I'm looking for a library to which nodes and edges can be supplied and which generates a coordinate list of all the nodes laid out nicely. However, it should be possible to supply fixed positions for some, but not all nodes which the layout algorithm should respect.
I have tried graphviz (fdp, neato) so far, which does not seem able to keep the position of certain nodes and built the layout around them.
The library has to be usable with python, so it should be either python or c/c++ so we could write our own binding.
The following pictures illustrates exactly what I'm looking for (this is the uDraw-project, which does not seem to exist as a library).
You can do this in graphviz in reverse, if that is useful to you. To do that, you would plot the right-hand graph first, and then plot the left-hand graph with nodes 15, 16 and 17 set to style=invis. That would give you much the same layout as is shown here.
A problem that I could perceive with plotting the left-hand graph first is that the software (dot or something else) would naturally try to plot a "nice-looking" graph without nodes 15, 16 and 17 and that might not leave enough space for nodes 15, 16 and 17 to be fitted in if they're needed later. For example, if we tried to insert a node 12a between nodes 11 and 12, there wouldn't be room for that node in the graphs shown above. On the other hand, if node 12a was initially plotted but invisible, then the software would allocate the space for it, where it could be included later.
Related
For one of my classes, I made a 3D graphing application (using Visual Basic). It takes in a string (z=f(x,y)) as input, parses it into RPN notation, then evaluates and graphs the equation. While it did work, it took about 20 seconds to graph. I would have liked to add slide bars to rotate the graph vertically and horizontally, but it was definitely too slow to allow that.
Does anyone know what programming languages would be best for this type of thing? Ideally, I will be able to smoothly rotate the function once it is graphed.
Also, I’m trying to find a better way to rotate the function. Right now, I evaluate it at a bunch of points, and then plot the points to the screen. Every time it is rotated, it must be re-evaluated and plot all the new points. This takes just as long as the original graph process, as it basically treats it as a completely new function.
Lastly, I need a better way to display the graph. Currently (using VB with visual studio) I plot 200,000 points to a chart, but this does not look great by any means. Eventually, I would like to be able to change color based on height, and other graphics manipulation to make it look better.
To be clear, I am not asking for someone to do any of this for me, but rather the means to go about coding this in an efficient way. I will greatly appreciate any advice anyone can give to help with any of these three concerns.
So I will explain how I would go about it using C++ and OpenGL. This doesn't mean those are the tools that you must use, it's just those are standard graphics tools.
Your function's surface is essentially a 2D manifold, which has the nice property of having an intuitive mapping to a 2D space. What is commonly referred to as UV mapping.
What you should do is pick the ranges for the rectangle domain you want to display (minimum x, maximum x, minimum y, maximum y) And make 2 nested for loops of the form:
// Pseudocode
for (x=minimum; x<maximum; x++)
for (y=minimum; y=maximum; y++)
3D point = (x,y, f(x,y))
Store all of these points into a container (std vector for c++ works fine) and this will be your "mesh".
This is done once, prior to rendering. You then render those points using, for example GL_POINTS, and rotate your graph mesh using rotations on the GPU.
This will only show scattered points, not a surface.
If you also wish to show the surface of your function, and not just the points, you can triangulate that set of points fairly easily.
Group each 4 contiguous vertices (i.e the vertices at indices <x,y>, <x+1,y>, <x+1,y>, <x+1,y+1>) and create the 2 triangles:
(<x,y>, <x+1,y>, <x,y+1>), (<x+1,y>, <x+1,y+1>, <x,y+1>)
This will fill triangulate the surface of your mesh.
Essentially you only need to build your mesh once, and this way rendering should be 60 fps for something with 20 000 vertices, regardless of whether you only render points or triangles too.
Programming language is mostly not relevant, so VB itself is probably not the issue. You can have the same issues in Python, C#, C++, etc. Of course you must master the programming language you choose.
One key aspect is using the right algorithms and data-structures. Proper use of memory allocations and memory layout for maximizing CPU (and GPU) cache are also key. Then you must take advantage of the platform and hardware capabilities (GPU and Multithreading). For the last point you definetely need to use a graphics library such as OpenGL or Vulkan.
I'm looking for a python 3 module that can generate a visual representation of a graph. Ideally I would give it a list of nodes and a list of connection, as well as some small amount of data associated with those things, and it would open a window (but an image saved on disk is fine) showing said nodes connected as specified. I don't want to specify the positions of the nodes, instead I'd like the software to arrange them in a way that minimizes edge crossings at least approximately.
Is there any such module? All I've been able to find are plotters and such...
If there is none, an easy-to-learn graphics module would do: I have never done any graphics things.
You can take a look at networkx. It offers the possibility to draw graphs with matplotlib
STL is the most popular 3d model file format for 3d printing. It records triangular surfaces that makes up a 3d shape.
I read the specification the STL file format. It is a rather simple format. Each triangle is represented by 12 float point number. The first 3 define the normal vector, and the next 9 define three vertices. But here's one question. Three vertices are sufficient to define a triangle. The normal vector can be computed by taking the cross product of two vectors (each pointing from a vertex to another).
I know that a normal vector can be useful in rendering, and by including a normal vector, the program doesn't have to compute the normal vectors every time it loads the same model. But I wonder what would happen if the creation software include wrong normal vectors on purpose? Would it produce wrong results in the rendering software?
On the other hand, 3 vertices says everything about a triangle. Include normal vectors will allow logical conflicts in the information and increase the size of file by 33%. Normal vectors can be computed by the rendering software under reasonable amount of time if necessary. So why should the format include it? The format was created in 1987 for stereolithographic 3D printing. Was computing normal vectors to costly to computers back then?
