In case somebody doesn't know: A cartogram is a type of map where some country/region-dependent numeric property scales the respective regions so that that property's density is (close to) constant. An example is
from worldmapper.org. In this example, countries are scaled according to their population, resulting in near-constant population density.
Needless to say, this is really cool. Does anyone know of a Matplotlib-based library for drawing such maps? The method used at worldmapper.org is described in (1), so it would surprise me if no one has implemented this yet...
I'm also interested in hearing about other cartogram libraries, even if they're not made for Matplotlib.
(1) Michael T. Gastner and M. E. J. Newman,
Diffusion-based method for producing density-equalizing maps,
Proc. Nat. Acad. Sci. USA, 101, 7499-7504 (2004). Available at arXiv.
There's this, though it's based and a different algorithm (and though it's on the ESRI site, it doesn't require ArcGIS). Of course, once you have the cartogram you can plot it in matplotlib.
Here is a Javascript plugin to make cartograms using D3. It is a good, simple solution if you are not too concerned about the regions being sized accurately. If accuracy is important, there are other options available that give you more freedom to play with the algorithm's parameters to get to a more accurate result.
Here are two great standalone programs I know of:
Scapetoad
Carto3F
Scapetoad is very easy to use. Just give it a shapefile, tell it which attribute to use for the scaling, and set a few accuracy parameters. If there is any doubt, this post describes the process.
Carto3F is more complex and allows for greater accuracy, though it is a bit trickier to figure out - lots of parameter settings without much documentation explaining them.
There is also a QGIS cartogram plugin, written in Python. Though I have not been able to get it to work, so cannot comment on that one.
In short, no. But Newman has an excellent little implementation of his and Gastner's method on his website. Installing it is easy and it works from the command line. Here's an example of a workflow using this software that worked for me.
Compute a grid of density estimates over some region, e.g. in Python. Store it as a matrix of numbers.
Run the cart program with your density matrix as input from the command line or from as subprocess in Python.
The program returns a list of new coordinates for each grid point.
Pipe your shapefile points through the interp program and into a new shapefile to get the transformed map.
There are nice instructions on the main page.
The geoplot.cartogram function in
Geoplot: geospatial data visualization — geoplot 0.2.0
says it is a high-level Python geospatial plotting library, and an extension to cartopy and matplotlib.
Try this library if you are using geopandas, it is quick and doesnt require much customization. https://github.com/mthh/cartogram_geopandas
Related
I am currently working on a (school-)project involving a robot having to navigate a corn field.
We need to make the complete software in NI Labview.
Because of the tasks the robot has to be able to perform the robot has to know it's position.
As sensors we have a 6-DOF IMU, some unrealiable wheel encoders and a 2D laser scanner (SICK TIM351).
Until now I am unable to figure out any algorithms or tutorials, and thus really stuck on this problem.
I am wondering if anyone ever attempted in making SLAM work in labview, and if so are there any examples or explanations to do this?
Or is there perhaps a toolkit for LabVIEW that contains this function/algorithm?
Kind regards,
Jesse Bax
3rd year mechatronic student
As Slavo mentioned, there's the LabVIEW Robotics module that contains algorithms like A* for pathfinding. But there's not very much there that can help you solve the SLAM problem, that I am aware of. The SLAM problem consist of the following parts: Landmark extraction, data association, state estimation and updating of state.
For landmark extraction, you have to pick one or multiple features that you want the robot to recognize. This can for example be a corner or a line(wall in 3D). You can for example use clustering, split and merge or the RANSAC algorithm. I believe your laser scanner extract and store the points in a list sorted by angle, this makes the Split and Merge algorithm very feasible. Although RANSAC is the most accurate of them, but also has a higher complexity. I recommend starting with some optimal data points for testing the line extraction. You can for example put your laser scanner in a small room with straight walls and perform one scan and save it to an array or a file. Make sure the contour is a bit more complex than just four walls. And remove noise either before or after measurement.
I haven't read up on good methods for data association, but you could for example just consider a landmark new if it is a certain distance away from any existing landmarks or update an old landmark if not.
