Scientific visualisation in 2D and 3D
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1 Scientific visualisation in 2D and 3D Roman Putanowicz Some rights reserved (CC) See License slide. 1
2 Right tool for the right job gnuplot All sorts of 2D visualisation and simple 3D visualisation octave More advanced 2D visualisations that require extensive data manipulations octave + octaviz Simple 3D programming VTK Advanced computer graphics and 3D programming ParaView, OpenDX 3D visualisations 2
3 Part I Gnuplot Overview 3
4 Gnuplot Home page: Portable: MS Windows, GNU/Linux, UNIX, and OSX. Book: Gnuplot in Action. Understanding Data with Graphs, Philipp K. Janert, Manning Publications Co.,
5 Plotting functions given by formulas 1 f(x) = 1/(1+(x*sin(x))**2) 2 plot f(x) 5
6 Axes setup 1 f(x) = 1/(1+(x*sin(x))**2) 2 plot f(x) 3 set xrange[-5:5] 4 set yrange[0:1.3] 5 replot 6
7 Labels and graph tytle 1 f(x) = 1/(1+(x*sin(x))**2) 2 plot f(x) 3 set xrange[-5:5] 4 set yrange[0:1.3] 5 set xlabel "Temperature [K]" 6 set ylabel "Distance [m]" 7 set title \ 8 "Temperature distribution" 9 replot 7
![3] 5 set xlabel "Temperature [K]" 6 set ylabel](/docs-images/40/8943707/images/page_7.jpg "\"Distance [m]\" 7 set title \ 8 \"Temperature")
8 Setting lines and markers style 1 f(x) = 1/(1+(x*sin(x))**2) 2 set xrange[-5:5] 3 set yrange[0:1.3] 4 set xlabel "Temperature [K]" 5 set ylabel "Distance [m]" 6 set title \ 7 "Temperature distribution" 8 set style lines 1 lw 0 linecolor rgb "green" pt 5 ps 2 pointinterval 5 9 set style lines 2 lc rgb "red" 10 plot f(x) with linespoints ls 1, f(x) notitle ls 2 8
![3] 4 set xlabel "Temperature [K]" 5 set ylabel "Distance [m]" 6 set title \ 7 "Temperature](/docs-images/40/8943707/images/page_8.jpg "distribution\" 8 set style lines 1 lw 0 linecolor rgb \"green\" pt 5 ps 2 pointinterval 5 9")
9 Legend 1 f(x) = 1/(1+(x*sin(x))**2) 2 set xrange[-5:5] 3 set yrange[0:1.3] 4 set xlabel "Temperature [K]" 5 set ylabel "Distance [m]" 6 set title \ 7 "Temperature distribution" 8 set style lines 1 lc rgb "red" 9 set style lines 2 lw 0 linecolor rgb "green" pt 5 ps 2 pointinterval 5 10 set style lines 3 linecolor rgb "blue" lw 3 11 set key left width 1 height 1 box ls 3 12 plot f(x) w linespoint title "f(x) samples" ls 2, f(x) ls 1 9
10 Plotting many functions 1 f(x) = 1/(1+x**2) 2 set xrange[-5:5] 3 plot f(x), sin(x) 4 replot cos(x) w points 10
![xrange[-5:5] 3 plot f(x),](/docs-images/40/8943707/images/page_10.jpg "sin(x) 4 replot cos(x) w")
11 Filled functions 1 f1(x) = 0.2*cos(x) 2 f2(x) = 0.5*sin(x) 3 f3(x) = 1/(1+x**2) 4 t1 = "0.2*cos(x)" 5 t2 = "0.5*sin(x)" 6 t3 = "1/(1+x**2)" 7 set clip two 8 unset colorbox 9 set xrange [-5:5] 10 set style fill solid 1.00 noborder 11 set style function filledcurves y1=0 12 set title "Solid filled curves" 13 plot 0.2*cos(x) fs solid 1.0 lc rgb "forest-green" title t1 14 replot 0.5*sin(x) lc rgb "gold" title t2 15 replot 1/(1+x**2) lc rgb "red" title t3 11
12 Transparent filling 12
13 Saving figures Selected formats: Nazwa Description canvas HTML Canvas object cgm Computer Graphics Metafile corel EPS format for CorelDRAW dumb ascii art for anything that prints text dxf dxf-file for AutoCad (default size 120x80) fig FIG graphics language for XFIG graphics editor gif GIF images using libgd and TrueType fonts jpeg JPEG images using libgd and TrueType fonts latex LaTeX picture environment pdfcairo pdf terminal based on cairo png PNG images using libgd and TrueType fonts pngcairo png terminal based on cairo postscript PostScript graphics, including EPSF embedded files (*.eps) svg W3C Scalable Vector Graphics driver wxt wxwidgets cross-platform windowed terminal x11 X11 Window System 13
