I am playing around with rgl and I have created a 3D rendering of the mouse brain, in which structures can be isolated and coloured separately.
The original data is a 3D array containing evenly spaced voxels.
Every voxel is coded with a structure ID.
Every structure is rendered separately as a mesh by marching cubes, and smoothed using Laplacian smoothing as implemented by Rvcg.
Some of these structures can be quite small, and it would make sense to look at them within the context of the whole brain structure.
One of the options is to create a low-threshold mesh of the whole set of voxels, so that only the outer surface of the brain is included in the mesh.
This surface can be smoothed and represented using a low alpha in rgl::shade3d colouring faces. This however seems to be quite taxing for the viewport as it slows down rotation etc especially when alpha levels are quite low.
I was wondering if there is any way to implement some sort of cel shading in rgl, e.g. outlining in solid colours the alpha hull of the 2D projection to the viewport in real time.
In case my description was not clear, here's a photoshopped example of what I'd need.
Ideally I would not render the gray transparent shell, only the outline.
Cel shading example
Does anybody know how to do that without getting deep into OpenGL?
Rendering transparent surfaces is slow because OpenGL requires the triangles making them up to be sorted from back to front. The sort order changes as you rotate, so you'll be doing a lot of sorting.
I can't think of any fast way to render the outline you want. One thing that might work given that you are starting from evenly spaced voxels is to render the outside surface using front="points", back="points", size = 1. Doing this with the ?surface3d example gives this fake transparency:
If that's not transparent enough, you might be able to improve it by getting rid of lighting (lit = FALSE), plotting in a colour close to the background (color = "gray90"), or some other thing like that. Doing both of those gives this:
You may also be able to cull your data so the surface has fewer vertices.
Related
There was a gif on the internet where someone used some sort of CAD and drew multiple vector pictures in it. On the first frame they zoom-in on a tiny dot, revealing there a whole new different vector picture just on a different scale, and then they proceed to zoom-in further on another tiny dot, revealing another detailed picture, repeating several times. here is the link to the gif
Or another similar example: imagine you have a time-series with a granularity of a millisecond per sample and you zoom out to reveal years-worth of data.
My questions are: how such a fine-detailed data, in the end, gets rendered, when a huge amount of data ends up getting aliased into a single pixel.
Do you have to go through the whole dataset to render that pixel (i.e. in case of time-series: go through million records to just average them out into 1 line or in case of CAD render whole vector picture and blur it into tiny dot), or there are certain level-of-detail optimizations that can be applied so that you don't have to do this?
If so, how do they work and where one can learn about it?
This is a very well known problem in games development. In the following I am assuming you are using a scene graph, a node-based tree of objects.
Typical solutions involve a mix of these techniques:
Level Of Detail (LOD): multiple resolutions of the same model, which are shown or hidden so that only one is "visible" at any time. When to hide and show is usually determined by the distance between camera and object, but you could also include the scale of the object as a factor. Modern 3d/CAD software will sometimes offer you automatic "simplification" of models, which can be used as the low res LOD models.
At the lowest level, you could even just use the object's bounding
box. Checking whether a bounding box is in view is only around 1-7 point checks depending on how you check. And you can utilise object parenting for transitive bounding boxes.
Clipping: if a polygon is not rendered in the view port at all, no need to render it. In the GIF you posted, when the camera zooms in on a new scene, what is left from the larger model is a single polygon in the background.
Re-scaling of world coordinates: as you zoom in, the coordinates for vertices become sub-zero floating point numbers. Given you want all coordinates as precise as possible and given modern CPUs can only handle floats with 64 bits precision (and often use only 32 for better performance), it's a good idea to reset the scaling of the visible objects. What I mean by that is that as your camera zooms in to say 1/1000 of the previous view, you can scale up the bigger objects by a factor of 1000, and at the same time adjust the camera position and focal length. Any newly attached small model would use its original scale, thus preserving its precision.
This transition would be invisible to the viewer, but allows you to stay within well-defined 3d coordinates while being able to zoom in infinitely.
On a higher level: As you zoom into something and the camera gets closer to an object, it appears as if the world grows bigger relative to the view. While normally the camera space is moving and the world gets multiplied by the camera's matrix, the same effect can be achieved by changing the world coordinates instead of the camera.
