Merge pull request 'Python package' (#1) from python_package into main

Reviewed-on: #1
This commit is contained in:
h4kor 2022-11-20 16:14:55 +00:00
commit 407a08d1f7
15 changed files with 518 additions and 247 deletions

2
.gitignore vendored
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@ -1,2 +1,4 @@
/target /target
result/ result/
venv/

3
.vscode/settings.json vendored Normal file
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@ -0,0 +1,3 @@
{
"editor.formatOnSave": true,
}

254
Cargo.lock generated
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@ -2,6 +2,18 @@
# It is not intended for manual editing. # It is not intended for manual editing.
version = 3 version = 3
[[package]]
name = "autocfg"
version = "1.1.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
[[package]]
name = "bitflags"
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[[package]] [[package]]
name = "cfg-if" name = "cfg-if"
version = "1.0.0" version = "1.0.0"
@ -20,24 +32,157 @@ dependencies = [
] ]
[[package]] [[package]]
name = "graph" name = "graph_force"
version = "0.1.0" version = "0.1.0"
dependencies = [ dependencies = [
"pyo3",
"rand", "rand",
] ]
[[package]]
name = "indoc"
version = "1.0.7"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "adab1eaa3408fb7f0c777a73e7465fd5656136fc93b670eb6df3c88c2c1344e3"
[[package]] [[package]]
name = "libc" name = "libc"
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source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "fc7fcc620a3bff7cdd7a365be3376c97191aeaccc2a603e600951e452615bf89" checksum = "fc7fcc620a3bff7cdd7a365be3376c97191aeaccc2a603e600951e452615bf89"
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"redox_syscall",
"smallvec",
"windows-sys",
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"indoc",
"libc",
"memoffset",
"parking_lot",
"pyo3-build-config",
"pyo3-ffi",
"pyo3-macros",
"unindent",
]
[[package]]
name = "pyo3-build-config"
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"pyo3-build-config",
]
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name = "pyo3-macros"
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dependencies = [
"proc-macro2",
"pyo3-macros-backend",
"quote",
"syn",
]
[[package]]
name = "pyo3-macros-backend"
version = "0.17.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "c8df9be978a2d2f0cdebabb03206ed73b11314701a5bfe71b0d753b81997777f"
dependencies = [
"proc-macro2",
"quote",
"syn",
]
[[package]]
name = "quote"
version = "1.0.21"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "bbe448f377a7d6961e30f5955f9b8d106c3f5e449d493ee1b125c1d43c2b5179"
dependencies = [
"proc-macro2",
]
[[package]] [[package]]
name = "rand" name = "rand"
version = "0.8.5" version = "0.8.5"
@ -68,8 +213,115 @@ dependencies = [
"getrandom", "getrandom",
] ]
[[package]]
name = "redox_syscall"
version = "0.2.16"
source = "registry+https://github.com/rust-lang/crates.io-index"
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]
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"windows_i686_gnu",
"windows_i686_msvc",
"windows_x86_64_gnu",
"windows_x86_64_gnullvm",
"windows_x86_64_msvc",
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@ -1,9 +1,13 @@
[package] [package]
name = "graph" name = "graph_force"
version = "0.1.0" version = "0.1.0"
edition = "2021" edition = "2021"
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
[lib]
name = "graph_force"
crate-type = ["cdylib"]
[dependencies] [dependencies]
rand = "0.8.5" rand = "0.8.5"
pyo3 = { version = "0.17.3", features = ["extension-module"] }

25
README.md Normal file
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@ -0,0 +1,25 @@
# Graph Force
A python/rust library for embedding graphs in 2D space, using force-directed layouts.
## Development
### Setup
```
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
```
### Build
```
maturin develop
```
## Usage
```python
import graph_force
edges = [(0, 1), (1, 2), (2, 3), (3, 0)]
pos = graph_force.layout_from_edge_list(4, edges)
```

14
pyproject.toml Normal file
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@ -0,0 +1,14 @@
[build-system]
requires = ["maturin>=0.14,<0.15"]
build-backend = "maturin"
[project]
name = "graph_force"
requires-python = ">=3.7"
classifiers = [
"Programming Language :: Rust",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
]

1
requirements.txt Normal file
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@ -0,0 +1 @@
maturin==0.14.1

