I have various point clouds defining RT-STRUCTs called ROI from DICOM files. DICOM files are formed by tomographic scanners. Each ROI is formed by point cloud and it represents some 3D object.
The goal is to get 2D curve which is formed by plane, cutting ROI's cloud point. The problem is that I can't just use points which were intersected by plane. What I probably need is to intersect 3D concave hull with some plane and get resulting intersection contour.
Is there any libraries which have already implemented these operations? I've found PCL library and probably it should be able to solve my problem, but I can't figure out how to achieve it with PCL. In addition I can use Matlab as well - we use it through its runtime from C++.
Has anyone stumbled with this problem already?
P.S. As I've mentioned above, I need to use a solution from my C++ code - so it should be some library or matlab solution which I'll use through Matlab Runtime.
P.P.S. Accuracy in such kind of calculations is really important - it will be used in a medical software intended for work with brain tumors, so you can imagine consequences of an error (:
You first need to form a surface from the point set.
If it's possible to pick a 2d direction for the points (ie they form a convexhull in one view) you can use a simple 2D Delaunay triangluation in those 2 coordinates.
otherwise you need a full 3D surfacing function (marching cubes or Poisson)
Then once you have the triangles it's simple to calculate the contour line that a plane cuts them.
See links in Mesh generation from points with x, y and z coordinates
Perhaps you could just discard the points that are far from the plane and project the remaining ones onto the plane. You'll still need to reconstruct the curve in the plane but there are several good methods for that. See for instance http://www.cse.ohio-state.edu/~tamaldey/curverecon.htm and http://valis.cs.uiuc.edu/~sariel/research/CG/applets/Crust/Crust.html.
Related
I have a set of 2D points of a known density I want to mesh by taking the holes in account. Basically, given the following input:
I want something link this:
I tried PCL ConcaveHull, but it doens't handle the holes and splitted mesh very well.
I looked at CGAL Alpha shapes, which seems to go in the right direction (creating a polygon from a point cloud), but I don't know how to get triangles after that.
I though of passing the resulting polygons to a constrained triangulation algorithm and mark domains, but I didn't find how to get a list of polygons.
The resulting triangulated polygon is about a two step process at the least. First you need to triangulate your 2D points (using something like a Delaunay2D algorithm). There you can set the maximum length for the triangles and get the the desired shape. Then you can decimate the point cloud and re-triangulate. Another option is to use the convex hull to get the outside polygon, then extract the inside polygon through a TriangulationCDT algorithm, the apply some PolygonBooleanOperations, obtain the desired polygon, and finaly re-triangulate.
I suggest you look into the Geometric Tools library and specifically the Geometric Samples. I think everything you need is in there, and is much less library and path heavy than CGAL (the algorithms are not free for this type of work unless is a school project) or the PCL (I really like the library for segmentation, but their triangulation breaks often and is slow).
If this solves your problem, please mark it as your answer. Thank you!
I realize there are many cans of worms related to what I'm asking, but I have to start somewhere. Basically, what I'm asking is:
Given two photos of a scene, taken with unknown cameras, to what extent can I determine the (relative) warping between the photos?
Below are two images of the 1904 World's Fair. They were taken at different levels on the wireless telegraph tower, so the cameras are more or less vertically in line. My goal is to create a model of the area (in Blender, if it matters) from these and other photos. I'm not looking for a fully automated solution, e.g., I have no problem with manually picking points and features.
Over the past month, I've taught myself what I can about projective transformations and epipolar geometry. For some pairs of photos, I can do pretty well by finding the fundamental matrix F from point correspondences. But the two below are causing me problems. I suspect that there's some sort of warping - maybe just an aspect ratio change, maybe more than that.
My process is as follows:
I find correspondences between the two photos (the red jagged lines seen below).
I run the point pairs through Matlab (actually Octave) to find the epipoles. Currently, I'm using Peter Kovesi's
Peter's Functions for Computer Vision.
In Blender, I set up two cameras with the images overlaid. I orient the first camera based on the vanishing points. I also determine the focal lengths from the vanishing points. I orient the second camera relative to the first using the epipoles and one of the point pairs (below, the point at the top of the bandstand).
For each point pair, I project a ray from each camera through its sample point, and mark the closest covergence of the pair (in light yellow below). I realize that this leaves out information from the fundamental matrix - see below.
As you can see, the points don't converge very well. The ones from the left spread out the further you go horizontally from the bandstand point. I'm guessing that this shows differences in the camera intrinsics. Unfortunately, I can't find a way to find the intrinsics from an F derived from point correspondences.
In the end, I don't think I care about the individual intrinsics per se. What I really need is a way to apply the intrinsics to "correct" the images so that I can use them as overlays to manually refine the model.
Is this possible? Do I need other information? Obviously, I have little hope of finding anything about the camera intrinsics. There is some obvious structural info though, such as which features are orthogonal. I saw a hint somewhere that the vanishing points can be used to further refine or upgrade the transformations, but I couldn't find anything specific.
Update 1
I may have found a solution, but I'd like someone with some knowledge of the subject to weigh in before I post it as an answer. It turns out that Peter's Functions for Computer Vision has a function for doing a RANSAC estimate of the homography from the sample points. Using m2 = H*m1, I should be able to plot the mapping of m1 -> m2 over top of the actual m2 points on the second image.