State estimation and updating of state can be achieved with the complementary filter or the Extended Kalman Filter (EKF). EKF is the de facto for nonlinear state estimation [1] and tend to work very well in practice. The theory behind EKF is quite though, but it should be a tad easier to implement. I would recommend using the MathScript module if you are going to program EKF. The point of these two filters are to estimate the position of the robot from the wheel encoders and landmarks extracted from the laser scanner.
As the SLAM problem is a big task, I would recommend program it in multiple smaller SubVI's. So that you can properly test your parts without too much added complexity.
There's also a lot of good papers on SLAM.
http://www.cs.berkeley.edu/~pabbeel/cs287-fa09/readings/Durrant-Whyte_Bailey_SLAM-tutorial-I.pdf
http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf
The book "Probabalistic Robotics".
https://wiki.csem.flinders.edu.au/pub/CSEMThesisProjects/ProjectSmit0949/Thesis.pdf
LabVIEW provides LabVIEW Robotics module. There are also plenty of templates for robotics module. Firstly you can check the Starter Kit 2.0 template Which will provide you simple working self driving robot project. You can base on such template and develop your own application from working model, not from scratch.
I want to explain the convergence in a bugs model with the command plot(). An example of the output is in the follow figure
I don't sure that I can read this output well, thanks to everyone :)
Unfortunately, it does not look as if you can confirm convergence from the figure that you are showing (EDIT: There is at least some information, see below). The left hand side of the figure is just a caterpillar plot, which effectively just shows the 95% intervals of the distribution for each parameter.
Assessing convergence is a much more nuanced process, as there are multiple ways to decide if your model has converged. What you will want to determine is that your model has appropriately explored the parameter space for each parameter (through trace plots, traceplot function in the coda library), between and within chain variance (the gelman-rubin diagnostic, gelman.diag in the coda library), and auto-correlation in your chains (autocorr.plot in coda). There are a variety of other measures that others have suggested to assess if your model has converged, and looking through the rest of the coda package will illustrate this.
I highly suggest that you go through the WINBUGS tutorial in their user manual (link to pdf), it has a section that addresses checking model convergence. You want to ensure that the traceplots are well-mixed (look to tutorial to see what that means), that your Gelman Rubin diagnostic is < 1.10 for each parameter (general rule), and that your chains are not too correlated (this will reduce your effective sample size in your chains).
Good luck, and read up a bit on the subject, it will greatly benefit you if you are interested in Bayesian inference!
Edit
As #jacobsocolar pointed out, and I completely missed, the plots that are available in this question do at least have some information that indicates the model did converge. I did not see the R-hat plot on the right side of the left plot. These values should be less than 1.1 for each parameter if the model did indeed converge. Eyeballing the above plot does hint that the model converged, but this would be far easier to see if there was a vertical line at the 1.1 mark on the plot, which there is not.
Your output figure is indeed enough to (begin to) assess convergence, contra M_Fidino's answer. Next to the caterpillar plot, there is a plot of 'r-hat' values. These are the Gelman-Rubin statistic--the ratio of between-chain variance to within-chain variance, and they are all < 1.10
This is an encouraging first sign that the model has converged, assuming that the initial values were chosen to be nicely overdispersed.
Otherwise, I agree with everything in M_Fidino's answer.
Background
I'm working on a project where a user gets scanned by a Kinect (v2). The result will be a generated 3D model which is suitable for use in games.
The scanning aspect is going quite well, and I've generated some good user models.
Example:
Note: This is just an early test model. It still needs to be cleaned up, and the stance needs to change to properly read skeletal data.
Problem
The problem I'm currently facing is that I'm unsure how to place skeletal data inside the generated 3D model. I can't seem to find a program that will let me insert the skeleton in the 3D model programmatically. I'd like to do this either via a program that I can control programmatically, or adjust the 3D model file in such a way that skeletal data gets included within the file.
What have I tried
I've been looking around for similar questions on Google and StackOverflow, but they usually refer to either motion capture or skeletal animation. I know Maya has the option to insert skeletons in 3D models, but as far as I could find that is always done by hand. Maybe there is a more technical term for the problem I'm trying to solve, but I don't know it.