14 Saving in vector formats fig gnuplot> set output rys.fig gnuplot> set term fig Terminal type set to fig Options are color small pointsmax 1000 landscape inches \ dashed textnormal font Times Roman fontsize 10 linewidth 1\ depth 10 version 3.2 PostScript gnuplot> set output rys.ps gnuplot> set term postscript color Terminal type set to postscript Options are landscape noenhanced defaultplex leveldefault color \ colortext dashed dashlength 1.0 linewidth 1.0 butt noclip \ palfuncparam 2000,0.003 Helvetica 14 14
15 Saving in raster formats GIF gnuplot> set output rys.gif gnuplot> set term gif Terminal type set to gif Options are truecolor nocrop \ font /usr/share/fonts/truetype/ttf liberation/liberationsans Regular.ttf 12\ size 640,480 PNG gnuplot> set output rys.png gnuplot> set term png Terminal type set to png Options are truecolor nocrop font /usr/share/fonts/truetype/ttf liberation/liberationsans Regular.ttf 12\ size 640,480 15
16 Data visualisation Data file: Script: 1 set xzeroaxis 2 plot data w l 16
17 Operation on data stream and data filtering Gnuplot provides tools for filtering input data stream and selecting data to be plotted. selecting data records option every selecting data columns option using selecting data sets option index data interpolation and approximation option smooth filtering through external programs 17
18 Overlays 1 set object 1 rect from graph 0, 0 to graph 0.6, 0.7 front fc rgb "green" 2 set key left 3 set multiplot 4 plot sin(x) 5 unset object 1 6 set key outside center top 7 set size 0.5,0.6 8 set origin 0.1, plot cos(x) lc rgb "black" 18
19 Subwindows 1 set multiplot layout 2, 2 2 set key outside center top 3 plot sin(x) 4 plot cos(x) 5 plot x*x 6 plot 1/(1+x**2) 19
20 Histograms Script and data taken form gnuplot distribution. 20
21 Histograms 1 set boxwidth 0.9 absolute 2 set style fill solid 1.00 border 1 3 set style histogram clustered gap 1 title offset character 0, 0, 0 4 set datafile missing 5 set style data histograms 6 set xtics border in scale 1,0.5 nomirror rotate by 45 offset character 0, 0, 0 7 set xtics ( , , , , , , , ) 8 set title US immigration from Northern Europe\n Plot selected data columns as histogram of clustered boxes 9 set yrange [ : ] noreverse nowriteback 10 plot immigration.dat using 6:xtic(1) ti col, u 12 ti col, u 13 ti col, u 14 ti col 21
22 Pie plots 1 circ="circle at 0,0 size 1" 2 wedge(color, s, e, title)= sprintf("set obj arc [%d:%d] fc rgb c%d;\ 3 replot -2 linecolor rgb c%d title \"%s\"",color,s,e,color,color,title) 4 set style fill solid 1.0 border -1 5 set key outside horizontal center top 6 set size square 7 set notics 8 set xrange [-1.2:1.2] 9 set yrange [-1.2:1.2] 10 c1="red" 11 c2="orange" 12 c3="yellow" 13 c4="forest-green" 14 c5="dark-turquoise" 15 c6="dark-magenta" 16 set style function filledcurves 17 set macro 18 plot -2 notitle 19 eval wedge(1,0,40, "Carbon 11.1%") 20 eval wedge(2,40,70, "Gold 8.3%") 21 eval wedge(3,70,90, "Mercury 5.5%") 22 eval wedge(4,90,120, "Iron 8.3%") 23 eval wedge(5,120,220, "Silver 27.7%") 24 eval wedge(6,220,360, "Tungsten 38.8%") 22
23 Plotting parametric curves 1 set xrange[-10:10] 2 set yrange[-10:10] 3 set size square 4 set parametric 5 set termoption enhanced 6 R=4 7 set key Left left 8 plot R*cos(t),R*sin(t) title "Circle R=4" 9 replot 0.5*t**2, t title "Parabole:\n x=t^2/2\n\r y=t" 23
24 Interactive elements New terminal type based on wx library allows some user interaction like rotating, panning and zooming with mouse. It also provides the way to define keyboard short-cuts for user commands. 24
25 Visualisation of function of two variables 1 f(x,y) = x*x-y*y 2 set isosamples 25, 25 3 unset key 4 set style fill solid 0.50 border 5 set hidden3d front offset 1 trianglepattern 3 undefined 1 altdiagonal bentover 6 set xyplane at 0 7 set palette rgbformulae 31, -11, 32 8 set colorbox vertical origin screen 0.9, 0.2, 0 size screen 0.05, 0.6, 0 front bdefault 9 splot f(x,y) with pm3d 10 replot f(x,y) with lines lt 1 lc rgb "#000000" 25
