
\end{figure}
......@@ -442,8 +442,8 @@ For the non-smooth artificial viscosity model the added artificial viscosity is
\end{equation}
\begin{figure}[!htbp]
\begin{center}
\includegraphics[width = 0.47 \textwidth]{Figures/Mach_P4.pdf}
\includegraphics[width = 0.47 \textwidth]{Figures/ArtVisc_P4.pdf}
\includegraphics[width = 0.47 \textwidth]{img/Mach_P4.pdf}
\includegraphics[width = 0.47 \textwidth]{img/ArtVisc_P4.pdf}
\caption{(a) Steady state solution for $M=0.8$ flow at $\alpha = 1.25^\circ$ past a NACA 0012 profile, (b) Artificial viscosity ($\epsilon$) distribution}
\label{fig:}
\end{center}
......
......@@ -236,7 +236,7 @@ where $\sigma=\left\| \mathbf{u'}(\tau)\right\|$. This is no other that the sing
\begin{figure}[!htbp]
\centering
\label{TG}
{\includegraphics[width=1 \textwidth]{Figures/transient_growth.png}}
{\includegraphics[width=1 \textwidth]{img/transient_growth.png}}
\caption {Geometric interpretation of the transient growth. Adapted from Schmid, 2007 }
\end{figure}
......@@ -870,8 +870,8 @@ The result should look similar to that shown in Figure~\ref{f:incns:kovaflow}.
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/KF2DCVP8.png}
\includegraphics[width=7cm]{Figures/KF2DCVP8SL.png}
\includegraphics[width=7cm]{img/KF2DCVP8.png}
\includegraphics[width=7cm]{img/KF2DCVP8SL.png}
\caption{Velocity profiles for the Kovasznay Flow (2D).}
\label{f:incns:kovaflow}
\end{center}
......@@ -948,8 +948,8 @@ Figure~\ref{f:incns:kovaflow2d_hobc}.
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/KF2DCVP8HOBC_U.png}
\includegraphics[width=7cm]{Figures/KF2DCVP8HOBC_V.png}
\includegraphics[width=7cm]{img/KF2DCVP8HOBC_U.png}
\includegraphics[width=7cm]{img/KF2DCVP8HOBC_V.png}
\caption{Velocity profiles for the Kovasznay Flow in truncated domain (2D).}
\label{f:incns:kovaflow2d_hobc}
\end{center}
......@@ -1083,8 +1083,8 @@ Figure~\ref{f:incns:laminar2d}.
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/CF2DSKP3PR.png}
\includegraphics[width=7cm]{Figures/CF2DSKP3.png}
\includegraphics[width=7cm]{img/CF2DSKP3PR.png}
\includegraphics[width=7cm]{img/CF2DSKP3.png}
\caption{Pressure and velocity profiles for the laminar channel flow (2D).}
\label{f:incns:laminar2d}
\end{center}
......@@ -1180,8 +1180,8 @@ The expected results are shown in Figure~\ref{f:incns:laminar3d}.
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/CF3DP8PR.png}
\includegraphics[width=7cm]{Figures/CF3DP8.png}
\includegraphics[width=7cm]{img/CF3DP8PR.png}
\includegraphics[width=7cm]{img/CF3DP8.png}
\caption{Pressure and velocity profiles for the laminar channel flow (full 3D).}
\label{f:incns:laminar3d}
\end{center}
......@@ -1269,7 +1269,7 @@ Figure~\ref{f:incns:turbchanmesh}.
\begin{figure}
\begin{center}
\includegraphics[width=10cm]{Figures/ChanMesh.png}
\includegraphics[width=10cm]{img/ChanMesh.png}
\caption{Mesh used for the turbulent channel flow.}
\label{f:incns:turbchanmesh}
\end{center}
......@@ -1363,7 +1363,7 @@ Figure~\ref{f:incns:turbchanflow}.
\begin{figure}
\begin{center}
\includegraphics[width=12cm]{Figures/ChanCont.png}
\includegraphics[width=12cm]{img/ChanCont.png}
\caption{Velocity profile of the turbulent channel flow (quasi-3D).}
\label{f:incns:turbchanflow}
\end{center}
......@@ -1384,7 +1384,7 @@ Figure~\ref{f:incns:turbpipemesh}.