I do have a train of thought on how to achieve the skeleton insertion. I imagine it to go like this:
Scan the user and generate a 3D model with Kinect;
1.2. Clean user model, getting rid of any deformations or unnecessary information. Close holes that are left in the clean up process.
Scan user skeletal data using the Kinect.
2.2. Extract the skeleton data.
2.3. Get joint locations and store as xyz-coordinates for 3D space. Store bone length and directions.
Read 3D skeleton data in a program that can create skeletons.
Save the new model with inserted skeleton.
Question
Can anyone recommend (I know, this is perhaps "opinion based") a program to read the skeletal data and insert it in to a 3D model? Is it possible to utilize Maya for this purpose?
Thanks in advance.
Note: I opted to post the question here and not on Graphics Design Stack Exchange (or other Stack Exchange sites) because I feel it's more coding related, and perhaps more useful for people who will search here in the future. Apologies if it's posted on the wrong site.
A tricky part of your question is what you mean by "inserting the skeleton". Typically bone data is very separate from your geometry, and stored in different places in your scene graph (with the bone data being hierarchical in nature).
There are file formats you can export to where you might establish some association between your geometry and skeleton, but that's very format-specific as to how you associate the two together (ex: FBX vs. Collada).
Probably the closest thing to "inserting" or, more appropriately, "attaching" a skeleton to a mesh is skinning. There you compute weight assignments, basically determining how much each bone influences a given vertex in your mesh.
This is a tough part to get right (both programmatically and artistically), and depending on your quality needs, is often a semi-automatic solution at best for the highest quality needs (commercial games, films, etc.) with artists laboring over tweaking the resulting weight assignments and/or skeleton.
There are algorithms that get pretty sophisticated in determining these weight assignments ranging from simple heuristics like just assigning weights based on nearest line distance (very crude, and will often fall apart near tricky areas like the pelvis or shoulder) or ones that actually consider the mesh as a solid volume (using voxels or tetrahedral representations) to try to assign weights. Example: http://blog.wolfire.com/2009/11/volumetric-heat-diffusion-skinning/
However, you might be able to get decent results using an algorithm like delta mush which allows you to get a bit sloppy with weight assignments but still get reasonably smooth deformations.
Now if you want to do this externally, pretty much any 3D animation software will do, including free ones like Blender. However, skinning and character animation in general is something that tends to take quite a bit of artistic skill and a lot of patience, so it's worth noting that it's not quite as easy as it might seem to make characters leap and dance and crouch and run and still look good even when you have a skeleton in advance. That weight association from skeleton to geometry is the toughest part. It's often the result of many hours of artists laboring over the deformations to get them to look right in a wide range of poses.
Is there a programmatic way to convert two images into an animation sequence (e.g., an animated GIF) like the following example?
This image sequence, taken from a http://memrise.com course, doesn't seem to have manually-edited frames, but seems automatically transformed using some kind shape morphing algorithm. Is there a common term used to describe such an animation or algorithm? Is there a feature in ImageMagick or Photoshop/Gimp that generates such animations, given a pair of images?
Ideally the technique could be scriptable so I could create animations for several pairs of start-end images.
Edit: I have just been told about Gimp's tool under Filters->Animation->Blend, which appears to do the same thing as jQuery morph: each frame i is start + (finish - start)/N*i. In other words, you're transitioning each pixel independently from the start value to the finish value, without any shape morphing. The example gives is more complicated, as it modifies the contours of both images to achieve its compelling effect.
Other examples:
http://static.memrise.com/uploads/mems/32000121024054535.gif
http://static.memrise.com/uploads/mems/225428000121109232837.gif
I have written a tool that doesn't require setting manual keypoints and is not restricted to a domain (like faces). Anyway, the images have to be similar (e.g. two faces or two cars from the same perspective).
https://github.com/kallaballa/Poppy
There is also a web-version created with emscripten.
I generated the above animation using following command line:
poppy flame.png glyph.png flame.png
Although this is an old question, since ImageMagick is mentioned, for anyone who comes here from google it may be worth looking at this imagemagick plugin called shapemorph.