First, you can use caching. With tiles, like it's done in cartography. You'll still need to go over all the points, but after that you'll be able zoom-in/zoom-out quite rapidly.
But if you don't have extra memory for cache (not so much actually, much less than the data itself), or don't have time to go over all the points you can use probabilistic approach.
It can be as simple as peeking only every other point (or every 10th point or whatever suits you). It yields decent results for some data. Again in cartography it works quite well for shorelines, but not so well for houses or administrative boarders - anything with a lot of straight lines.
Or you can take a more hardcore probabilistic approach: randomly peek some points, and if, for example, there're 100 data points that hit pixel one and only 50 hit pixel two, then you can more or less safely assume that if you'll continue to peek points still pixel one will be twice as likely to be hit that pixel two. So you can just give up and draw pixel one with a twice more heavy color.
Also consider how much data you can and want to put in a pixel. If you'll draw a pixel in black and white, then there're only 256 variants of color. And you don't need to be more precise. Or if you're going to draw a pixel in full color then you still need to ask yourself: will anyone notice the difference between something like rgb(123,12,54) and rgb(123,11,54)?
I am writing a drawing program that is vector-based but should have drawing tools that behave more like raster-based tools. For example - when you draw with a graphics tablet pen, the resultant vector stroke, with pressure differences and all, is actually a fill. The vector curve just fits to the outside of the stroke. Also, if you pick up the eraser and erase part of this stroke, it only erases exactly where you erase at. It does not just delete vector points, but creates new ones where it has to. These pen and eraser strokes will also be of any geometry - with not only outlines on the outside, but also holes in the middle.
I puzzled for a long time over how to do this, and last night I got the idea of drawing the pen input to an offscreen bitmap (where each pixel is one bit - either touched or untouched by the pen stroke) and then when the stroke ends (pen is lifted up) the program vectorizes this bitmap, and then either places down the vector fill with appropriate color, or performs a boolean operation with the vectors underneath in order to erase.
I can make this work with raster drawing tools (so that you're not constantly drawing lines right on the visible surface, which doesn't look good if you're drawing with transparency), but I don't know how I would fit a vector curve to this one-bit bitmap. The operation has to be fast but not real-time, as it is done once after the pen is lifted up. It also has to create optimized geometry so that only the minimum number of bezier curve points needed to describe the geometry are used.
Does anyone have any suggestions, solutions, pointers, or references for how to do this? Or, is there maybe another way?
Let me explain my problem:
I have a black vector shape (let's say it's a series of joined, straight lines for now, but it'd be nice if I could also support quadratic curves).
I also have a rectangle of a predefined width and height. I'm going to place it on top of the black shape, and then take the union of the two.
My first issue is that I don't know how to quickly extract vector unions, but I think there is a well-defined formula I can figure out for myself.
My second, and more tricky issue is how to efficiently detect the position the rectangle needs to be in (i.e., what translation and rotation are needed by the matrices), in order to maximize the black, remaining after the union (see figure, below).
The red outlined shape below is ~33% black; the green is something like 85%; and there are positions for this shape & rectangle wherein either could have 100% coverage.
Obviously, I can brute-force this by trying every translation and rotation value for every point where at least part of the rectangle is touching the black shape, then keep track of the one with the most black coverage. The problem is, I can only try a finite number of positions (and may therefore miss the maximum). Apart from that, it feels very inefficient!
Can you think of a more efficient way of tackling this problem?
Something from my Uni days tells me that a Fourier transform might improve the efficiency here, but I can't figure out how I'd do that with a vector shape!
Three ideas that have promise of being faster and/or more precise than brute force search:
Suppose you have a 3d physics engine. Define a "cone-shaped" surface where the apex is at say (0,0,-1), the black polygon boundary on the z=0 plane with its centroid at the origin, and the cone surface is formed by connecting the apex with semi-infinite rays through the polygon boundary. Think of a party hat turned upside down and crumpled to the shape of the black polygon. Now constrain the rectangle to be parallel to the z=0 plane and initially so high above the cone (large z value) that it's easy to find a place where it's definitely "inside". Then let the rectangle fall downward under gravity, twisting about z and translating in x-y only as it touches the cone, staying inside all the way down until it settles and can't move any farther. The collision detection and force resolution of the physics engine takes care of the complexities. When it settles, it will be in a position of maximal coverage of the black polygon in a local sense. (If it settles with z<0, then coverage is 100%.) For the convex case it's probably a global maximum. To probabilistically improve the result for non-convex cases (like your example), you'd randomize the starting position, dropping the polygon many times, taking the best result. Note you don't really need a full blown physics engine (though they certainly exist in open source). It's enough to use collision resolution to tell you how to rotate and translate the rectangle in a pseudo-physical way as it twists and slides uniformly down the z axis as far as possible.