\begin{figure}
\begin{center}
\includegraphics[width=10cm]{Figures/PipeDomain.png}
\includegraphics[width=10cm]{img/PipeDomain.png}
\caption{Domain for the turbulent pipe flow problem.}
\label{f:incns:turbpipemesh}
\end{center}
......@@ -1431,7 +1431,7 @@ Figure~\ref{f:incns:turbpipeflow}.
\begin{figure}
\begin{center}
\includegraphics[width=12cm]{Figures/PipeCont.png}
\includegraphics[width=12cm]{img/PipeCont.png}
\caption{Velocity profile of the turbulent pipe flow (quasi-3D).}
\label{f:incns:turbpipeflow}
\end{center}
......@@ -1458,7 +1458,7 @@ The geometry under consideration is a segment of a rabbit descending aorta with
\begin{figure}
\begin{center}
\includegraphics[width=10cm]{Figures/IntercostalGeometry.png}
\includegraphics[width=10cm]{img/IntercostalGeometry.png}
\caption{Reduced region of rabbit descending thoracic aorta.}
\end{center}
\end{figure}
......@@ -1467,7 +1467,7 @@ In order to capture the physics of the flow in the boundary layer, a thin layer
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/spherigons.png}
\includegraphics[width=7cm]{img/spherigons.png}
\caption{Surface mesh indicating curved surface elements at a branch location.}
\end{center}
\end{figure}
......@@ -1561,7 +1561,7 @@ We can visualise the internal velocity field by applying a volume render filter
\begin{figure}
\begin{center}
\includegraphics[width=10cm]{Figures/velocityRendered.png}
\includegraphics[width=10cm]{img/velocityRendered.png}
\caption{The solved-for velocity field.}
\end{center}
\end{figure}
......@@ -1570,7 +1570,7 @@ It is possible to visualise the wall shear stress distribution by running the Fl
\begin{figure}
\begin{center}
\includegraphics[width=12cm]{Figures/WSS.png}
\includegraphics[width=12cm]{img/WSS.png}
\caption{Non-dimensional wall shear stress distribution.}
\end{center}
\end{figure}
......@@ -1633,8 +1633,8 @@ The simulation results are illustrated in spanwise vorticity contours in Figure
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/strip-16-time-100.png}
\includegraphics[width=7cm]{Figures/strip-16-time-600.png}
\includegraphics[width=7cm]{img/strip-16-time-100.png}
\includegraphics[width=7cm]{img/strip-16-time-600.png}
\caption{Spanwise vorticity contours in standing wave and traveling wave patterns predicted in finite strip modeling.}
\label{f:incns:finite-strip-modeling}
\end{center}
......@@ -1812,13 +1812,13 @@ The stability simulation takes about 250 iterations to converge and the dominant
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/chan_u.png}}
{\includegraphics[width=1 \textwidth]{img/chan_u.png}}
\caption {}
\end{figure}
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/chan_v}}
{\includegraphics[width=1 \textwidth]{img/chan_v}}
\caption {}
\end{figure}
......@@ -1936,13 +1936,13 @@ The equations will then be evolved backwards in time (consistently with the nega
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/chan_u_adj.png}}
{\includegraphics[width=1 \textwidth]{img/chan_u_adj.png}}
\caption {}
\end{figure}
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/chan_v_adj}}
{\includegraphics[width=1 \textwidth]{img/chan_v_adj}}
\caption {}
\end{figure}
......@@ -1952,7 +1952,7 @@ In this section it will be described how to perform a transient growth stability
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/bfs_geo}}
{\includegraphics[width=1 \textwidth]{img/bfs_geo}}
\caption {}\label{bfs_geo}
\end{figure}
......@@ -2116,13 +2116,13 @@ The solution will be evolved forward in time using the operator $\mathcal{A}$, t
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/bfs_eig_u}}
{\includegraphics[width=1 \textwidth]{img/bfs_eig_u}}
\caption {}
\end{figure}
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/bfs_eig_v}}
{\includegraphics[width=1 \textwidth]{img/bfs_eig_v}}
\caption {}
\end{figure}
......@@ -2131,7 +2131,7 @@ It is possible to visualise the transient growth plotting the energy evolution o
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/energy_bfs}}
{\includegraphics[width=1 \textwidth]{img/energy_bfs}}
\caption {}
\end{figure}
......@@ -2141,7 +2141,7 @@ It is possible to visualise the transient growth plotting the energy evolution o
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/cylinder_geo}}
{\includegraphics[width=1 \textwidth]{img/cylinder_geo}}
\caption {}
\end{figure}
......@@ -2200,7 +2200,7 @@ The stability simulation takes about 20 cycles to converge and the leading eigen
\begin{figure}[!htbp]
\centering
{\includegraphics[width=1 \textwidth]{Figures/floquet}}
{\includegraphics[width=1 \textwidth]{img/floquet}}
\caption {}
\end{figure}
......@@ -164,7 +164,7 @@ in order to test convergence $h$-refinement is required.