26 Command line history history show the complete history history 5 show last 5 entries in the history history quiet 5 show last 5 entries without entry numbers history hist.gp write the complete history to file hist.gp history hist.gp append append the complete history to file hist.gp history 10 head -5 >>diary.gp write 5 history commands using pipe history 10 hist.gp write last 10 commands to file hist.gp history?load show all history entries starting with load history? set c like above, several words enclosed in quotes hi!reread execute last entry starting with reread hist! set xr like above, several words enclosed in quotes hi!hi guess yourself :-)) 26
27 Gnuplot scripts Gnuplot scripts can be run in terminal during interactive gnuplot session using load command. 27
28 Other gnuplot features More gnuplot features can be seen at gnuplot demo pages: 28
29 Part II VTK Overview 29
30 VTK Visualization Toolkit The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization. Book: The Visualization Toolkit, An Object-Oriented to 3D Graphics, 2nd edition, Prentice-Hall Software: 30
31 VTK Applications 31
32 VTK Applications cont. 32
33 VTK Applications cont. 33
34 VTK Applications cont. 34
35 VTK on jinx Which packages: dpkg l grep i vtk Visualization Toolkit - A high level 3D visualization library VTK header files for building C++ code Python bindings for VTK Tcl bindings for VTK VTK class reference documentation C++, Tcl and Python example programs/scripts 35
36 Technical Overview C++ implementation Open source Scripting interface: Tcl/Tk, Python, Java Portable Supports parallelization Commercial support Not super-fast graphics engine Very large not a toy Requires decent system to use it effectively 36
37 VTK: 3D Graphics Surface Rendering: OpenGL, gl, starbase, xgl Volume Rendering Flexible ray casting implementation Support for VoumePRO volume rendering hardware Supports mixing opaque surface geometry and volume rendering Rendering primitives: points, lines, polygons, tringle strips, volumes 37
38 VTK: Datasets Types Structured Points Rectlinear Grid Polygonal Data Structured Grid Unstructured Points Unstructured Grid 38
39 VTK: Cell Types Vertex Polyline Pixel Tetrahedron Polyvertex Triangle strip Quad Hexahedron Line Triangle Polygon Voxel 39
40 VTK: Atribute Types Scalars (single valued + grayscale, grayscale-alpha, rgb, rgb-alpha) Vectors 3x3 Tensors Texture Coordinates (1-3D) Field Data 40
41 VTK: Scalar Algorithms 41
42 VTK: Scalar Algorithms cont. 42
43 VTK: Scalar Algorithms cont. 43
44 VTK: Scalar Algorithms cont. 44
45 VTK: Vector Algorithms 45
46 VTK: Vector Algorithms cont. 46
47 VTK: Tensor Algorithms 47
48 VTK: Multidimensional solution 48
49 VTK: Modeling Algorithms 49
50 VTK: Modeling Algorithms cont. 50
51 VTK: Modeling Algorithms cont. 51
52 VTK:Imaging 52
53 VTK: Visualization Pipeline Demand-driven data-flow with automatic network updates Network looping and feedback supported Supports multiple input/multiple output filters vtkspheresource vtkpolydatamapper vtkactor vtkrenerer vtkrendererwindow vtkrenderer WindowInteractor 53
54 VTK: Programming - Tcl/Tk 1 vtkspheresource sphere 2 sphere SetRadius sphere SetThetaResolution 18 4 sphere SetPhiResolution 18 5 vtkpolydatamapper map 6 map SetInput [sphere GetOutput] 7 vtkactor asphere 8 asphere SetMapper map 9 [asphere GetProperty] SetColor vtkrenderwindow renwin 11 vtkrenderer ren1 12 renwin AddRenderer ren1 13 vtkrenderwindowinteractor iren 14 iren SetRenderWindow renwin 15 ren1 AddActor asphere 16 ren1 SetBackground renwin Render 18 wm withdraw. 54
55 Mayavi free scientific data visualizer implemented in Python + Tkinter + VTK A pipeline browser can browse and edit objects in the VTK pipeline. Visualize computational grids. Visualize scalar, vector and tensor data. A modular design so you can add your own modules and filters. Output to: PostScript, PPM/BMP/TIFF/JPEG/PNG, Open Inventor, VRML or RenderMan. 55
