Questions relating to graphing and displaying the results of scientific computations.

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0
votes
1answer
31 views

VTK File: How do I save data on a cell face?

I am writing a program that creates a vtk file with a Rectilinear Grid. I am able to save data to each one of the cells using CELL_DATA, but now, I need to save data to each one of the cell faces ...
2
votes
1answer
73 views

Unwrap cylinder to plane in Paraview

I want to extract the data from the boundary surface of a cylinder (in a .vtu file) and plot it onto a plane, where the coordinates are theta (rotation angle) and ...
4
votes
2answers
79 views

Line Integral Convolution (LIC) Requirements

I'm trying to plot some vector fields using LIC technique. More specifically, I'm using the Python solution for this kind of plot. Before applying that approach, I was plotting my vectors as quiver. ...
0
votes
1answer
35 views

Visualizing certain sets

I'm not sure if this question is appropriate for this site, so I appologize in advance if it's not. For the purpose of a certain project I am working on, I would like to have the following sets ...
5
votes
4answers
160 views

Should I use a database to handle large amounts of results?

Background: I am currently running a large amount parameter variation experiments. They are being run in Python 2.6+, using numpy. These experiments are going to take about 2 weeks to run. Roughly I ...
1
vote
1answer
119 views

WRL and VRML to Matplotlib/Numpy

I would like to import (or parse ??) a WRL/VRML file format in python in order to work the data with Matplotlib. Is there any way of converting this file format into plottable numpy arrays ? I ...
2
votes
2answers
196 views

visualization of 3D probability flow

I have a master equation for $P(N_A^+,N_B^+,N_C^+,t)$, with $N_A^+,N_B^+,N_C^+$ all discrete. The numerical integration is done by this Matlab program using Euler's method. Despite the crude Euler's ...
0
votes
1answer
61 views

Plotting 3d dimensional histogarm in a spatial grid

Is there any tool to plot 3d dimensional histogram in a spatial grid? Preferably are there any filters or operators in Paraview or Visit for this?
6
votes
3answers
932 views

Visualizing finite element solutions in MATLAB

On my triangular mesh, I have the $(x,y,z)$ coordinates of each vertex of each triangle. For higher order elements, I refine each element a few times so I have more points to work with. If I just need ...
1
vote
1answer
68 views

How to interpret Turing Machine illustrations on p79 of Stephen Wolfram's “A New Kind of Science” book?

I am reading Stephen Wolfram's "A New Kind of Science". At present, I cannot understand how the cellular automata illustrations on p79 are created. In the patterns, the active cell, representing the ...
5
votes
4answers
907 views

How do I calculate the numerical difference between two fields stored in two different VTK files with the same structure?

Suppose I have two VTK files, both in structured grid format. The structured grids are the same (they have the same list of points, in the same order), and there is a field, call it "Phi", in each VTK ...
1
vote
2answers
86 views

Converting VTK point dataset of scalar values to a smooth surface

Does Paraview or Visit have any filters to draw a smooth surface for a set of points?
3
votes
1answer
143 views

Is there an Implementation of the Hilbert curve from $[0,1]$ to $[0,1]^n$, where $n$ is large? ($n=10,000$, say)

I would like to map each point in $[0,1]$ to $[0,1]^n$ with a Hilbert curve, where $n=10,000$. That is $$ f: [0,1] \to [0,1]^n, $$ is the $n$-dimensional Hilbert curve. I found the library of ...
3
votes
4answers
160 views

Finding a molecular dynamics visualization library for C

I asked this question over at stackoverflow, and got blasted for it. I am currently working with legacy MD code written in C that my university uses, and haven't moved to a more modern library like ...
5
votes
3answers
917 views

Python scripting in Paraview

I've been using the basic visualization features of Paraview. Now, I want to go further by writing python macros to handle some specific tasks. My question for the advanced users: Are there any ...
2
votes
1answer
62 views

Equal Area Sampling on Curved Surface:

I have a quantity $\beta(\mathbf{x}) \in \mathbb{R}$ that I wish to compute on a curved, smooth surface defined by $\{\mathbf{x}: \Gamma(\mathbf{x})=0\} \subset \mathbb{R}^{3}$. (This surface is ...
12
votes
2answers
1k views

Binary vs. ASCII file size

I need to write some data from a computation, that will be read later by Paraview (.vtu or vtk file). When it comes to file size , should I go for the ASCII format or the Binary format ?
3
votes
2answers
154 views

VTK file format to image file

Is there a way to convert vtk file without visualizing into a image file such as png in the bash terminal itself? I have found that for the vtk files that I visualize to take longer time than its ...
0
votes
1answer
92 views

Setting background image with respect to a point in Paraview

How to set image with respect to a point in Paraview? I have a vtk file within a rectangular domain starting with the lower left point -1842,10000, I want to set a background image whose lower left ...
3
votes
2answers
115 views

VTK: Subset of Points with same color

I have a set of points, among which a subset needs to have the same color in vtk file format. For ex. all agents with table value 0.0, 0.0, 0.0, 0.0 will have same color. Here is my vtk ...
2
votes
2answers
439 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
votes
2answers
114 views

Which visualisation software for a layered graph?

I have produced a CSV file in the following format: position number, list of positions it links to, second list of positions it links to,....., sixth list of positions it links to. All the items are ...
6
votes
2answers
615 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
2k 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 ...
3
votes
1answer
2k 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
vote
1answer
468 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
277 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
0answers
805 views

Tecplot: Overlapping of 2 contour plot data from a single file, in a 2D Cartesian grid

I have a rectangular grid ASCII .dat file that looks like this ...
0
votes
1answer
44 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
187 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
votes
1answer
102 views

Looking for parMetis visualizer?

Is there any visualizer for parMetis (mpmetis), which can visualize FEM mesh grids after partitioning?
20
votes
4answers
2k 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 ...
4
votes
0answers
89 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 ...
7
votes
1answer
244 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
251 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
116 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 ...
3
votes
2answers
2k 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 ...
26
votes
14answers
5k 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
4answers
2k 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
129 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 ...
4
votes
5answers
2k 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
128 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?
4
votes
5answers
633 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?
30
votes
6answers
1k 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 ...