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@ -1,3 +1,4 @@
use rand::Rng;
use std::sync::{Arc, RwLock}; use std::sync::{Arc, RwLock};
pub struct Node { pub struct Node {
pub x: f32, pub x: f32,
@ -10,3 +11,26 @@ pub struct Edge {
pub type EdgeMatrix = Arc<RwLock<Vec<Vec<Edge>>>>; pub type EdgeMatrix = Arc<RwLock<Vec<Vec<Edge>>>>;
pub type NodeVector = Arc<Vec<RwLock<Node>>>; pub type NodeVector = Arc<Vec<RwLock<Node>>>;
pub fn new_edge_matrix(size: usize) -> EdgeMatrix {
let mut matrix = Vec::with_capacity(size);
for _ in 0..size {
let mut row = Vec::with_capacity(size);
for _ in 0..size {
row.push(Edge { weight: 0.0 });
}
matrix.push(row);
}
Arc::new(RwLock::new(matrix))
}
pub fn new_node_vector(size: usize) -> NodeVector {
let mut nodes = Vec::with_capacity(size);
for _ in 0..size {
nodes.push(RwLock::new(Node {
x: rand::thread_rng().gen_range(-0.5..0.5),
y: rand::thread_rng().gen_range(-0.5..0.5),
}));
}
Arc::new(nodes)
}

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src/lib.rs Normal file
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@ -0,0 +1,25 @@
mod graph;
mod runner;
mod spring_model;
mod utils;
use pyo3::prelude::*;
/// Formats the sum of two numbers as string.
#[pyfunction(number_of_nodes, edges, "*", iter = 500, threads = 0)]
fn layout_from_edge_list(
number_of_nodes: usize,
edges: Vec<(u32, u32)>,
iter: usize,
threads: usize,
) -> PyResult<Vec<(f32, f32)>> {
let r = runner::Runner::new(iter, threads);
Ok(r.layout(number_of_nodes, edges))
}
/// A Python module implemented in Rust.
#[pymodule]
fn graph_force(_py: Python, m: &PyModule) -> PyResult<()> {
m.add_function(wrap_pyfunction!(layout_from_edge_list, m)?)?;
Ok(())
}

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@ -1,116 +0,0 @@
mod utils;
mod spring_model;
mod my_model;
mod graph;
use rand::Rng;
use std::fs::File;
use std::io::prelude::*;
use std::sync::{Arc, RwLock};
use std::thread;
use graph::{EdgeMatrix, NodeVector, Node, Edge};
fn nodes_list(size: usize) -> NodeVector {
let mut nodes = Vec::new();
for _ in 0..size {
let node = RwLock::new(Node {
x: rand::thread_rng().gen_range(-0.5..0.5),
y: rand::thread_rng().gen_range(-0.5..0.5),
});
nodes.push(node);
}
Arc::new(nodes)
}
fn connection_matrix(size: usize) -> EdgeMatrix {
let mut matrix = Vec::with_capacity(size);
for _ in 0..size {
let mut row = Vec::with_capacity(size);
for _ in 0..size {
row.push(Edge { weight: 0.0 });
}
matrix.push(row);
}
Arc::new(RwLock::new(matrix))
}
/**
* Read Graph data from file
* Format:
* - Little endian
* - 4 bytes: number of nodes(int)
* - 12 bytes: nodeA(int), nodeB(int), weight(float)
*/
fn read_graph(file_name: &str) -> (usize, EdgeMatrix) {
let mut file = File::open(file_name).expect("file not found");
let mut size_buffer = [0; 4];
file.read_exact(&mut size_buffer).expect("buffer overflow");
let size = u32::from_le_bytes(size_buffer) as usize;
let matrix_ptr = connection_matrix(size);
{
let mut matrix = matrix_ptr.write().unwrap();
let mut buffer = [0; 12];
while file.read_exact(&mut buffer).is_ok() {
let node_a = u32::from_le_bytes(buffer[0..4].try_into().unwrap()) as usize;
let node_b = u32::from_le_bytes(buffer[4..8].try_into().unwrap()) as usize;
let weight = f32::from_le_bytes(buffer[8..12].try_into().unwrap());
matrix[node_a][node_b].weight = weight;
matrix[node_b][node_a].weight = weight;
}
}
(size, matrix_ptr)
}
fn main() -> std::io::Result<()> {
const ITER: usize = 5000;
const THREADS: usize = 8;
// let edges = connection_matrix(size);
let (size, edges): (usize, EdgeMatrix) = read_graph("../debug_graph.bin");
println!("Size: {}", size);
let mut nodes = nodes_list(size);
let mut nodes_next = nodes_list(size);
// let model = Arc::new(RwLock::new(spring_model::InitialModel::new(edges, size)));
let model = Arc::new(RwLock::new(my_model::MyModel::new(edges, size, ITER)));
let chunks = utils::gen_chunks(size, THREADS);
for epoch in 0..ITER {
model.write().unwrap().prepare(&nodes);
let mut handles = vec![];
for i in 0..THREADS {
let nodes = nodes.clone();
let nodes_next = nodes_next.clone();
let chunk = chunks[i].clone();
let model = model.clone();
let handle = thread::spawn(move || {
for n in chunk {
let update = model.read().unwrap().step(&nodes,n);
let mut result = nodes_next[n].write().unwrap();
result.x = update.x;
result.y = update.y;
}
});
handles.push(handle);
}
for handle in handles {
handle.join().unwrap();
}
// swap nodes and nodes_next
let tmp = nodes.clone();
nodes = nodes_next.clone();
nodes_next = tmp.clone();
let mut file = File::create(format!("result/{:04}.txt", epoch))?;
for i in 0..size {
let node = nodes[i].read().unwrap();
// println!("{} {}", node.x, node.y);
file.write_all(format!("{} {}\n", node.x, node.y).as_bytes())?;
}
}
Ok(())
}

