GLSL truncated signed distance representation (TSDF) implementation - c++

I am looking forward to implement a model reconstruction of RGB-D images. Preferred on mobile phones. For that I read, it is all done with an TSDF-representation. I read a lot of papers now over hierarchical structures and other ideas to speed this up, but my problem is, that I still hat no clue how to actually implement this representation.
If I have a volume grid of size n, so n x n x n and I want to store in each voxel the signed distance, weight and color information. My only guess is, that I have to build a discrete set of points, for each voxel position. And with GLSL "paint" all these points and calculate the nearest distance. But that don't seem quite good or efficient to calculate this n^3 times.
How can I imagine to implement such a TSDF-representation?
The problem is, my only idea is to render the voxel grid to store in the data of signed distances. But for each depth map I have to render again all voxels and calculate all distances. Is there any way to render it the other way around?
So can't I render the points of the depth map and store informations in the voxel grid?
How is the actual state of art to render such a signed distance representation in an efficient way?

You are on the right track, it's an ambitious project but very cool if you can do it.
First, it's worth getting a good idea how these things work. The original paper identifying a TSDF was by Curless and Levoy and is reasonably approachable - a copy is here . There are many later variations but this is the starting point.
Second, you will need to create nxnxn storage as you have said. This very quickly gets big. For example, if you want 400x400x400 voxels with RGB data and floating point values for distance and weight then that will be 768MB of GPU memory - you may want to check how much GPU memory you have available on a mobile device. Yup, I said GPU because...
While you can implement toy solutions on CPU, you really need to get serious about GPU programming if you want to have any kind of performance. I built an early version on an Intel i7 CPU laptop. Admittedly I spent no time optimising it but it was taking tens of seconds to integrate a single depth image. If you want to get real time (30Hz) then you'll need some GPU programming.
Now you have your TSFD data representation, each frame you need to do this:
1. Work out where the camera is with respect to the TSDF in world coordinates.
Usually you assume that you are the origin at time t=0 and then measure your relative translation and rotation with regard to the previous frame. The most common way to do this is with an algorithm called iterative closest point (ICP) You could implement this yourself or use a library like PCL though I'm not sure if they have a mobile version. I'd suggest you get started without this by just keeping your camera and scene stationary and build up to movement later.
2. Integrate the depth image you have into the TSDF This means updating the TSDF with the next depth image. You don't throw away the information you have to date, you merge the new information with the old.
You do this by iterating over every voxel in your TSDF and :
a) Work out the distance from the voxel centre to your camera
b) Project the point into your depth camera's image plane to get a pixel coordinate (using the extrinsic camera position obtained above and the camera intrinsic parameters which are easily searchable for Kinect)
c) Lookup up the depth in your depth map at that pixel coordinate
d) Project this point back into space using the pixel x and y coords plus depth and your camera properties to get a 3D point corresponding to that depth
e) Update the value for the current voxel's distance with the value distance_from_step_d - distance_from_step_a (update is usually a weighted average of the existing value plus the new value).
You can use a similar approach for the voxel colour.
Once you have integrated all of your depth maps into the TSDF, you can visualise the result by either raytracing it or extracting the iso surface (3D mesh) and viewing it in another package.
A really helpful paper that will get you there is here. This is a lab report by some students who actually implemented Kinect Fusion for themselves on a PC. It's pretty much a step by step guide though you'll still have to learn CUDA or similar to implement it
You can also check out my source code on GitHub for ideas though all normal disclaimers about fitness for purpose apply.
Good luck!

After I posted my other answer I thought of another approach which seems to match the second part of your question but it definitely is not reconstruction and doesn't involve using a TSDF. It's actually a visualisation but it is a lot simpler :)
Each frame you get an RGB and a Depth image. Assuming that these images are registered, that is the pixel at (x,y) in the RGB image represents the same pixel as that at (x,y) in the depth image then you can create a dense point cloud coloured using the RGB data. To do this you would:
For every pixel in the depth map
a) Use the camera's intrinsic matrix (K), the pixel coordinates and the depth value in the map at that point to project the point into a 3D point in camera coordinates
b) Associate the RGB value at the same pixel with that point in space
So now you have an array of (probably 640x480) structures like {x,y,z,r,g,b}
You can render these using on GLES just by creating a set of vertices and rendering points. There's a discussion on how to do this here
With this approach you throw away the data every frame and redo from scratch. Importantly, you don't get a reconstructed surface, and you don't use a TSDF. You can get pretty results but it's not reconstruction.

