Questions tagged [visualization]

Questions relating to graphing and displaying numerical data

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2
votes
2answers
1k views

Best VTK visualizing software?

I have a large VTK file with rectangular data, it seems Paraview cannot handle the size of the file, so it crashes and Visit navigation is extremely slow? Can anyone point me to good open source ...
5
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2answers
140 views

Which visualisation software for a layered graph?

I have produced a CSV file in the following format: ...
3
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1answer
91 views

Best file format for bond connectivity?

I need to generate an output file from my molecular data that can be loaded into VMD to visualize the bond connectivity. I'm not sure what the best choice is. I know the PDB format has a HETATOM ...
4
votes
2answers
632 views

High quality molecular renderings

I would like to use a high-quality renderer (physically based path-tracing or MLT) to generate some images of molecular systems I have. Right now I'm just using some of the simple renderers in VMD, ...
7
votes
2answers
4k views

Is there a fast way to compute histograms for high-dimensional large datasets?

Currently the way I compute histograms for data is by generating grid in $N$ dimensions (where $N$ is the dimension of the data) and searching through the $M$ data points in each dimension to see in ...
5
votes
1answer
7k views

How to generate sloped streamslice plot of magnetic field in Matlab

I am currently working on my bachelor thesis, where I am calculating trajectory of electrons and ions in Hall Effect Ion Thruster. However, to be sure what I am calculating, I need to know how does ...
4
votes
2answers
13k views

plotting a 2D animated data surface on MatPlotLib

I'm trying to get an animated 2D data surface on MatPlotLib. After a bit of search on the internet, i've found an example that almost works: ...
1
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1answer
3k views

matlab set center of output figure to [0 0 0]

I have a few set of data of three dimensional matrices, n x 3 with x, y and z coordinates. I viewed the matrices in the figure window. ...
3
votes
1answer
721 views

How to do local FFT on huge 3D vector data cell mesh and visualize it spatially?

Simulation type: I'm running a simulation with the OOMMF micromagnetics package http://math.nist.gov/oommf/ where are magnet is represented by a mesh of 3 million cells, it gets excited by a ...
0
votes
1answer
94 views

mapping data with a spike to a heat map

I have the following dataset that I need to display on the heat map: [30, 15, 66, 7, 9999, 78, 42, 132] So if I map the values to the color scale using a linear function I only see the spike while ...
0
votes
3answers
245 views

CAD like visualisation of 3D vector data?

It looks like MATLAB and Mathematica is often used for post-processing and data visualization of 3D vector data. Now consider you are simulating 3D objects and get out gradient fields etc., is there ...
3
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0answers
2k views

Create 2D plot from two data sets in ParaView

I'm currently running a CFD simulation for an internal flow and need to compare my computed results to experimental data. The experimental data is saved as a comma separated file with columns for x,y,...
6
votes
1answer
742 views

how to visualize lattice with periodic, helical, etc. boundary conditions?

I am trying to write a special hexagonal lattice generator, with several kinds of boundary conditions, such as helical BC, periodic BC, and I find it hard to verify whether it works correctly. I tried ...
2
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4answers
3k views

Magnetic field simulation and visualization on Mac OS X?

Does somebody know about any tool for simulation and visualization of magnetic fields either of permanent magnets or solenoids, that can be used on Mac OS X? Maybe there is some software for Linux, ...
4
votes
3answers
156 views

Offline (visualisation) rendering in scientific computing

I need to simulate the movement of a large number of agents. The processes that govern the agents' movement are complex and so the entire process requires parallelisation. The output from this ...
3
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1answer
236 views

Looking for parMetis visualizer?

Is there any visualizer for parMetis (mpmetis), which can visualize FEM mesh grids after partitioning?
26
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6answers
8k views

Visualizing very large link graphs

I am looking for a tool to visualize very large directional link graphs. I currently have ~2million nodes with ~10million edges. I have tried a few different things, but most take hours to even do ...
10
votes
3answers
353 views

Ways of visualizing event data in search of performance issues

I'm trying to optimize an MPI application with a highly asynchronous communication pattern. Each rank has a list of things to compute, and sends messages as necessary if the inputs or outputs reside ...
15
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1answer
2k views

Visualizing discontinuous Galerkin/finite element data

I would like to visualize simulation results, obtained using the discontinuous Galerkin (DG) approach, within ParaView. Similarly to finite volume methods, the problem domain is divided into cube-...
4
votes
0answers
107 views

Existing software/scripts for spiral graphs?

