Graph layout algorithm for ontologies (directed acyclic graphs) - layout

I'm looking for a way to display an ontology (DAG). Preferably I'd like to generate a structure like:
I've been playing around with the layout algorithms in igraph but haven't found anything close to what I want.

You are basically looking for a radial tree layout algorithm. igraph includes a tree layout algorithm (the Reingold-Tilford algorithm, but it does not produce radial layouts by default as it lays out the tree in a top-down manner. You can experiment with transforming the layout generated by the Reingold-Tilford algorithm into a radial layout (just use the Y coordinate as the radius and the X coordinate as the angle around the origin). This will probably provide a good starting point, but I suspect that the resulting layout can be improved further by passing it to a force-directed layout (like the Fruchterman-Reingold algorithm) that is able to refine an initial "seed" layout.
Note: using the Fruchterman-Reingold layout algorithm out-of-the-box probably wouldn't work because if you don't provide it with a seed layout, then it starts from a random layout. The random layout is probably very far from the optimal tree-like layout and thus it is harder for the Fruchterman-Reingold algorithm to disentangle the crossing edges.

Related

Is there any code for an interactive plotting application for a two dimensional curves

Plotting packages offer a variety of methods for displaying data. Write an interactive plotting application for two dimensionsional curves. Your application should be able to allow the user to choose the mode (line strip or polyline display of the data, bar chart or pie charts), colours, and line styles.
You should start with the GUI editation like this:
Does anyone know of a low level (no frameworks) example of a drag & drop, re-order-able list?
and change it to your primitives (more points per primitive instead of one ... handle each point as (sub)object so you can change its position later).
Then just add tools like add object,del object,... For hand drawing tool use piece wise interpolation cubics
The grid can be done like this:
How to draw dynamic 2D grid that adjusts according to camera zoom: OpenGL
Mouse zooming/panning is also important
Zooming graphics based on current mouse position
Putting all above together into simple editor looks like this:
Using GPU for curve rendering might give you some nice speed and functionality boost:
Is it possible to express "t" variable from Cubic Bezier Curve equation?
Mouse selection of objects might be a speed problem if your scene contains too many objects so in such case its best to use index buffers where you can mouse select with pixel perfect precision for almost free in O(1):
OpenGL 3D-raypicking with high poly meshes
The example is for 3D , in 2D is much simpler ...
Also do not forget to implement save/load functionality to some vector file format. I recommend using SVG it might be complicated to start with it but you can quickly check it contents in any SVG viewer or browser also in notepad as its just a text file. If you use just basic path elements and ignore the rest of SVG features you will see the parsing and creating SVG is not that hard for example See these:
Get Vertices/Edges From BMP or SVG (C#)
Discrete probability distribution plot with given values
For really big datasets you might want to use spatial subdivision techniques (Bounding (Volume)Area Hierarchy, or Quad tree) to ease up the operations...
More in depth implementation details about 2D vector gfx editors depends on language, OS, gfx api and GUI api you using and task you are aiming for ...

Silhouette below 3D model

There are some 3D applications which can cast shadow or silhouette below 3D models. They render pretty fast and smooth. I wonder what kind of technology is the standard procedure to get 3D model shadow/silhouette.
For example is there any C++ library like libigl or CGAL to get shadow/silhouette pretty fast? Or maybe GLSL shading is used? Any hint would be appreciated on the standard technology stack.
For rendering, it's trivial. Just project the vertices to the surface (for the case of the XY plane, this just entails setting the Z coordinate to 0) and render the triangles. There'll be a lot of overlap, but since you're just rendering that won't matter.
If you're trying to build a set of polygons representing the silhouette shape, you'll need to instead union the projected triangles using something like the Vatti clipping algorithm.
Computing shadows is a vast and uneasy topic. In the real world, light sources are extended and the shadow edges are not sharp (there is penumbra). Then there are cast shadows, and even self-shadows.
If you limit yourself to punctual light sources (hence sharp shadows), there is a simple principle: if you place an observer at the light source, the faces he will see are illuminated by that light source. Conversely, the hidden surfaces are in the shadow.
For correct rendering, the shadowed areas should be back-projected to the scene and painted black.
By nature, the ray-tracing techniques make this process easy to implement.

