GraphViz: fixing only the y position of nodes - graphviz

I want to pin the y position of nodes, but have the x positions aligned automatically according to force direction.
Each y position is individual because it corresponds to a coordinate on the y axis, and there are several thousand nodes, so I don't think using a sub graph for each node is reasonable.

Wrote my own Java2D / PDFGraphics2D function with a simple force directed layout. GraphViz is quite annoying when you have already a quite clear idea about how the layout should look.

Related

BVH trees - ways to determine child nodes intersection order?

just to mention that my math skills are not great and i need to ask for a little help here !
I am now trying to implement a stack less BVH traversal function using this paper:
https://graphics.cg.uni-saarland.de/fileadmin/cguds/papers/2011/hapala_sccg2011/hapala_sccg2011.pdf
I am having it working except i am likely not having the both child traversal order correct which results in wrong image.
In point ( 3 Algorithm outline ) they mention a couple of methods to determine the right order:
For the traversal order there are various different alternatives. One
often-used option is to store, for each node, the coordinate axis
along which the builder split the parent node, and to use the ray’s
direction sign in this dimension to determine the two nodes’ traversal
order.
Let's say i am having the split axis index as 0, 1, 2 for X, Y, Z and the ray direction... It can determine the split axis by computing the maximum separation axis of both nodes centroids on the fly which i am also having...
So, the question is what would be the way (math) to determine the nodes traversal order by using the ray direction and the split axis ?
use the ray’s direction sign in this dimension to determine the two nodes’ traversal order.
Suppose your ray has direction (0.707, 0, -0.707).
For that ray:
If you determine the parent's split axis to be X (i.e. two children share a boundary on the YZ plane), then your ray's direction sign in X is positive (0.707), and you should traverse the child whose centroid has the higher X centroid coordinate first.
If you determine the parent's split axis to by Y (i.e. two children share a boundary on the XZ plane), then your ray's direction in Y is unsigned (0) and you'll have to decide what to do. The details of what you do in this case are up to you (pick a direction, move on to the next coordinate, etc) but acting consistently is the key.
If you determine the parent's split axis to be Z (i.e. to children share a boundary on the XY plane), then your ray's direction in Z is negative (-.707), and you should traverse the child whose centroid has the lower Z coordinate first.

too many collisions in D3 Sankey when x-Position of nodes is fixed

I adopted the trick from
d3 sankey charts - manually position node along x axis
to manually control the x-position of my nodes. But many of the links end up crossing over each other:
(I set the node widths to zero). I know a Sankey diagram with no link overlaps can be achieved, because the data corresponds to a dendrogram.
Increasing the number of iterations in the .layout(...) command does not solve the problem. Can someone please help?

Meaning of node size in force layout and calculating radius

What is the node size parameter in a D3.js force-layout?
Is it the pixel area on the screen, the radius or something completely different?
Lastly, how do I calculate the radius from that size value?
Edit: I've been confused about a D3 example, which had a size variable for the nodes objects and I thought that this variable was used in the force-layout similar to the source and target parameters. That is not the case. Consequently, this question doesn't make sense.
The size is in screen coordinates, i.e. pixels. Note that this is not a hard limit, i.e. nodes may move outside of this area. I assume that by "radius" you mean the radius of the node circles -- the simple answer is that the two are completely unrelated.

marching cubes efficiency- you can reduce 3/4rs of the edge calculations?