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@ -1,97 +0,0 @@
use crate::graph::{EdgeMatrix, NodeVector, Node};
pub struct MyModel {
edges: EdgeMatrix,
ranks: Vec<f32>,
size: usize,
opt_dist: f32,
c: f32,
dc: f32,
}
impl MyModel {
pub fn new(edges: EdgeMatrix, size: usize, iterations: usize) -> MyModel {
let opt_dist = 1.0;
let c = 0.1;
let mut ranks = vec![0.0; size];
{
let edges = edges.read().unwrap();
for i in 0..size {
ranks[i] = edges[i].iter().map(|e| e.weight).sum();
}
}
MyModel{
edges,
ranks,
size,
opt_dist,
c: c,
dc: c / ((iterations + 1) as f32)
}
}
pub fn prepare(& mut self, _nodes: &NodeVector) {
self.c -= self.dc;
}
pub fn step(&self, nodes: &NodeVector, i_node: usize) -> Node {
let node = nodes[i_node].read().unwrap();
let edges = self.edges.read().unwrap();
let node_x = node.x;
let node_y = node.y;
let mut sum_x = 0.0;
let mut sum_y = 0.0;
for o in 0..self.size {
if o == i_node {
continue;
}
let o_x: f32;
let o_y: f32;
{
let other = nodes[o].read().unwrap();
o_x = other.x;
o_y = other.y;
}
let d_x = o_x - node_x;
let d_y = o_y - node_y;
let dist = (d_x * d_x + d_y * d_y).sqrt();
let unit_x = d_x / dist;
let unit_y = d_y / dist;
let edge = edges[i_node][o].weight;
if edge == 0.0 {
let f_rep = dist.powi(2).recip().min(self.opt_dist);
let f_rep_x = f_rep * unit_x;
let f_rep_y = f_rep * unit_y;
sum_x -= f_rep_x;
sum_y -= f_rep_y;
} else {
let f_spring = 0.5 * (dist - self.opt_dist);
let f_spring_x = f_spring * unit_x;
let f_spring_y = f_spring * unit_y;
sum_x += f_spring_x;
sum_y += f_spring_y;
}
}
// limit the movement
// TODO: find a good upper bound
let sum_l = (sum_x * sum_x + sum_y * sum_y).sqrt().max(1e-6).recip() * self.c;
let sum_x = sum_x * sum_l;
let sum_y = sum_y * sum_l;
Node {
x: node_x + sum_x,
y: node_y + sum_y,
}
}
}