Different physics model. Suppose the black area is an attractive field generator in 2d following the usual inverse square rule like gravity and magnetism. Now let the rectangle drift in a damping medium responding to this field. It ought to settle with a maximal area overlapping the black area. There are problems with "nulls" like at the center of a donut, but I don't think these can ever be stable equillibria. Can they? The simulation could be easily done by modeling both shapes as particle swarms. Or since the rectangle is a simple shape and you are a physicist, you could come up with a closed form for the integral of attractive force between a point and the rectangle. This way only the black shape needs representation as particles. Come to think of it, if you can come up with a closed form for torque and linear attraction due to two triangles, then you can decompose both shapes with a (e.g. Delaunay) triangulation and get a precise answer. Unfortunately this discussion implies it can't be done analytically. So particle clouds may be the final solution. The good news is that modern processors, particularly GPUs, do very large particle computations with amazing speed. Edit: I implemented this quick and dirty. It works great for convex shapes, but concavities create stable points that aren't what you want. Using the example:
This problem is related to robot path planning. Looking at this literature may turn up some ideas In RPP you have obstacles and a robot and want to find a path the robot can travel while avoiding and/or sliding along them. If the robot is asymmetric and can rotate, then 2d planning is done in a 3d (toroidal) configuration space (C-space) where one dimension is rotation (so closes on itself). The idea is to "grow" the obstacles in C-space while shrinking the robot to a point. Growing the obstacles is achieved by computing Minkowski Differences.) If you decompose all polygons to convex shapes, then there is a simple "edge merge" algorithm for computing the MD.) When the C-space representation is complete, any 1d path that does not pierce the "grown" obstacles corresponds to continuous translation/rotation of the robot in world space that avoids the original obstacles. For your problem the white area is the obstacle and the rectangle is the robot. You're looking for any open point at all. This would correspond to 100% coverage. For the less than 100% case, the C-space would have to be a function on 3d that reflects how "bad" the intersection of the robot is with the obstacle rather than just a binary value. You're looking for the least bad point. C-space representation is an open research topic. An octree might work here.
Lots of details to think through in both cases, and they may not pan out at all, but at least these are frameworks to think more about the problem. The physics idea is a bit like using simulated spring systems to do graph layout, which has been very successful.
I don't believe it is possible to find the precise maximum for this problem, so you will need to make do with an approximation.
You could potentially render the vector image into a bitmap and use Haar features for this - they provide a very quick O(1) way of calculating the average colour of a rectangular region.
You'd still need to perform this multiple times for different rotations and positions, but it would bring it algorithmic complexity down from a naive O(n^5) to O(n^3) which may be acceptably fast. (with n here being the size of the different degrees of freedom you are scanning)
Have you thought to keep track of the remaining white space inside the blocks with something like if whitespace !== 0?
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.
Banging my head on the wall with this one...
Google searches so far null...
I have a ton of over lapping circles in a mapping program...they represent radar ranges for installations such as fixed operating bases, strategic facilities, anti-aircraft assets...
Most if not all overlap one or many of their bretheren...some may stand alone...Imagine an outlying installation with limited range...
I am trying to draw the UNION of the aggregated collection of circle objects...technically ellipses bound by rectangles...
I am trying to draw the outside boundary of the air defense system...I want to eliminate all drawing of the portion of the child ellipses that fall within that outer boundry...
If an outlying station is standing alone so to speak it should be drawn as a simple circle...
Should I link a picture?
What the heck here it is...image is a bit big so I linked it
image 1024x1024
What I want to draw is union outline of the British and then of the Germans...
So far I can't figure out how to this in C# GDI...
I Do not want to fill the path using the Winding Mode Flag...I want to Draw the OUTLINE..
Any help greatly appreciated...
Oneway
Create a new image, render the circles in solid colour to that area, then overlay that image on your map at, say, 50% opacity.
Alternatively, run an edge detect on that solid-colour image to find the overall outline.