Normal marching cubes finds 12 edges per cube, but you can do 3 edges per cube, save the edges inside an array, and then go through the cubes again, referencing the edges from the cubes adjacent rather than calculating them.
The process to reference adjacent cubes isn't clearly discussed on the Internet so anyone using marching cubes would be welcome to help find the details of the solution. do you know an implementation already?
here is a picture showing the 3 edges in yellow that you need for each cube, instead of 12.
EDIT- I just found this solution, although it's just a part of it:
Imagine 3 edges coming from the corner of the cube with lowerest coordinates. Then all other edges just belong to other cubes. If our cube has coordinates (x,y,z), the neiboring cubes have coordinates (x+1,y,z), (x,y+1,z), (x,y,z+1), (x+1,y+1,z), (x+1,y,z+1), (x,y+1,z+1). You can imagine the edge as a vector. Then the corner of the cube have edges (1,0,0), (0,1,0), (0,0,1). The cube with coordinates (x+1,y,z) have edges (0,1,0) and (0,0,1) that belong to our cube. The cube (x+1,y+1,z) has only one edge (0,0,1) that belongs to our cube. So if you store 4 elements for the cube you can access them like that:
edge1 = cube[x][y][z][0];
edge2 = cube[x][y][z][1];
edge3 = cube[x][y][z][2];
edge4 = cube[x+1][y][z][1];
edge5 = cube[x+1][y][z][2];
edge6 = cube[x][y+1][z][0];
edge7 = cube[x][y+1][z][2];
edge8 = cube[x][y][z+1][0];
edge9 = cube[x][y][z+1][1];
edge10 = cube[x+1][y+1][z][2];
edge11 = cube[x+1][y][z+1][1];
edge12 = cube[x][y+1][z+1][0];
Now which points edge7 connect? The answer is (x,y+1,z) and (x,y+1,z)+(0,0,1)=(x,y+1,z+1).
Now which cubes edge7 connect? It is more harder. We see that coordinate z is changes along the edge this means that neibour cube has the same z coordinate. Now all others coordinates change. Where we have +1, the cube has large coordinate. Where we have +0, the cube has smaller coordinates. So the edge connects cubes (x,y,z) and (x-1,y+1,z). Other 2 cubes that has the same edge are (x,y+1,z) and (x-1,y,z).
-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=--=-=
EDIT2-
So I am doing this, and it isn't so simple. I have a loop which simultaneously calculate 8 points, 12 edges, the interpolation of edges, the bit values and a vertex the values for the edges, all in one loop.
so I am doing a new loop previous to it to calculate as much as possible and place it in arrays to used in the complicated loop.
I can recycle the interpolated values of the intersection points along edges, in an array, although I will have to recalculate all the points again in the complicated loop, because the values of the points I used to decide bit numbers that reference values in the vertex table. That confuses me! I thought that once I have the edge intersection values, I could use those directly to get the triangle tables, without having to calculate the points all over again!
in fact no.
anyway, here is another bit of information with someone that already did it, if only it was readable!
http://www.new-npac.org/projects/sv2all/sv2/vtk/patented/vtkImageMarchingCubes.cxx
scroll to this line: Cubes are responsible for edges on their min faces.
A simple way to reduce edge calculations in the way you are suggesting is to compute cubes one axis aligned plane at a time.
If you kept all of the cubes, with their edges, in memory, it would be easy to compute each edge only once and to find adjacent edges by indexing. However, you usually don't want to keep all the cubes in memory at once because of the space requirements.
A solution to this is to compute one plane of cubes at a time. i.e. an axis aligned cross-section, starting from one side and progressing to the opposite side. You then only need to keep at most two full planes of cubes in memory at a time. As you move through each plane you can reference shared edges in the previous plane and previously computed cubes in the current plane. As you move to the next plane you can deallocate the plane you will no longer need.
Edit: This article discusses doing just what I suggest:
http://alphanew.net/index.php?section=articles&site=marchoptim&lang=eng
Funny, because when I implemented my own MCs I came up with similar solution.
When you start working with MCs you treat them as a distinct cubes but if you want to go for high performance you'll need to create entire mesh as a whole, and creating vertex indices etc. is not so easy here. It gets even more interesting when you want to add smooth per-vertex normals :).
To solve this I created a simple index cache mechanism to store vertex indices for each edge.
Then, for each computed edge I have cube position x,y,z and edge index and I do as follows:
For each axis:
if the edge is on '+' side of axis:
replace edge index with its '-' side sibling
increment cube position along axis
This simple operation gives me the correct cube position, and edge index of 0,1,2. Then I compute a total cache index from x,y,z,edgeIndex values with simple bit rotations.
When I have cache index I check if it's bigger than -1. If it is then there was an already computed vertex at this edge and I can reuse it. If it's -1 I need to create a new vertex and store its index in the cache. This way you'll compute each vertex only once, and you can even add a normal value shared between every triangle containing your vertex.
Yes, I think I do it similar to kolenda. I have a struct with 5 ints: (cube)index and 4 vertexindices (A, B, C, D).
for the most inner loop (x), I have just lastXCache and nextXCache. On the 4 edges pointing in the -x direction, i ask if lastXCache.A != -1 and if so, assign the previously calculated value, etc.
In the +x direction I store calculated vertices in nextXCache. when cube is done: lastXCache = nextXCache;
For y and z direction it needs to be a list (unity term for mutable array), next y is next row (so sizex) and next z is the next plane (so sizex * sizey)
only diadvantage is that this way it has to run cube after cube, so serially. But you can calculate different chunks in parallel.
Another way I thought of that could be more parallel would need 2 passes: 1. calculate 3 edges every cube, when 1 is done -> 2. draw the triangles.
Don't really know what is better, but the way it actually works seems to be fast enough. even better with unity jobs. Create one IJob for 1 chunk/mesh.