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src/reader.rs Normal file
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@ -0,0 +1,26 @@
/**
* Read Graph data from file
* Format:
* - Little endian
* - 4 bytes: number of nodes(int)
* - 12 bytes: nodeA(int), nodeB(int), weight(float)
*/
fn read_graph(file_name: &str) -> (usize, EdgeMatrix) {
let mut file = File::open(file_name).expect("file not found");
let mut size_buffer = [0; 4];
file.read_exact(&mut size_buffer).expect("buffer overflow");
let size = u32::from_le_bytes(size_buffer) as usize;
let matrix_ptr = connection_matrix(size);
{
let mut matrix = matrix_ptr.write().unwrap();
let mut buffer = [0; 12];
while file.read_exact(&mut buffer).is_ok() {
let node_a = u32::from_le_bytes(buffer[0..4].try_into().unwrap()) as usize;
let node_b = u32::from_le_bytes(buffer[4..8].try_into().unwrap()) as usize;
let weight = f32::from_le_bytes(buffer[8..12].try_into().unwrap());
matrix[node_a][node_b].weight = weight;
matrix[node_b][node_a].weight = weight;
}
}
(size, matrix_ptr)
}

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src/runner.rs Normal file
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@ -0,0 +1,99 @@
use crate::graph::{new_edge_matrix, new_node_vector, EdgeMatrix};
use crate::spring_model;
use crate::utils;
use std::sync::{Arc, RwLock};
use std::thread;
pub struct Runner {
iterations: usize,
threads: usize,
}
impl Runner {
pub fn new(iterations: usize, threads: usize) -> Self {
if threads == 0 {
match std::thread::available_parallelism() {
Ok(threads) => Runner {
iterations,
threads: threads.get(),
},
Err(_) => Runner {
iterations,
threads: 1,
},
}
} else {
Runner {
iterations,
threads,
}
}
}
pub fn layout(
self: &Self,
number_of_nodes: usize,
edge_list: Vec<(u32, u32)>,
) -> Vec<(f32, f32)> {
// let edges = connection_matrix(size);
let edges = edge_matrix_from_edge_list(number_of_nodes, edge_list);
let mut nodes = new_node_vector(number_of_nodes);
let mut nodes_next = new_node_vector(number_of_nodes);
// let model = Arc::new(RwLock::new(spring_model::InitialModel::new(edges, number_of_nodes)));
let model = Arc::new(RwLock::new(spring_model::MyModel::new(
edges,
number_of_nodes,
self.iterations,
)));
let chunks = utils::gen_chunks(number_of_nodes, self.threads);
for _epoch in 0..self.iterations {
model.write().unwrap().prepare(&nodes);
let mut handles = vec![];
for i in 0..self.threads {
let nodes = nodes.clone();
let nodes_next = nodes_next.clone();
let chunk = chunks[i].clone();
let model = model.clone();
let handle = thread::spawn(move || {
for n in chunk {
let update = model.read().unwrap().step(&nodes, n);
let mut result = nodes_next[n].write().unwrap();
result.x = update.x;
result.y = update.y;
}
});
handles.push(handle);
}
for handle in handles {
handle.join().unwrap();
}
// swap nodes and nodes_next
let tmp = nodes.clone();
nodes = nodes_next.clone();
nodes_next = tmp.clone();
}
let mut result = vec![];
for node in nodes.iter() {
let node = node.read().unwrap();
result.push((node.x, node.y));
}
result
}
}
fn edge_matrix_from_edge_list(number_of_nodes: usize, edge_list: Vec<(u32, u32)>) -> EdgeMatrix {
let matrix_ptr = new_edge_matrix(number_of_nodes as usize);
{
let mut matrix = matrix_ptr.write().unwrap();
for (node_a, node_b) in edge_list {
matrix[node_a as usize][node_b as usize].weight = 1.0;
matrix[node_b as usize][node_a as usize].weight = 1.0;
}
}
matrix_ptr
}