Related

GPU-Computation (CUDA) tex2d/tex3d - How to deal with anisotropic pixel/voxel

I am quite new to cuda programming and i have a question about the texXD function. My goal is to implement a simple GPU-based ray tracer using the optimized CUDA functionality.
See CUDA texture API that is used by NVIDIA.
At my research I have to deal with images that have a different resolution for every dimension (like CT images, (x,y) have a different resolution as (z)). Resampling to an isotropic pixel/voxel size might bring up some problems (especially for medical diagnosis).
For example i have an image with size (100px x 50px) and a resolution of (2px/mm x 1px/mm). The ray enters the image at an arbitrary point and leaves is somewhere else. The ray is sampled in the direction form entrance to leaving point. At each sample point (pos.x,pos.y) the tex2D function carries out an (bicubicbilinear) interpolation taking the neighbour pixel values into account weighted by their distance from the sample point.
example image:
In both shapes the corner points are named the same way(x1,y1),.... The only difference is the physical space between the corner points. The interpolation point is (x,y). I computed an example using the formula for rectangular grids and yield a different results for both grids. But if I use the ratio of areas of the numbered rectangles I got a different result.
My Question: Will CUDA take care of the different resolutions of the dimensions or does CUDA see all pixel in the same distance (and therefore as a squared grid)?
The formula used by CUDA seems to be the one for a squared grid (google:CUDA Texture fetching).
Or can I resample the image to squared grid before using tex2D without a substantial information loss?
Any suggestions are recommended. If you need some more clarification, feel free to ask. I will specifiy my question.
I don't believe what (I think it is) you are trying to do can be achieved using textures. The sole filtering mode supported using textures is described here.
Some salient points:
Textures don't have resolution. The just have dimensions.
Textures data is implicitly uniformly spaced in all dimensions.
Texture interpolation is done in a reduced accuracy fixed point arithmetic format which gives 8 bits of representational accuracy
None of this seems like anything that would be useful for the interpolation on a non-uniform grid which you are describing. At a minimum you would need to perform a coordinate transformation before you could use the uniform filtering mode. The amount of effort and expense would be about the same as just writing an interpolation routine yourself in user code.

How do you store voxel data?