What formula or algorithm can I use to draw a 3D Sphere without using OpenGL-like libs?

I know that there are 4 techniques to draw 3D objects:
(1) Wireframe Modeling and rendering, (2) Additive Modeling, (3) Subtractive Modeling, (4) Splines and curves.
Then, those models go through hidden surface removal algorithm.
Am I correct?
Be that way, What formula or algorithm can I use to draw a 3D Sphere?
I am using a low-level library named WinBGIm from colorado university.
there are 4 techniques to draw 3D objects:
(1) Wireframe Modeling and rendering, (2) Additive Modeling, (3) Subtractive Modeling, (4) Splines and curves.
These are modelling techniques and not rendering techniques. They allow you to mathematically define your mesh's geometry. How you render this data on to a 2D canvas is another story.
There are two fundamental approaches to rendering 3D models on a 2D canvas.
Ray Tracing
The basic idea of ray tracing is to pass a ray from the camera's origin, through the point on the canvas whose colour needs to be determined. Determine which models get hit by it and pick the closest one, determine how it's lit to compute the colour there. This is done by further tracing rays from the hit point to all the light sources in the scene. If you notice, this approach eliminates the need to use hidden surface determination algorithms like the back face culling, z-buffer, etc. since the basic idea is rooted on a hidden surface algorithm (ray tracing).
There are packages, libraries, etc. that help you do this. However, it's common that ray tracers are written from scratch as a college-level project. However, this approach takes more time to render (not to code), but the results are generally more pleasing than the below one. This approach is more popular when you want to render non-interactive visuals like movies.
Rasterization
This approach takes primitives (triangles and quads) that define the models in the scene and sample them at regular intervals (screen pixels they cover) and write it on to a colour buffer. Here hidden surface is usually eliminated using the Z-buffer; a buffer that stores the z-order of the fragment and the closer one wins, when writing to the colour buffer.
Rasterization is the more popular approach with cheap hardware support for it available on most modern computers due to years of research and money that has gone in to it. Libraries like OpenGL and Direct3D are readily available to facilitate development. Although the results are less pleasing than ray tracing, it's faster to render and thus is widely used in interactive, real-time rendering like games.
If you want to not use those libraries, then you have to do what is commonly known as software rendering i.e. you will end up doing what these libraries do.
What formula or algorithm can I use to draw a 3D Sphere?
Depends on which one of the above you choose. If you simply rasterize a 3D sphere in 2D with orthographic projection, all you have to do is draw a circle on the canvas.
If you are looking for hidden lines removal (drawing the edges rather than the inside of the faces), the solution is easy: "back face culling".
Every edge of your model belongs to two faces. For every face you can compute the normal vector and check if it is facing to the observer (by the sign of the dot product of the normal and the direction of the projection line); in other words, if the observer is located in the outer half-space defined by the plane of the face. Then an edge is wholly visible if and only if it belongs to at least one front face.
Usual discretization of the sphere are made by drawing equidistant parallels and meridians. It may be advantageous to adjust the spacing of the parallels so that all tiles are about the same area.