The only problem is, I'm not sure I believe what I'm seeing. Even on an image pair that lines up pretty well using the epipoles from F, the mapping from the homography looks pretty bad.
I'll try to capture an understandable image, but is there anything wrong with my reasoning?
A couple answers and suggestions (in no particular order):
A homography will only correctly map between point correspondences when either (a) the camera undergoes a pure rotation (no translation) or (b) the corresponding points are all co-planar.
The fundamental matrix only relates uncalibrated cameras. The process of recovering a camera's calibration parameters (intrinsics) from unknown scenes, known as "auto-calibration" is a rather difficult problem. You'd need these parameters (focal length, principal point) to correctly reconstruct the scene.
If you have (many) more images of this scene, you could try using a system such as Visual SFM: http://ccwu.me/vsfm/ It will attempt to automatically solve the Structure From Motion problem, including point matching, auto-calibration and sparse 3D reconstruction.
I am currently reading into the topic of stereo vision, using the book of Hartley&Zimmerman alongside some papers, as I am trying to develop an algorithm capable of creating elevation maps from two images.
I am trying to come up with the basic steps for such an algorithm. This is what I think I have to do:
If I have two images I somehow have to find the fundamental matrix, F, in order to find the actual elevation values at all points from triangulation later on. If the cameras are calibrated this is straightforward if not it is slightly more complex (plenty of methods for this can be found in H&Z).
It is necessary to know F in order to obtain the epipolar lines. These are lines that are used in order to find image point x in the first image back in the second image.
Now comes the part were it gets a bit confusing for me:
Now I would start taking a image point x_i in the first picture and try to find the corresponding point x_i’ in the second picture, using some matching algorithm. Using triangulation it is now possible to compute the real world point X and from that it’s elevation. This process will be repeated for every pixel in the right image.
In the perfect world (no noise etc) triangulation will be done based on
x1=P1X
x2=P2X
In the real world it is necessary to find a best fit instead.
Doing this for all pixels will lead to the complete elevation map as desired, some pixels will however be impossible to match and therefore can't be triangulated.
What confuses me most is that I have the feeling that Hartley&Zimmerman skip the entire discussion on how to obtain your point correspondences (matching?) and that the papers I read in addition to the book talk a lot about disparity maps which aren’t mentioned in H&Z at all. However I think I understood correctly that the disparity is simply the difference x1_i- x2_i?
Is this approach correct, and if not where did I make mistakes?
Your approach is in general correct.
You can think of a stereo camera system as two points in space where their relative orientation is known. This are the optical centers. In front of each optical center, you have a coordinate system. These are the image planes. When you have found two corresponding pixels, you can then calculate a line for each pixel, wich goes throug the pixel and the respectively optical center. Where the two lines intersect, there is the object point in 3D. Because of the not perfect world, they will probably not intersect and one may use the point where the lines are closest to each other.
There exist several algorithms to detect which points correspond.
When using disparities, the two image planes need to be aligned such that the images are parallel and each row in image 1 corresponds to the same row in image 2. Then correspondences only need to be searched on a per row basis. Then it is also enough to know about the differences on x-axis of the single corresponding points. This is then the disparity.
I have some 3D Points that roughly, but clearly form a segment of a circle. I now have to determine the circle that fits best all the points. I think there has to be some sort of least squares best fit but I cant figure out how to start.
The points are sorted the way they would be situated on the circle. I also have an estimated curvature at each point.
I need the radius and the plane of the circle.
I have to work in c/c++ or use an extern script.
You could use a Principal Component Analysis (PCA) to map your coordinates from three dimensions down to two dimensions.
Compute the PCA and project your data onto the first to principal components. You can then use any 2D algorithm to find the centre of the circle and its radius. Once these have been found/fitted, you can project the centre back into 3D coordinates.
Since your data is noisy, there will still be some data in the third dimension you squeezed out, but bear in mind that the PCA chooses this dimension such as to minimize the amount of data lost, i.e. by maximizing the amount of data that is represented in the first two components, so you should be safe.
A good algorithm for such data fitting is RANSAC (Random sample consensus). You can find a good description in the link so this is just a short outline of the important parts:
In your special case the model would be the 3D circle. To build this up pick three random non-colinear points from your set, compute the hyperplane they are embedded in (cross product), project the random points to the plane and then apply the usual 2D circle fitting. With this you get the circle center, radius and the hyperplane equation. Now it's easy to check the support by each of the remaining points. The support may be expressed as the distance from the circle that consists of two parts: The orthogonal distance from the plane and the distance from the circle boundary inside the plane.
Edit:
The reason because i would prefer RANSAC over ordinary Least-Squares(LS) is its superior stability in the case of heavy outliers. The following image is showing an example comparision of LS vs. RANSAC. While the ideal model line is created by RANSAC the dashed line is created by LS.
The arguably easiest algorithm is called Least-Square Curve Fitting.
You may want to check the math,
or look at similar questions, such as polynomial least squares for image curve fitting
However I'd rather use a library for doing it.
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/