I've been looking online and I'm impressed by the capabilities of using voxel data, especially for terrain building and manipulation. The problem is that voxels are never clearly explained on any site that i visited or how to use/implement them. All i find is that voxels are volumetric data. Please provide a more complete answer; what is volumetric data. It may seem like a simple question but I'm still unsure.
Also, how would you implement voxel data? (I aim to implement this into a c++ program.) What sort of data type would you use to store the voxel data to enable me to modify the contents at run time as fast as possible. I have looked online and i couldn't find anything which explained how to store the data. Lists of objects, arrays, ect...
How do you use voxels?
EDIT:
Since I'm just beginning with voxels, I'll probably start by using it to only model simple objects but I will eventually be using it for rendering terrain and world objects.
In essence, voxels are a three-dimensional extension of pixels ("volumetric pixels"), and they can indeed be used to represent volumetric data.
What is volumetric data
Mathematically, volumetric data can be seen as a three-dimensional function F(x,y,z). In many applications this function is a scalar function, i.e., it has one scalar value at each point (x,y,z) in space. For instance, in medical applications this could be the density of certain tissues. To represent this digitally, one common approach is to simply make slices of the data: imagine images in the (X,Y)-plane, and shifting the z-value to have a number of images. If the slices are close to eachother, the images can be displayed in a video sequence as for instance seen on the wiki-page for MRI-scans (https://upload.wikimedia.org/wikipedia/commons/transcoded/4/44/Structural_MRI_animation.ogv/Structural_MRI_animation.ogv.360p.webm). As you can see, each point in space has one scalar value which is represented as a grayscale.
Instead of slices or a video, one can also represent this data using voxels. Instead of dividing a 2D plane in a regular grid of pixels, we now divide a 3D area in a regular grid of voxels. Again, a scalar value can be given to each voxel. However, visualizing this is not as trivial: whereas we could just give a gray value to pixels, this does not work for voxels (we would only see the colors of the box itself, not of its interior). In fact, this problem is caused by the fact that we live in a 3D world: we can look at a 2D image from a third dimension and completely observe it; but we cannot look at a 3D voxel space and observe it completely as we have no 4th dimension to look from (unless you count time as a 4th dimension, i.e., creating a video).
So we can only look at parts of the data. One way, as indicated above, is to make slices. Another way is to look at so-called "iso-surfaces": we create surfaces in the 3D space for which each point has the same scalar value. For a medical scan, this allows to extract for instance the brain-part from the volumetric data (not just as a slice, but as a 3D model).
Finally, note that surfaces (meshes, terrains, ...) are not volumetric, they are 2D-shapes bent, twisted, stretched and deformed to be embedded in the 3D space. Ideally they represent the border of a volumetric object, but not necessarily (e.g., terrain data will probably not be a closed mesh). A way to represent surfaces using volumetric data, is by making sure the surface is again an iso-surface of some function. As an example: F(x,y,z) = x^2 + y^2 + z^2 - R^2 can represent a sphere with radius R, centered around the origin. For all points (x',y',z') of the sphere, F(x',y',z') = 0. Even more, for points inside the sphere, F < 0, and for points outside of the sphere, F > 0.
A way to "construct" such a function is by creating a distance map, i.e., creating volumetric data such that every point F(x,y,z) indicates the distance to the surface. Of course, the surface is the collection of all the points for which the distance is 0 (so, again, the iso-surface with value 0 just as with the sphere above).
How to implement
As mentioned by others, this indeed depends on the usage. In essence, the data can be given in a 3D matrix. However, this is huge! If you want the resolution doubled, you need 8x as much storage, so in general this is not an efficient solution. This will work for smaller examples, but does not scale very well.
An octree structure is, afaik, the most common structure to store this. Many implementations and optimizations for octrees exist, so have a look at what can be (re)used. As pointed out by Andreas Kahler, sparse voxel octrees are a recent approach.
Octrees allow easier navigating to neighbouring cells, parent cells, child cells, ... (I am assuming now that the concept of octrees (or quadtrees in 2D) are known?) However, if many leaf cells are located at the finest resolutions, this data structure will come with a huge overhead! So, is this better than a 3D array: it somewhat depends on what volumetric data you want to work with, and what operations you want to perform.
If the data is used to represent surfaces, octrees will in general be much better: as stated before, surfaces are not really volumetric, hence will not require many voxels to have relevant data (hence: "sparse" octrees). Refering back to the distance maps, the only relevant data are the points having value 0. The other points can also have any value, but these do not matter (in some cases, the sign is still considered, to denote "interior" and "exterior", but the value itself is not required if only the surface is needed).
How to use
If by "use", you are wondering how to render them, then you can have a look at "marching cubes" and its optimizations. MC will create a triangle mesh from volumetric data, to be rendered in any classical way. Instead of translating to triangles, you can also look at volume rendering to render a "3D sampled data set" (i.e., voxels) as such (https://en.wikipedia.org/wiki/Volume_rendering). I have to admit that I am not that familiar with volume rendering, so I'll leave it at just the wiki-link for now.
Voxels are just 3D pixels, i.e. 3D space regularly subdivided into blocks.
How do you use them? It really depends on what you are trying to do. A ray casting terrain game engine? A medical volume renderer? Something completely different?
Plain 3D arrays might be the best for you, but it is memory intensive. As BWG pointed out, octree is another popular alternative. Search for Sparse Voxel Octrees for a more recent approach.
In popular usage during the 90's and 00's, 'voxel' could mean somewhat different things, which is probably one reason you have been finding it hard to find consistent information. In technical imaging literature, it means 3D volume element. Oftentimes, though, it is used to describe what is somewhat-more-clearly termed a high-detail raycasting engine (as opposed to the low-detail raycasting engine in Doom or Wolfenstein). A popular multi-part tutorial lives in the Flipcode archives. Also check out this brief one by Jacco.
There are many old demos you can find out there that should run under emulation. They are good for inspiration and dissection, but tend to use a lot of assembly code.
You should think carefully about what you want to support with your engine: car-racing, flying, 3D objects, planets, etc., as these constraints can change the implementation of your engine. Oftentimes, there is not a data structure, per se, but the terrain heightfield is represented procedurally by functions. Otherwise, you can use an image as a heightfield. For performance, when rendering to the screen, think about level-of-detail, in other words, how many actual pixels will be taken up by the rendered element. This will determine how much sampling you do of the heightfield. Once you get something working, you can think about ways you can blend pixels over time and screen space to make them look better, while doing as little rendering as possible.