\begin{figure}
\begin{center}
\includegraphics[width=0.5\textwidth]{Figures/l-shape}
\includegraphics[width=0.5\textwidth]{img/l-shape}
\end{center}
\caption{Solution of the $u$ displacement field for the L-shaped domain.}
\label{fig:elas:ldomain}
......@@ -197,9 +197,9 @@ figure~\ref{fig:elas:bl}.
\begin{figure}
\begin{center}
\includegraphics[width=0.3\textwidth]{Figures/bl-0}
\includegraphics[width=0.3\textwidth]{Figures/bl-1}
\includegraphics[width=0.3\textwidth]{Figures/bl-2}
\includegraphics[width=0.3\textwidth]{img/bl-0}
\includegraphics[width=0.3\textwidth]{img/bl-1}
\includegraphics[width=0.3\textwidth]{img/bl-2}
\end{center}
\caption{Figures that show the initial domain (left), after 50 steps (middle)
and final deformation of the domain (right).}
......
......@@ -37,7 +37,7 @@ Typically 1D arterial networks are made up of a connection of different base uni
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/PulseWaveBifurcation.png}
\includegraphics[width=7cm]{img/PulseWaveBifurcation.png}
\caption{Model of bifurcating artery. The bifurcation is made of three domains and 15 vertices. Vertex V[0] is the inlet and vertices V[10] and V[15] the outlets.}
\end{center}
\end{figure}
......@@ -224,8 +224,8 @@ are set correctly and how each arterial segment gets its correct physiological
data.
\begin{figure}
\includegraphics[width=0.49\linewidth]{Figures/55_artery_network.jpg}
\includegraphics[width=0.49\linewidth]{Figures/Data_Table.png}
\includegraphics[width=0.49\linewidth]{img/55_artery_network.jpg}
\includegraphics[width=0.49\linewidth]{img/Data_Table.png}
\end{figure}
First, we will set up the mesh where each arterial segment is represented by one
......@@ -342,8 +342,8 @@ The vertices where the network terminates are specified as boundary regions
based on their subsequent composite ids.
\begin{figure}
\includegraphics[width=0.49\linewidth]{Figures/Bifurcation.png}
\includegraphics[width=0.49\linewidth]{Figures/Network_Inflow.png}
\includegraphics[width=0.49\linewidth]{img/Bifurcation.png}
\includegraphics[width=0.49\linewidth]{img/Network_Inflow.png}
\end{figure}
\begin{lstlisting}[style=XmlStyle]
......@@ -432,7 +432,7 @@ values slightly differ from in vivo measurements due to the missing terminal
resistance, which will be added in future.
\begin{figure}
\includegraphics[width=\linewidth]{Figures/Network_Results.png}
\includegraphics[width=\linewidth]{img/Network_Results.png}
\end{figure}
These short examples should give an insight to the functionality of our
......@@ -449,7 +449,7 @@ In the following we will explain the usage of the \hyperref[PulseWaveSolver]{Pu
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/StentGeometry.png}
\includegraphics[width=7cm]{img/StentGeometry.png}
\caption{Model of straight artery with a stent in the middle.}
\end{center}
\end{figure}
......@@ -458,7 +458,7 @@ In the following we will explain the usage of the \hyperref[PulseWaveSolver]{Pu
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/StentDomain.png}
\includegraphics[width=7cm]{img/StentDomain.png}
\caption{1D arterial domain consisting of 30 elements and 31 vertices.}
\end{center}
\end{figure}
......@@ -488,7 +488,7 @@ These elements are combined to three different composites (shown below): composi
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/StentComposite.png}
\includegraphics[width=7cm]{img/StentComposite.png}
\caption{Three composites (C[0], C[1] and C[2]) for the stunted artery.}
\end{center}
\end{figure}
......@@ -553,7 +553,7 @@ Finally the domain is specified by the first composite by
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/StentPressureProfile.png}
\includegraphics[width=7cm]{img/StentPressureProfile.png}
\caption{Pressure profile applied at the inlet of the artery}
\end{center}
\end{figure}
......@@ -593,7 +593,7 @@ The simulation starts from the static equilibrium of the vessel with normalised
\paragraph{Functions:~} The stent is introduced by applying a variable material properties function ($\beta$ - see equation \ref{eqn:PA}) along the vessel in the x direction, shown graphically below
\begin{figure}
\begin{center}
\includegraphics[width=7cm]{Figures/StentMaterial.png}
\includegraphics[width=7cm]{img/StentMaterial.png}
\caption{material property variation along the artery. The stiff region in the middle represents the stent.}
\end{center}
\end{figure}
......@@ -621,8 +621,8 @@ area in that specific part of the artery compared to the normal vessel
(Fig.~\ref{f:pulsewave:stented:vessels}).