Algorithm for cutting a mesh using another mesh

I am looking for an algorithm that given two meshes could clip one using another.
The simplest form of this is clipping a mesh using a plane. I've already implemented that by following something similar to what is described here.
What it does is basically inspecting all mesh vertices and triangles with respect to the plane (the plane's normal and point are given). If the triangle is completely above the plane, it is left untouched. If it falls completely below the plane, it is discarded. If some of the edges of the triangle intersect with the plane, the intersecting points with the plane are calculated and added as the new vertices. Finally a cap is generated for the hole on the place the mesh was cut.
The problem is that the algorithm assumes that the plane is unlimited, therefore whatever is in its path is clipped. In the simplest form, I need an extension of this without the assumption of a plane of "infinite" size.
To clarify, imagine that we have a 3D model of a desk with 2 boxes on it. The boxes are adjacent (but not touching or stacked). The user will define a cutting plane of a limited width and height underneath the first box and performs the cut. We end up with a desk model (mesh) with a box on it and another box (mesh) that can be freely moved around/manipulated.
In the general form, I'd like the user to be able to define a bounding box for the box he/she wants to separate from the desk model and perform the cut using that bounding box.
If I could extend the algorithm I already have to an algorithm with limited-sized planes, that would be great for now.
What you're looking for are constructive solid geometry/boolean algorithms with arbitrary meshes. It's considerably more complex than slicing meshes by an infinite plane.
Among the earliest and simplest research in this area, and a good starting point, is Constructive Solid Geometry for Polyhedral Objects by Trumbore and Hughes.
http://cs.brown.edu/~jfh/papers/Laidlaw-CSG-1986/main.htm
From the original paper:
More elaborate solutions extend upon this subject with a variety of data structures.
The real complexity of the operation lies in the slicing algorithm to slice one triangle against another. The nightmare of implementing robust CSG lies in numerical precision. It's easy when you involve objects far more complex than a cube to run into cases where a slice is made just barely next to a vertex (at which point you have the tough decision of merging the new split vertex or not prior to carrying out more splits), where polygons are coplanar (or almost), etc.
So I suggest initially erring on the side of using very high-precision floating point numbers, possibly even higher than double precision to focus on getting something working correctly and robustly. You can optimize later (first pass should be to use an accelerator like an octree/kd-tree/bvh), but you'll avoid many headaches this way in your first iteration.
This is vastly simpler to implement at render time if you're focusing on a raytracer rather than a modeling software, e.g. With raytracers, all you have to do to do this kind of arbitrary clipping is pretend that an object used to subtract from another has its polygons flipped in the culling process, e.g. It's easy to solve robustly at the ray level, but quite a bit harder to do robustly at the geometric level.
Another thing you can do to make your life so much easier if you can afford it is to voxelize your object, find subtractions/additions/unions of voxels, and then translate the voxels back into a mesh. This is so much easier to make robust, but harder to do efficiently and the voxel->polygon conversion can get quite involved if you want better results than what marching cubes provide.
It's a really tough area to do extremely well and requires perseverance, and thus the reason for the existence of things like this: http://carve-csg.com/about.
If someone is interested, currently there is a solution for this problem in CGAL library. It allows clipping one triangular mesh using another mesh as bounding volume. The usage example can be found here.

Non-Affine image transformations in .NET

Are there any classes, methods in the .NET library, or any algorithms in general, to perform non-affine transformations? (i.e. transformations that involve more than just rotation, scale, translation and shear)
e.g.:
(source: last100.com)
Is there another term for non-affine transformations?
I am not aware of anything integrated in .Net letting you do non affine transforms.
I guess you are trying to have some sort of 3D texture mapping? If that's the case you need an homogenous affine transform, which is not available in .Net. I'm also not aware of any integrated way to make pixel displacement transforms in .Net.
However, the currently voted solution might be good for what you are trying to do, just be aware that it won't do perspective correction out of the box.
For instance:
The picture on the left was generated using the single quad distort library provided by Neil N. The picture on the right was generated using a single quad (two triangles actually) in DirectX.
This may not have any impact on what you are trying to do, but this is something to keep in mind if you want to do 3D stuff, it will look very weird without perspective correct mapping.
All of the example images you posted can be done with a Quadrilateral Distortion. Though I cant say for certain that a quad distort will cover ALL non affine transforms.
Heres a link to a not so good implementation of it in C#... it works, but is slow. Poke around Wikipedia for the many different optimizations available for these kinds of calculations
http://www.vcskicks.com/image-distortion.html
-Neil
You can do this in wpf using a the Viewport3d control and a non-affine transform matrix. Rendering this to a bitmap again may be interesting.... Which I "fixed" by including an invisible <image> control with the same image as on my textured plane... (Also, I've had to work around the max texture size issues by splitting up the plane and cropping images...)
http://www.charlespetzold.com/blog/2007/08/060605.html
In my case I wanted the reverse of this (transform so arbitrary points on the warped become the corners of my rectangular window), which is the Inverse of the matrix to do the opposite.

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