56 Mayavi - examples 56
57 57
58 58
59 Credits Most of the figures in this part and Tcl/Tk example come from VTK distribution. 59
60 Part III VTK Programming 60
61 VTK: Visualization Pipe vtkconesource vtkpolydatamapper vtkactor vtkrenerer vtkrendererwindow vtkrenderer WindowInteractor 61
62 VTK: Programming - C++ 1 #include vtkconesource.h 2 #include vtkpolydatamapper.h 3 #include vtkrenderwindow.h 4 #include vtkrenderwindowinteractor.h 5 #include vtkactor.h 6 #include vtkrenderer.h 7 8 int main( int argc, char argv[] ) { 9 10 vtkconesource cone = 11 vtkconesource::new(); 12 cone >SetHeight( 3.0 ); 13 cone >SetRadius( 1.0 ); 14 cone >SetResolution( 5 ); 15 vtkpolydatamapper conemapper = 16 vtkpolydatamapper::new(); 17 conemapper >SetInput( 18 cone >GetOutput() ); vtkactor coneactor = 21 vtkactor::new(); 22 coneactor >SetMapper( conemapper ); 23 vtkrenderer ren1= 24 vtkrenderer::new(); 25 ren1 >AddActor( coneactor ); 26 ren1 >SetBackground(0.1, 0.2, 0.4); 27 vtkrenderwindow renwin = 28 vtkrenderwindow::new(); 29 renwin >AddRenderer( ren1 ); 30 renwin >SetSize( 400, 400 ); vtkrenderwindowinteractor iren = 33 vtkrenderwindowinteractor::new(); 34 iren >SetRenderWindow(renWin); iren >Initialize(); 37 iren >Start(); return 0; 40 } 62
63 VTK: Programming - Makefile 1 CXX = g++ g Wall 2 3 # for queen VTK #INCLUDES = I. I/home/pracow/putanowr/include/vtk 5 #LDFLAGS = L/home/pracow/putanowr/lib/vtk \ 6 L/usr/X11R6/lib 7 #LDADD = lvtkcommon lvtkio lvtkgraphics \ 8 lvtkrendering lgl lx11 lm 9 10 #for jinx VTK INCLUDES = I. I/usr/include/vtk 12 LDFLAGS = L/usr/lib/vtk L/usr/X11R6/lib 13 LDADD = lvtkcommon lvtkgraphics lgl \ 14 lxt lx11 lm #for foo VTK #INCLUDES = I. I/opt/include/vtk 18 #LDFLAGS = L/opt/lib/vtk L/usr/X11R6/lib 19 #LDADD = lvtkcommon lvtkio lvtkgraphics \ 20 lvtkrendering lgl lx11 lm %.o : %.cxx 23 $(CXX) c $(INCLUDES) $< o $@ Cone1 : Cone1.o 26 $(CXX) $ˆ $(LDFLAGS) $(LDADD) o $@ PHONY : clean distclean 29 clean : 30 /bin/rm rf.o 31 distclean : 32 rm f Cone1 63
64 VTK: Programming - Tcl/Tk 1 package require vtk 2 package require vtkinteraction 3 4 vtkconesource cone 5 cone SetHeight cone SetRadius cone SetResolution vtkpolydatamapper conemapper 10 conemapper SetInput [cone GetOutput] vtkactor coneactor 13 coneactor SetMapper conemapper vtkrenderer ren1 16 ren1 AddActor coneactor 17 ren1 SetBackground vtkrenderwindow renwin 19 renwin AddRenderer ren1 20 renwin SetSize vtkrenderwindowinteractor iren 23 iren SetRenderWindow renwin 24 iren Initialize wm withdraw. 64
65 Part IV OpenDX Overview 65
66 OpenDX Open source software project based on IBM s Visualization Data Explored (DX) Powerful, full-featured visualization system Visual programming, advanced GUI Modular design, object-oriented, self-describing data model C implementation Scripting Python and Tcl/Tk wrappers 66
67 Visual Programs Gradient 67
68 Visual Programs Gradient 68
69 Visual Programs Gradient 69
70 Visual Programs Streamlines 70
71 Visual Programs Streamlines 71
72 Visual Programs isosurfaces 72
73 Visual Programs Isosurfaces 73
74 Credits All figures in this presentation come from OpenDx distribution. 74
75 References 1. Gnuplot home page 2. Gnuplot demo page 3. GNU Octave 4. Octaviz 5. VTK - The Visualization Toolkit 6. OpenDX 7. Own materials 75
76 Thank you for your attention 76
77 License This work is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported License. To view a copy of this license, either visit or, send a letter to Creative Commons, 171 2nd Street, Suite 300, San Francisco, California, 94105, USA. You are free: to share to copy, distribute and transmit the work to remix to adapt the work Under the following conditions: attribution You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). share alike If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one. 77
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