OpenCV Image stiching when camera parameters are known

We have pictures taken from a plane flying over an area with 50% overlap and is using the OpenCV stitching algorithm to stitch them together. This works fine for our version 1. In our next iteration we want to look into a few extra things that I could use a few comments on.
Currently the stitching algorithm estimates the camera parameters. We do have camera parameters and a lot of information available from the plane about camera angle, position (GPS) etc. Would we be able to benefit anything from this information in contrast to just let the algorithm estimate everything based on matched feature points?
These images are taken in high resolution and the algorithm takes up quite amount of RAM at this point, not a big problem as we just spin large machines up in the cloud. But I would like to in our next iteration to get out the homography from down sampled images and apply it to the large images later. This will also give us more options to manipulate and visualize other information on the original images and be able to go back and forward between original and stitched images.
If we in question 1 is going to take apart the stitching algorithm to put in the known information, is it just using the findHomography method to get the info or is there better alternatives to create the homography when we actually know the plane position and angles and the camera parameters.
I got a basic understanding of opencv and is fine with c++ programming so its not a problem to write our own customized stitcher, but the theory is a bit rusty here.
Since you are using homographies to warp your imagery, I assume you are capturing areas small enough that you don't have to worry about Earth curvature effects. Also, I assume you don't use an elevation model.
Generally speaking, you will always want to tighten your (homography) model using matched image points, since your final output is a stitched image. If you have the RAM and CPU budget, you could refine your linear model using a max likelihood estimator.
Having a prior motion model (e.g. from GPS + IMU) could be used to initialize the feature search and match. With a good enough initial estimation of the feature apparent motion, you could dispense with expensive feature descriptor computation and storage, and just go with normalized crosscorrelation.
If I understand correctly, the images are taken vertically and overlap by a known amount of pixels, in that case calculating homography is a bit overkill: you're just talking about a translation matrix, and using more powerful algorithms can only give you bad conditioned matrixes.
In 2D, if H is a generalised homography matrix representing a perspective transformation,
H=[[a1 a2 a3] [a4 a5 a6] [a7 a8 a9]]
then the submatrixes R and T represent rotation and translation, respectively, if a9==1.
R= [[a1 a2] [a4 a5]], T=[[a3] [a6]]
while [a7 a8] represents the stretching of each axis. (All of this is a bit approximate since when all effects are present they'll influence each other).
So, if you known the lateral displacement, you can create a 3x3 matrix having just a3, a6 and a9=1 and pass it to cv::warpPerspective or cv::warpAffine.
As a criteria of matching correctness you can, f.e., calculate a normalized diff between pixels.

OpenGL Dynamic Object Motion Blur

I've been following the GPU Gems 3 tutorial on how to blur based on camera movement. However I'm wanting to implement a blur based on object movement too. The solution is presented in the article (see quote below), however I'm curious as to how exactly to implement this.
At the moment I'm multiplying the object's matrix by the view-projection, then separately again for the previous-view-projection and then passing them into the pixel shader to calculate the velocity instead of just the view-projections.
If that is in fact the correct method, then why am I not simply able to pass in the model-view-projection? I would have assumed they would be the same value?
GPU Gems 3 Motion Blur
To generate a velocity texture for rigid dynamic objects, transform the object by using the current frame's view-projection matrix and the last frame's view-projection matrix, and then compute the difference in viewport positions the same way as for the post-processing pass. This velocity should be computed per-pixel by passing both transformed positions into the pixel shader and computing the velocity there.
Check out my research I did a few months ago on this topic: https://slu-files.s3.us-east-1.amazonaws.com/Fragment_shader_dynamic_blur.pdf
(source: stevenlu.net)
(source: stevenlu.net)
Sadly I did not implement textured objects when producing this material, but do use your imagination. I am working on a game engine so when that finally sees the light of day in the form of a game, you can be sure that I'll come and post breadcrumbs here.
It primarily addresses how to implement this effect in 2D, and in cases where objects do not overlap. There is not really a good way to handle using a fragment shader to "sweep" samples in order to generate "accurate" blur. While the effect approaches pixel-perfection as the sample count is cranked up, the geometry that must be generated to cover the sweep area has to be manually assembled using some "ugly" techniques.
In full 3D it's a rather difficult problem to know which pixels a dynamic object will sweep over during the course of a frame. Even with static geometry and a moving camera the solution proposed by the GPU Gems article is incorrect when moving past things quickly because it is unable to address that issue of requiring blending of the area swept out by something moving...
That said, if this approximation which neglects the sweep is sufficient (and it may be) then what you can do to extend to dynamic objects is to take their motion into account. You'll need to work out the details of course but look at lines 2 and 5 in the second code block on the article you linked: They are the current and previous screen space "positions" of the pixel. You simply have to somehow pass in the matrices that will allow you to compute the previous position of each pixel, taking into account the dynamic motion of your object.
It shouldn't be too bad. In the pass where you render your dynamic object you send in an extra matrix that represents its motion over the last frame.
Update:
I found that this paper describes an elegant and performant approach that provides somewhat high quality physically correct blurring for a 3D pipeline. It'll be hard to do much better than this within the constraint of rendering the full scene no more than one time for performance reasons.
I noticed with some of the examples the quality of the velocity buffer could be better. for example a rotating wheel should have some curves in the velocity space. I believe if they can be set properly (may require custom fragment shaders to render the velocity out...) they will look intuitively correct like the spinning cube seen above from my 2D exploration into dynamic motion blurring.