View File

@ -1,38 +1,41 @@
use crate::graph::{EdgeMatrix, NodeVector, Node}; use crate::graph::{EdgeMatrix, Node, NodeVector};
pub struct MyModel {
const C_REP: f32 = 0.1;
const C_SPRING: f32 = 0.1;
pub struct InitialModel {
edges: EdgeMatrix, edges: EdgeMatrix,
size: usize, size: usize,
opt_dist: f32, opt_dist: f32,
t: f32, c: f32,
dc: f32,
} }
impl InitialModel { impl MyModel {
pub fn new(edges: EdgeMatrix, size: usize, iterations: usize) -> MyModel {
let opt_dist = 1.0;
let c = 0.1;
pub fn new(edges: EdgeMatrix, size: usize) -> InitialModel { MyModel {
let opt_dist = 1.0 / (size as f32).sqrt(); edges,
InitialModel{ edges, size, opt_dist, t: 0.1 } size,
opt_dist,
c: c,
dc: c / ((iterations + 1) as f32),
}
} }
pub fn prepare(& mut self, nodes: &NodeVector) { pub fn prepare(&mut self, _nodes: &NodeVector) {
self.t = 0.1 * f32::max( self.c -= self.dc;
nodes.iter().map(|n| n.read().unwrap().x.abs()).reduce(|a, b| a.max(b)).unwrap(),
nodes.iter().map(|n| n.read().unwrap().y.abs()).reduce(|a, b| a.max(b)).unwrap()
);
} }
pub fn step(&self, nodes: &NodeVector, i_node: usize) -> Node { pub fn step(&self, nodes: &NodeVector, i_node: usize) -> Node {
let node = nodes[i_node].read().unwrap(); let node = nodes[i_node].read().unwrap();
let edges = self.edges.read().unwrap(); let edges = self.edges.read().unwrap();
let mut node_x = node.x; let node_x = node.x;
let mut node_y = node.y; let node_y = node.y;
let mut sum_x = 0.0;
let mut sum_y = 0.0;
for o in 0..self.size { for o in 0..self.size {
if o == i_node { if o == i_node {
continue; continue;
@ -47,30 +50,37 @@ impl InitialModel {
let d_x = o_x - node_x; let d_x = o_x - node_x;
let d_y = o_y - node_y; let d_y = o_y - node_y;
let dist = (d_x * d_x + d_y * d_y).sqrt().max(0.01); let dist = (d_x * d_x + d_y * d_y).sqrt();
let unit_x = d_x / dist; let unit_x = d_x / dist;
let unit_y = d_y / dist; let unit_y = d_y / dist;
let edge = edges[i_node][o].weight; let edge = edges[i_node][o].weight;
if edge == 0.0 { if edge == 0.0 {
let f_rep = (C_REP / (dist).powi(2)).min(self.t); let f_rep = dist.powi(2).recip().min(self.opt_dist);
let f_rep_x = f_rep * unit_x; let f_rep_x = f_rep * unit_x;
let f_rep_y = f_rep * unit_y; let f_rep_y = f_rep * unit_y;
node_x -= f_rep_x; sum_x -= f_rep_x;
node_y -= f_rep_y; sum_y -= f_rep_y;
} else { } else {
let f_spring = (C_SPRING * (dist / self.opt_dist).log(2.0)).min(self.t); let f_spring = 0.5 * (dist - self.opt_dist);
let f_spring_x = f_spring * unit_x; let f_spring_x = f_spring * unit_x;
let f_spring_y = f_spring * unit_y; let f_spring_y = f_spring * unit_y;
node_x += f_spring_x; sum_x += f_spring_x;
node_y += f_spring_y; sum_y += f_spring_y;
} }
} }
// limit the movement
// TODO: find a good upper bound
let sum_l = (sum_x * sum_x + sum_y * sum_y).sqrt().max(1e-6).recip() * self.c;
let sum_x = sum_x * sum_l;
let sum_y = sum_y * sum_l;
Node { Node {
x: node_x, x: node_x + sum_x,
y: node_y, y: node_y + sum_y,
} }
} }
} }

View File

@ -15,7 +15,7 @@ pub fn gen_chunks(n: usize, chunks: usize) -> Vec<Range<usize>> {
borders borders
} }
#[cfg(test)]
mod test { mod test {
use super::*; use super::*;
@ -36,5 +36,4 @@ mod test {
let borders = gen_chunks(10, 1); let borders = gen_chunks(10, 1);
assert_eq!(borders, vec![(0..10)]); assert_eq!(borders, vec![(0..10)]);
} }
} }