I am looking for existing software or scripts to generate spiral graphs from cyclical (time) data, as presented by Webber and Muller. The graphs shown in the paper look like a great means of ...
24
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4answers
3k views

Algorithms for (adaptive?) function plotting

I am looking for algorithms to draw standard 2d-graphs for functions that may or may not have singularities. The purpose is to write a "Mini-CAS", so I have no a priori knowledge of the types of ...
12
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4answers
1k views

Making a Molecular editor/visualizer: Object oriented programming, data structures, and molecules

I am new to programming and I am trying to solve my first big problem and write my first big program. I have looked for open source examples of code to learn from, but so far have only found code in ...
7
votes
1answer
406 views

Generalized least squares gradient of a vector field

For computing the gradient of a scalar field, one can use the weighted least squares method as described in the paper Revisiting the Least-squares Procedure for Gradient Reconstruction on Unstructured ...
6
votes
2answers
453 views

Tools for computing an electric field based on location of charges?

I have the positions of a large number of charges (the strengths are known, but are also variables). Are there any tools that will allow me to visualize the electric field induced by these charges (or ...
1
vote
1answer
238 views

Error message when trying to get PETSc to draw to an X terminal by passing -mat_view_draw

I've made a matrix, and now I want to draw it on the screen to make a basic check of correctness. The documentation for MatAssemblyEnd() states that I can pass an ...
5
votes
1answer
1k views

Drawing isocontour data of 3d discrete volume with mayavi2

I'm trying to visualize the propagation of heat in a discrete sphere surface. The sphere is hollow, only the voxels of the boundary have value. Visualization in matlab using isosurface shows correct ...
4
votes
2answers
4k views

Can gnuplot's PNG terminal use superscripts and subscipts?

I know that gnuplot's epslatex terminal can display superscipts and subscripts in titles and label axes. Is this also possible when using gnuplot's ...
42
votes
14answers
19k views

Which software and workflow is recommend for publication of scientific data and graphs?

Which software provides a good workflow from simple plotting of a few datapoints up to the creation of publication level graphics with detailed styles, mathematical typesetting and "professional ...
5
votes
1answer
10k views

How do I plot a transparent cylinder in matlab? [closed]

I know that I can use the following commands to create an opaque cylinder in matlab: N=100; [X,Y,Z]=cylinder(R,N); surf(X,Y,Z); I want to plot an arrow inside ...
12
votes
2answers
897 views

How can one mathematically describe the “cartoon” type of representation of proteins?

Proteins are typically represented in a cartoon form, with β sheets as arrows and α helices as coils: I'm wondering, is there somewhere a reference that describes the construction of this ...
6
votes
4answers
5k views

Tools for visualizing large 3D volumes

I have a sequence of 2D images (png files) encoding the partitioning (segmentation) of a large biological 3D volume. In these files, each pixel has a color, representing the 3D object the pixel ...
9
votes
1answer
326 views

Given values on a mesh, what algorithm can I use to construct efficiently level set contours?

I have a mesh, faces $F$, edges $E$, and vertices $V$, and I have a list of predefined level set contours. What algorithm can I use to construct contours in the most efficient manner? A plot of the ...
4
votes
2answers
328 views

Tools/solutions for visualization of molecular simulation trajectories?

I have so far been using VMD to create visualizations of molecular trajectories. However, I find myself not entirely satisfied with the quality of the resulting animations—when you want to do snapshot-...
5
votes
6answers
18k views

How can I plot piece-wise defined function in some easily-accessed open-source tool?

I want to plot $$f_{n}(x) = \begin{cases} x-n & \text{for } n \leq x \leq n+1 \\ 2-x+n & \text{for } n+1\leq x \leq n+2 \\ 0 &...
2
votes
1answer
173 views

How can I set different axes for different plots in gnuplot?

I want to plot a few sets of data points on the same x-axis that have different units. How can I set different axes for each incompatible quantity?
5
votes
5answers
2k views

How do I create an animation from a 2D model or dataset?

I found the following thread in the physics stackexchange where I saw the video called output attached to the main post. The video can be found here. How would I go about creating such an animation?
35
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6answers
3k views

What attributes make a figure “professional-quality”?

I've heard people say that plots produced by ORIGIN tend to look polished and "professional," whereas plots produced by Mathematica do not. However, most plot-creation programs are quite configurable ...

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