GIMP can't do that directly, but over the years a series of (now poorly maintaind) plug-ins to do that where released by third parties. The keyword for searching for this is "morph" - you should find a bunch of stand alone programs to do that as well, from "gratis" to full fledged Free Software, such as xmorph
Given pairs of vector files (.wmf extension) it is possible to use linear interpolation of shapenodes in Visual Basic for Applications to create frames for GIF animations , though this would take along time to explain. For some examples see
http://www.giless.co.uk/animatorMorphGIFs.htm (it is like a slideshow)
I have made some improvements since then, as well!
We currently have a dynamically updated network graph with around 1,500 nodes and 2,000 edges. It's ever-growing. Our current layout engine uses Prefuse - the force directed layout in particular - and it takes about 10 minutes with a hefty server to get a nice, stable layout.
I've looked a little GraphViz's sfpd algorithm, but haven't tested it yet...
Are there faster alternatives I should look at?
I don't care about the visual appearance of the nodes and edges - we process that separately - just putting x, y on the nodes.
We do need to be able to tinker with the layout properties for specific parts of the graph, for instance, applying special tighter or looser springs for certain nodes.
Thanks in advance, and please comment if you need more specific information to answer!
EDIT: I'm particularly looking for speed comparisons between the layout engine options. Benchmarks, specific examples, or just personal experience would suffice!
I wrote a JavaScript-based graph drawing library VivaGraph.js.
It calculates layout and renders graph with 2K+ vertices, 8.5K edges in ~10-15 seconds. If you don't need rendering part it should be even faster.
Here is a video demonstrating it in action: WebGL Graph Rendering With VivaGraphJS.
Online demo is available here. WebGL is required to view the demo but is not needed to calculate graphs layouts. The library also works under node.js, thus could be used as a service.
Example of API usage (layout only):
var graph = Viva.Graph.graph(),
layout = Viva.Graph.Layout.forceDirected(graph);
graph.addLink(1, 2);
layout.run(50); // runs 50 iterations of graph layout
// print results:
graph.forEachNode(function(node) { console.log(node.position); })
Hope this helps :)
I would have a look at OGDF, specifically http://www.ogdf.net/doku.php/tech:howto:frcl
I have not used OGDF, but I do know that Fast Multipole Multilevel is a good performant algorithm and when you're dealing with the types of runtimes involved with force directed layout with the number of nodes you want, that matters a lot.
Why, among other reasons, that algorithm is awesome: Fast Multipole method. The fast multipole method is a matrix multiplication approximation which reduces the O() runtime of matrix multiplication for approximation to a small degree. Ideally, you'd have code from something like this: http://mgarland.org/files/papers/layoutgpu.pdf but I can't find it anywhere; maybe a CUDA solution isn't up your alley anyways.
Good luck.
The Gephi Toolkit might be what you need: some layouts are very fast yet with a good quality: http://gephi.org/toolkit/
30 secondes to 2 minutes are enough to layout such a graph, depending on your machine.
You can use the ForAtlas layout, or the Yifan Hu Multilevel layout.
For very large graphs (+50K nodes and 500K links), the OpenOrd layout wil
In a commercial scenario, you might also want to look at the family of yFiles graph layout and visualization libraries.
Even the JavaScript version of it can perform layouts for thousands of nodes and edges using different arrangement styles. The "organic" layout style is an implementation of a force directed layout algorithm similar in nature to the one used in Neo4j's browser application. But there are a lot more layout algorithms available that can give better visualizations for certain types of graph structures and diagrams. Depending on the settings and structure of the problem, some of the algorithms take only seconds, while more complex implementations can also bring your JavaScript engine to its knees. The Java and .net based variants still perform quite a bit better, as of today, but the JavaScript engines are catching up.
You can play with these algorithms and settings in this online demo.
Disclaimer: I work for yWorks, which is the maker of these libraries, but I do not represent my employer on SO.
I would take a look at http://neo4j.org/ its open source which is beneficial in your case so you can customize it to your needs. The github account can be found here.