Packing rectangles for compact representation

I am looking for pointers to the solution of the following problem: I have a set of rectangles, whose height is known and x-positions also and I want to pack them in the more compact form. With a little drawing (where all rectangles are of the same width, but the width may vary in real life), i would like, instead of.
-r1-
-r2--
-r3--
-r4-
-r5--
something like.
-r1- -r3--
-r2-- -r4-
-r5--
All hints will be appreciated. I am not necessarily looking for "the" best solution.
Your problem is a simpler variant, but you might get some tips reading about heuristics developed for the "binpacking" problem. There has been a lot written about this, but this page is a good start.
Topcoder had a competition to solve the 3D version of this problem. The winner discussed his approach here, it might be an interesting read for you.
Are the rectangles all of the same height? If they are, and the problem is just which row to put each rectangle in, then the problem boils down to a series of constraints over all pairs of rectangles (X,Y) of the form "rectangle X cannot be in the same row as rectangle Y" when rectangle X overlaps in the x-direction with rectangle Y.
A 'greedy' algorithm for this sorts the rectangles from left to right, then assigns each rectangle in turn to the lowest-numbered row in which it fits. Because the rectangles are being processed from left to right, one only needs to worry about whether the left hand edge of the current rectangle will overlap any other rectangles, which simplifies the overlap detection algorithm somewhat.
I can't prove that this is gives the optimal solution, but on the other hand can't think of any counterexamples offhand either. Anyone?
Something like this?
Sort your collection of rectangles by x-position
write a method that checks which rectangles are present on a certain interval of the x-axis
Collection<Rectangle> overlaps (int startx, int endx, Collection<Rectangle> rects){
...
}
loop over the collection of rectangles
Collection<Rectangle> toDraw;
Collection<Rectangle> drawn;
foreach (Rectangle r in toDraw){
Collection<Rectangle> overlapping = overlaps (r.x, r.x+r.width, drawn);
int y = 0;
foreach(Rectangle overlapRect in overlapping){
y += overlapRect.height;
}
drawRectangle(y, Rectangle);
drawn.add(r);
}
Put a tetris-like game into you website. Generate the blocks that fall and the size of the play area based on your paramters. Award points to players based on the compactness (less free space = more points) of their design. Get your website visitors to perform the work for you.
I had worked on a problem like this before. The most intuitive picture is probably one where the large rectangles are on the bottom, and the smaller ones are on top, kinda like putting them all in a container and shaking it so the heavy ones fall to the bottom. So to accomplish this, first sort your array in order of decreasing area (or width) -- we will process the large items first and build the picture ground up.
Now the problem is to assign y-coordinates to a set of rectangles whose x-coordinates are given, if I understand you correctly.
Iterate over your array of rectangles. For each rectangle, initialize the rectangle's y-coordinate to 0. Then loop by increasing this rectangle's y-coordinate until it does not intersect with any of the previously placed rectangles (you need to keep track of which rectangles have been previously placed). Commit to the y-coordinate you just found, and continue on to process the next rectangle.

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