Implementing Marching Cube Algorithm?

From My last question: Marching Cube Question
However, i am still unclear as in:
how to create imaginary cube/voxel to check if a vertex is below the isosurface?
how do i know which vertex is below the isosurface?
how does each cube/voxel determines which cubeindex/surface to use?
how draw surface using the data in triTable?
Let's say i have a point cloud data of an apple.
how do i proceed?
can anybody that are familiar with Marching Cube help me?
i only know C++ and opengl.(c is a little bit out of my hand)
First of all, the isosurface can be represented in two ways. One way is to have the isovalue and per-point scalars as a dataset from an external source. That's how MRI scans work. The second approach is to make an implicit function F() which takes a point/vertex as its parameter and returns a new scalar. Consider this function:
float computeScalar(const Vector3<float>& v)
{
return std::sqrt(v.x*v.x + v.y*v.y + v.z*v.z);
}
Which would compute the distance from the point and to the origin for every point in your scalar field. If the isovalue is the radius, you just figured a way to represent a sphere.
This is because |v| <= R is true for all points inside a sphere, or which lives on its interior. Just figure out which vertices are inside the sphere and which ones are on the outside. You want to use the less or greater-than operators because a volume divides the space in two. When you know which points in your cube are classified as inside and outside, you also know which edges the isosurface intersects. You can end up with everything from no triangles to five triangles. The position of the mesh vertices can be computed by interpolating across the intersected edges to find the actual intersection point.
If you want to represent say an apple with scalar fields, you would either need to get the source data set to plug in to your application, or use a pretty complex implicit function. I recommend getting simple geometric primitives like spheres and tori to work first, and then expand from there.
1) It depends on yoru implementation. You'll need to have a data structure where you can lookup the values at each corner (vertex) of the voxel or cube. This can be a 3d image (ie: an 3D texture in OpenGL), or it can be a customized array data structure, or any other format you wish.
2) You need to check the vertices of the cube. There are different optimizations on this, but in general, start with the first corner, and just check the values of all 8 corners of the cube.
3) Most (fast) algorithms create a bitmask to use as a lookup table into a static array of options. There are only so many possible options for this.
4) Once you've made the triangles from the triTable, you can use OpenGL to render them.
Let's say i have a point cloud data of an apple. how do i proceed?
This isn't going to work with marching cubes. Marching cubes requires voxel data, so you'd need to use some algorithm to put the point cloud of data into a cubic volume. Gaussian Splatting is an option here.
Normally, if you are working from a point cloud, and want to see the surface, you should look at surface reconstruction algorithms instead of marching cubes.
If you want to learn more, I'd highly recommend reading some books on visualization techniques. A good one is from the Kitware folks - The Visualization Toolkit.
You might want to take a look at VTK. It has a C++ implementation of Marching Cubes, and is fully open sourced.
As requested, here is some sample code implementing the Marching Cubes algorithm (using JavaScript/Three.js for the graphics):
http://stemkoski.github.com/Three.js/Marching-Cubes.html
For more details on the theory, you should check out the article at
http://paulbourke.net/geometry/polygonise/