I'm looking to plot the points in a 3D space. I find that languages like python with matplotlib, take a lot of time. What would be the simple way to do it in opencl ?
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I am working with networks which vertices are nodes of brain areas with specific coordinates.
I need to visualize these networks in a 3D enviroments in order to improve the understanding of my results.
Up to now I have tried to plot them using rglplot of igraph library in R, but the result is not so good in truth.
Currently I am plotting them using projection on each pair of axis (XY, XZ, YZ).
Futhermore I also have tried several tools like gephi, but it seems that 3D is not really supported.
There is some tool or software for visualizing a network in a 3D space?
It turns out that in fact Gephi supports 3d display of graphs, only to see the effect you have to pan the graph in the Overview Pane by keeping you mouse's scroll wheel pressed! Also the rotation options are limited to rotating on the x-axis
See the example below for the Les Miserables graph laid out with the Force Atlas 3d algorithm
You can also set the coordinates from within the Data Laboratory with the aid of the Data laboratory helper plugin. See a screenshot below
When drawing curved shapes in R, they are typically made up of a collection of short straight line segments (with circular line endings). The result looks good to the human eye but is a bit of a roundabout way of doing it as you need to interpolate the curve to get the coordinates of the segments. It also produces unnecessarily large files, although this is not a big problem unless the plot contains an extreme amount of curves.
Is there a way to create curved vector shapes the proper way using paths made up of anchor and pivot points as in the figure below?
Short answer: "No".
Long answer: R doesn't know if your output device supports describing curves from formulae - for example PDF and PostScript can (I think) have arcs and curves, but R doesn't know if its drawing to one of those or to a bitmap device.
Hence when you want to draw an arc on an R plot, it can't do:
0 0 moveto
25 25 pi arcto
(or whatever the PostScript is) to describe an arc that will be infinitely smoothly zoomable. It has to render the arc into segments.
If you run the example in help(bezierGrob) to a PDF device and zoom in, you can see the segments (zoomed in to 500%).
Mapping a point cloud onto a 3D "fabric" then flattening.
So I have a scientific dataset consisting of a point cloud in 3D, this point cloud comprises points on a surface that is curved. In order to perform quantitative analysis I however need to map these point clouds onto a surface I can then flatten. I thought about using mapping tools sort of like in the case of the 3d world being flattened onto a map, but not sure how to even begin as I have no experience in cartography and maybe I'm trying to solve an easy problem with the wrong tools.
Just to briefly describe the dataset: imagine entirely transparent curtains on the window with small dots on them, if I could use that dot pattern to fit the material the dots are on I could then "straighten" it and do meaningful analysis on the spread of the dots. I'm guessing the procedure would be to first manually fit the "sheet" onto the point cloud data by using contours or something along those lines then flattening the sheet thus putting the points into a 2d array. Ultimately I'll probably also reduce that into a 1D but I assume I need the intermediate 2D step as the length of the 2nd dimension is variable (i.e. one end of the sheet is shorter than the other but still corresponds to the same position in terms of contours) I'm using Matlab and Amira though I'm always happy to learn new tools!
Any advice or hints how to approach are much appreciated!
You can use a space filling curve to reduce the 3d complexity to a 1d complexity. I use a hilbert curve to index lat-lng pairs on a 2d map. You can do the same with a 3d space but it's easier to start with a simple curve for example a z morton order curve. Space filling curves are often used in mapping applications. A space filling curve also adds some proximity information and a new sort order to the 3d points.
You can try to build a surface that approximates your dataset, then unfold the surface with the points you want. Solid3dtech.com has the tool to unfold the surfaces with the curves or points.
I need to convert arbitrary triangulated 3D mesh to cloud of particles that are uniformly spaced.
First thought was to try find a way to fill one 3D triangle. And then fill each triangle of mesh, removing duplicated particles on edges, but that's just hard and too much work. I was hoping for some more-math way.
Can anyone point me to an algorithm which can help me do my task correctly... well, at least approximatively?
Thanks
There are two main options:
Voxelization of mesh. Easy to implement the conversion of mesh to voxels, but it's inaccurate since uniform spacing cannot be achieved: distance between cubes can be x, x*sqrt(2) or x*sqrt(3) depending if neighbor cubes are in same plane and adjacent.
Poisson disk sampling on surface. Hard to implement and lack of research material and code, but mathematically very correct. Some links:
http://research.microsoft.com/apps/pubs/default.aspx?id=135760
http://web.mysites.ntu.edu.sg/cwfu/public/Shared%20Documents/dualtiling/index.html
You could convert the TIN to raster using a GIS package or software such as R, then retrieve one point at the center of each pixel representing the value. (Example in ArcGIS)
EDIT: If the irregular 3D mesh has multiple heights per {x, y} a similar approach would be to sample the mesh using a voxel "grid" and keep one value per voxel. GRASS GIS has the functionality to take the vertices of the TIN (3d mesh) and convert them to voxels, then back to a regular 3d cloud.
This is something related with Mathematics as well. But this is useful in computing as well.
Lets say you have 10 coordinates. (x1,y1)(x2,y2)..... in 2D Space. (i.e on a X-Y Plane). Can we find a single smooth curve going across the each coordinate.
While expanding the question, If the space is 3D, then can we find an equation of a smooth surface that going across a given set of spacial coordinates?
Are there any Libraries (Any language) \ tools to perform such calculations?
What you should be looking for is some library implementing NURBS (or Non Uniform Rational B-Splines). This will solve your problem in both 2d and 3d, since 2d is just a special case of the 3d.
Roughly speaking, you are not interested in the actual equation, you are only interested in getting the points approximated with smooth curves or surfaces. This is done by finding "control points" in 2d or 3d space, which are multiplied with B-spline base functions. A NURBS library will do this for you.
Cheers !
Edit:
Have a look at this one
you can always fit an order-10 polynomial through the points. that's not necessarily what you want to do, though - fitting a smooth curve via a series of splines will give you a better-looking result. the curve-fitting article on wikipedia gives you a good overview of the various options.
In the 2D case you are asking for curve fitting. This actually exists in excel, where you plot your points (I usually use XY scatter if you have x and y listed) and then right-click on the curve. Select Add Trendline. There you can choose which kind of function you want to fit to and you can ask excel to display it in the image (Tab named Options, check the box "Display equation on chart"). Nice and quick.
Otherwise you can use matlab and use the lsqr (least square method). If you want to find the polynomial closest that best describes your data you could use the polyfit function. It uses the least square method, but returns coefficients. Matlab has a whole set of other algorithms for solving/finding "best" approximations to systems of linear equations. I mention lsqr because it is one of the simplest to implement yourself if you don't have matlab. On the other hand it is for solving sets of linear equations - I don't know anything about your data.
Have a look at splines
in wiki
an interactive introduction
Searching for 'spline interpolation library' might give some useful hints for implementations.