User: rhaas Date: 2012/04/05 12:36 AM
Added: /handson_viz/ Makefile, add_isosurface.png, add_pseudocolor.png, add_reflection.png, annotation_menu.png, change_colour_scheme.png, disable_x_axis.png, final_plot_snapshot.png, handson_viz.tex, initial_plot_snapshot.png, isocontour_options.png, movie_frame_options.png, open_file.png, pseudocolour_options.png, reflection_options.png, render_frames_menu.png, rendering_options.png
Log: add first version of visualization hands on
this is really just a collection of images of where to click on not quite sure how else to guide them through VisIt and still be done on time.
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File [added]: Makefile Delta lines: +10 -0 =================================================================== --- handson_viz/Makefile (rev 0) +++ handson_viz/Makefile 2012-04-05 05:36:03 UTC (rev 59) @@ -0,0 +1,10 @@ +all: handson_viz.pdf + +%.pdf: %.tex + pdflatex $* + +clean: + /bin/bash -exec "rm -f handson_viz.{aux,log,nav,out,snm,pdf,toc} *~" + +.PHONY: all clean +
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File [added]: handson_viz.tex Delta lines: +245 -0 =================================================================== --- handson_viz/handson_viz.tex (rev 0) +++ handson_viz/handson_viz.tex 2012-04-05 05:36:03 UTC (rev 59) @@ -0,0 +1,245 @@ +\input{../preamble.tex} +\usepackage{ragged2e} +\usepackage{amsmath} +\usepackage{listings} +\newcommand{\Heaviside}{\operatorname{\Theta}} + +\subtitle[Visualization hands-on]{{\large Einstein Toolkit +Workshop}\*[0.3em]Hands-on exercise: visualizing density oscillations and +gravitational waves} +\author{Roland Haas} +\date{Apr 05 2012} + +\usecolortheme[RGB={200,200,200}]{structure} + +\begin{document} + +\begin{frame} +\titlepage +\end{frame} + +\begin{frame} +\frametitle{Installing software} +To turn the rendered frames into a movie we will use \texttt{ffmpeg} which +unfortunately did not make it into the virtual machine. To install it, enter +on a command prompt: +\begin{alltt} + sudo apt-get install ffmpeg +\end{alltt} +Enter \texttt{etk-user} (ie. your password) when asked for the password. +\end{frame} + +\begin{frame} +\frametitle{TOV files to visualize} +You can either use the output files from the \texttt{fast_tov.par} run you +started yesterday, or download a (slightly different) dataset from +\url{http://www.physics.gatech.edu/~rhaas3/Workshop%5C_Spring%5C_2012/rho.rl4.h5.... +(about 4MB). Copy the file to a folder of your choice and decompress it via +\begin{alltt} + xz -d -f --keep path-to-folder/rho.rl4.h5.xz +\end{alltt} + +The former file will work but will be a bit boring. The later one I tweaked a +bit to get nice large oscillations. +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{itemize} + \item type \texttt{$HOME/VisIt/bin/visit} at a command prompt to start + visit + \item You can try enabling 3D acceleration, but at least on Intel graphics + chips this tends to make VisIt fail at startup. + \item open the output file of your choice +\end{itemize} +\begin{center} +\includegraphics[height=48mm]{open_file} +\end{center} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{columns} +\column{60mm} +\begin{itemize} +\item add a pseudocolor plot from the "Plots" drop-down button +\item we will display a number of isocontour lines in the star to show its oscillations +\item we will use the \texttt{IsoSurface} operator to compute the contour surfaces +\item \texttt{VisIt} also offers a \texttt{Contour} plot which however is limited in the transparency options compared to the \texttt{IsoSurface}, \texttt{PseudoColor} combination we use +\end{itemize} +\column{60mm} +\includegraphics[width=60mm]{add_pseudocolor} +\end{columns} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{itemize} +\item add \texttt{IsoSurface} operator from \texttt{Operators/Slicing/Isosurface} +\item add \texttt{Reflect} operator from \texttt{Operators/Transforms/Reflect}, to populate the ``missing'' octants +\end{itemize} +\begin{columns} +\column{60mm} +\includegraphics[width=60mm]{add_reflection} +\column{60mm} +\includegraphics[width=60mm]{add_isosurface} +\end{columns} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{columns} +\column{60mm} +\begin{itemize} +\item double-click on the \texttt{Pseudocolor} entry in the list of plots to display its options page. Your might have to expand the list using the triangle shaped button on the left first +\item add transparency by reducing the opacity to about 25% and set limits of $[10^{-8},10^{-3}]$ for the plot range. We will use the same range when creating isocontours in the next step +\item you have to click on \texttt{Apply} then on \texttt{Dismiss} to apply the new settings +\end{itemize} +\column{60mm} +\includegraphics[width=60mm]{pseudocolour_options} +\end{columns} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{itemize} +\item double click on the \texttt{Reflect} operator, change to \texttt{3D} and activate all octants except the original ($+X+Y+Z$) one and the $+X-Y+Z$ one, change the reflection point to the origin. +\end{itemize} +\begin{center} +\includegraphics[height=60mm]{reflection_options} +\end{center} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{itemize} +\item double click on the \texttt{IsoSurface} operator and select the range used for the \texttt{Pseudocolor} plot, use $6$ levels and leave the scaling at \texttt{linear} +\end{itemize} +\begin{center} +\includegraphics[width=60mm]{isocontour_options} +\end{center} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{itemize} +\item click on \texttt{Draw} to see how your plot looks like +\item rotate to an orientation that looks nice, by grabbing the plot with the mouse +\end{itemize} +\begin{center} +\includegraphics[width=60mm]{initial_plot_snapshot} +\end{center} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{columns} +\column{60mm} +\begin{itemize} +\item next we will change \texttt{VisIt}'s rendering options to add shadows and change the background to something more attractive +\item unfortunately this means we will eventually loose the transparancy (at least in the virtual machine) +\item first though open the \texttt{Annotation} control page +\end{itemize} +\column{60mm} +\includegraphics[width=60mm]{annotation_menu} +\end{columns} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{itemize} +\item in the \texttt{X-Axis} subtab of the \texttt{3D} tab, disable the axis title +\item repeat for the other two axes +\item in the \texttt{Colors} tab, change the background to black and the foreground to white +\item add a gradient to the background, with a dark gray as the second colour +\end{itemize} +\begin{center} +\includegraphics[width=58mm]{disable_x_axis} +\hfill +\includegraphics[width=58mm]{change_colour_scheme} +\end{center} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{columns} +\column{60mm} +\begin{itemize} +\item open \texttt{VisIt}'s rendering options from the \texttt{Options/Rendering...} menu +\item on the \texttt{Advanced} tab, enable \texttt{scalable rendering}, \texttt{Shadows} and \texttt{Depth Cueing} +\end{itemize} +\column{60mm} +\includegraphics[width=60mm]{rendering_options} +\end{columns} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{itemize} +\item click on \texttt{Draw} to see how your plot looks like +\end{itemize} +\begin{center} +\includegraphics[width=60mm]{final_plot_snapshot} +\end{center} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{columns} +\column{60mm} +\begin{itemize} +\item in this penultimate step we will let \texttt{VisIt} rendering frames of a small movie showing the oscillations +\item to start the movie wizard, select \texttt{Save movie...} from the \texttt{File} menu +\end{itemize} +\column{60mm} +\includegraphics[width=60mm]{render_frames_menu} +\end{columns} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{columns} +\column{60mm} +\begin{itemize} +\item in this penultimate step we will let \texttt{VisIt} rendering frames of a small movie showing the oscillations +\item to start the movie wizard, select \texttt{Save movie...} from the \texttt{File} menu +\end{itemize} +\column{60mm} +\includegraphics[width=60mm]{render_frames_menu} +\end{columns} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{columns} +\column{60mm} +\begin{itemize} +\item Finally, inside the wizard, change the frame size to approximately $640\times640$ pixels (multiples of $16$ are best) +\item choose \texttt{png} output +\item add the movie format to the list on the right using the \texttt{->} button +\item click on next and accept the defaults for all other steps, maybe choosing a different output directory for the frames +\end{itemize} +\column{60mm} +\includegraphics[width=60mm]{movie_frame_options} +\end{columns} +\end{frame} + +\begin{frame} +\frametitle{Visualizing density oscillations} +\begin{itemize} +\item once \texttt{VisIt} is done, which will take some minutes, we can render the frames into an actual movie +\item for this, \texttt{cd} into the folder containing the frames and enter +\begin{alltt} +ffmpeg -loop_input -vframes 200 -qscale 1 -b 1000 -i movie%04d.png movie.avi +\end{alltt} +\begin{itemize} +\item \texttt{-loop_input} makes \texttt{ffmpeg} wrap around when looking for frames +\item \texttt{-vframes 200} is the number of frames to include in the movie, we set this to twice as many as we have actual frames, ie. the movie will loop twice +\item \texttt{-qscale 1} sets the quality scale for the encoder. $1$ is best quality. +\item \texttt{-b 1000} asks for a bitrate of $1000$ kilobits per second +\item \texttt{-i movie%04d.png} tells \texttt{ffmpeg} the names of the input files, it accepts \texttt{printf} format specifiers to construct a file name based on the frame number. \texttt{ffmpeg} stops encoding once it generates a name for which no or no valid file is found. +\end{itemize} +\item play the movie using \texttt{ffplay} +\end{itemize} +\end{frame} +\end{document}
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