I read in a thread that Autodesk Meshmixer would disregard the normal vector and graph triangles according to the vertices. Providing wrong normal vector doesn't seem to change the result.
Why do Stereolithography (.STL) files require each triangle to have a normal vector?
At least when using Cura to slice a model, the direction of the surface normal can make a difference. I have regularly run into STL files that look just find when rendered as solid objects in any viewer, but because some faces have the wrong direction of the surface normal, the slicer "thinks" that a region (typically concave) which should be empty is part of the interior, and the slicer creates a "top layer" covering up the details of the concave region. (And this was with an STL exported from a Meshmixer file that was imported from some SketchUp source).
FWIW, Meshmixer has a FlipSurfaceNormals tool to help deal with this.
I'm halfway there please see the edit
OK here's my problem, I'm generating a graph of a python module, including all the files with their functions/methods/classes.
I want to arrange it so, that nodes gather in circles around their parent nodes, currently everything is on one gargantuan horizontal row, which makes the thing >50k pixels wide and also let's the svg converter fail(only renders about the half of the graph).
I went through the docs but couldn't find anything that seems to do the trick.
So the question is:
Is there a simple way to do this or do I have to layout the whole thing by myself? :/
EDIT:
Thanks to Andrews comment I've got the right layout, the only problem now is that it's a bit to "compact"... so the question now is, how to fix this?
i've mentioned all of the most significant parameters that influence your current layout and then suggested values for those parameters. Still, i suspect you can get the layout that you want just from applying a couple of these suggestions.
reduce the edge weight, eg, [weight=0.5]; this will make the
edges longer, causing the tight
clusters you currently see in your
graph to 'fan out'.
get rid of the node borders, node_A
[color=none; shape=plaintext];
especially for oval-shaped nodes, a
substantial fraction of the total
node space is 'unused' (ie, not used
to display the node label).
explicitly set the font size for
the nodes (the node borders are
enlarged so that they surround the
node text, which means that the font
size and amount of text for a given
node has a significant effect on its
size); [fontsize=11] should be large
enough to be legible yet also reduce
the 'cluttered' appearance (the
default size is 14).
increase minimum separation between
nodes, via 'nodesep'; eg, nodesep=2.0; this will
directly address your objection
regarding your graph being "too
compact." ('nodesep' and 'ranksep'
probably affect how dot draws a graph
more than any other parameters for
node, edge, or graph. In your case,
it looks like you have only two ranks
of nodes; 'ranksep' sets the minimum
distance between nodes of different
ranks--it looks like all of the nodes
that comprise your graph are of the
same rank (except for few top level
nodes in the centers).
explicitly set total graph size, eg,
size="7.75,10.25" (ensures that your
graph fits on an 8.5 x 11 page and
that it occupies the entire space)
And one purely aesthetic suggestion
that at most will only help your
graph appear less cluttered: the
default fontcolor for both edges and
nodes is black. The majority of the
ink on your graph is from those two
structures (particularly if you
remove the node borders), so i would
for instance set either the node
(text) fontcolor or the edge
fontcolor to "blue" to help the eye
distinguish the two sets of graph
structures.
If it is too compact, you will want to mess with the edge length. You have a couple options depending on the graph layout:
If your layout is sfdp or fdp, tweak the graph property K. Default is 0.3.
For neato (or fdp), tweak the edge property len. Default is 1.0 for neato and 0.3 for fdp.
For dot you can use the edge property minlen which is the minimum edge length. Default is 1.
You might also want to mess with the graph property model which determines clustering behavior. Specifically, try subset. I believe this handles len for you:
http://www.graphviz.org/doc/info/attrs.html#d:model
Also, you can remove overlaps all together with scaling techniques: http://www.graphviz.org/doc/info/attrs.html#d:overlap
I have around 500 nodes and used doug's recommendation.
This is my sample code that works (in python):
f = Digraph('companies',filename='companies.gv',
edge_attr={'weight':'1',
'fontsize':'11',
'fontcolor':'blue',
'len':'4'},
graph_attr={'fixedsize':'false',
'bgcolor':'transparent'},
node_attr={'fontsize':'11',
'shape':'plaintext',
'color':'none',
'fontcolor':'black'})
f.attr(layout="neato")
f.attr(nodesep='3')
f.attr(ranksep='3')
f.attr(size='5000,5000')
I am taking an input, e.g.
4
1 3
1 2
2 4
First line is number of nodes, lines after that are the edges. I have to attempt to color the graph, and if I can't, I need to list a cycle in the graph that is causing the error.
This is fine so far, except one of the graphs contains 1,000,000 nodes. Everytime I try to use it I get a Stack Overflow error, even though I streamlined it more, and raised the max heap size of eclipse to 1024m.
I'm not asking for code, just asking if I am doing something blatantly wrong to keep getting errors.
Maybe you could optimize your cycle detection algorithm.
This might help you: http://en.wikipedia.org/wiki/Cycle_detection
Other than that, a million nodes plus adjacency matrix might as well be too much to handle at once, so perhaps there's a way to just load parts of the graph at a time.
If it's a bipartite graph you can always colour it with only two colours (e.g. colour the first partition white, and the second partition black).
Usually when one thinks of colouring a graph he should specify the number of colours. You can always colour a graph by assigning to each node a different colour. Another example: for planar graphs only four colour are required. However, for most graphs the [chromatic number] of a graph is [NP].
[NP] http://en.wikipedia.org/wiki/Karp%27s_21_NP-complete_problems
[chromatic number] http://en.wikipedia.org/wiki/Graph_coloring
Well, this IS an NP complete problem (longest cycle), so this sort of thing IS likely to happen.
I'd probably just bump the heap again, and let it run...
EDIT: Never mind. got my reduction backwards.