\begin{figure}
\includegraphics[width=0.49\linewidth]{Figures/normal_vessel.jpg}
\includegraphics[width=0.49\linewidth]{Figures/stented_vessel.jpg}
\includegraphics[width=0.49\linewidth]{img/normal_vessel.jpg}
\includegraphics[width=0.49\linewidth]{img/stented_vessel.jpg}
\caption{}
\label{f:pulsewave:stented:vessels}
\end{figure}
......@@ -635,8 +635,8 @@ artery (right). Here, the stiffening at the stent causes reflections and thus
there are losses for total pressure at the medial (M) and distal (D) point.
\begin{figure}
\includegraphics[width=0.49\linewidth]{Figures/pressure_normal_vessel.jpg}
\includegraphics[width=0.49\linewidth]{Figures/pressure_stented_vessel.jpg}
\includegraphics[width=0.49\linewidth]{img/pressure_normal_vessel.jpg}
\includegraphics[width=0.49\linewidth]{img/pressure_stented_vessel.jpg}
\end{figure}
\section{Further Information}
......
......@@ -166,5 +166,5 @@ This will generate a file called \inltt{RossbyModon\_Nonlinear\_DG.dat} that
can be loaded directly into tecplot:
\begin{figure}
\includegraphics[width=\linewidth]{Figures/RossbyModon.png}
\includegraphics[width=\linewidth]{img/RossbyModon.png}
\end{figure}
\Preamble{html}
\Configure{graphics*}
{pdf}
{\Needs{"convert \csname Gin@base\endcsname.pdf
\csname Gin@base\endcsname.png"}%
\Picture[pict]{\csname Gin@base\endcsname.png}%
\special{t4ht+@File: \csname Gin@base\endcsname.png}
}
%% Use HTML for italics and bold
\Configure{emph}{\ifvmode\ShowPar\fi\HCode{<em>}}{\HCode{</em>}}
\Configure{textbf}{\ifvmode\ShowPar\fi\HCode{<b>}}{\HCode{</b>}}
......
......@@ -348,8 +348,8 @@ the surface elements producing leading edge closer to the underlying geometry:
\begin{figure}[!htbp]
\begin{center}
\includegraphics[width = 0.47 \textwidth]{Figures/noSphnoBL.jpg}
\includegraphics[width = 0.47 \textwidth]{Figures/SphnoBL.jpg}
\includegraphics[width = 0.47 \textwidth]{img/noSphnoBL.jpg}
\includegraphics[width = 0.47 \textwidth]{img/SphnoBL.jpg}
\caption{(a) Leading edge without spherigons, (b) Leading edge with
spherigons}
\end{center}
......@@ -439,8 +439,8 @@ of 2 and 7 integration points per element use the following command:
%
\begin{figure}[!htbp]
\begin{center}
\includegraphics[width = 0.47 \textwidth]{Figures/SphnoBL.jpg}
\includegraphics[width = 0.47 \textwidth]{Figures/SphBL.jpg}
\includegraphics[width = 0.47 \textwidth]{img/SphnoBL.jpg}
\includegraphics[width = 0.47 \textwidth]{img/SphBL.jpg}
\caption{(a) LE with Spherigons but only one prism layer for resolving the
boundary layer, (b) LE with Spherigons with 3 growing layers of prisms for
better resolving the boundary layer.}
......
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