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"windows_aarch64_msvc", + "windows_i686_gnu", + "windows_i686_msvc", + "windows_x86_64_gnu", + "windows_x86_64_gnullvm", + "windows_x86_64_msvc", +] + +[[package]] +name = "windows_aarch64_gnullvm" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "41d2aa71f6f0cbe00ae5167d90ef3cfe66527d6f613ca78ac8024c3ccab9a19e" + +[[package]] +name = "windows_aarch64_msvc" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dd0f252f5a35cac83d6311b2e795981f5ee6e67eb1f9a7f64eb4500fbc4dcdb4" + +[[package]] +name = "windows_i686_gnu" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fbeae19f6716841636c28d695375df17562ca208b2b7d0dc47635a50ae6c5de7" + +[[package]] +name = "windows_i686_msvc" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "84c12f65daa39dd2babe6e442988fc329d6243fdce47d7d2d155b8d874862246" + +[[package]] +name = "windows_x86_64_gnu" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bf7b1b21b5362cbc318f686150e5bcea75ecedc74dd157d874d754a2ca44b0ed" + +[[package]] +name = "windows_x86_64_gnullvm" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "09d525d2ba30eeb3297665bd434a54297e4170c7f1a44cad4ef58095b4cd2028" + +[[package]] +name = "windows_x86_64_msvc" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f40009d85759725a34da6d89a94e63d7bdc50a862acf0dbc7c8e488f1edcb6f5" diff --git a/Cargo.toml b/Cargo.toml index 2578eb0..29ba271 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,9 +1,13 @@ [package] -name = "graph" +name = "graph_force" version = "0.1.0" edition = "2021" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html +[lib] +name = "graph_force" +crate-type = ["cdylib"] [dependencies] rand = "0.8.5" +pyo3 = { version = "0.17.3", features = ["extension-module"] } diff --git a/README.md b/README.md new file mode 100644 index 0000000..0fab51f --- /dev/null +++ b/README.md @@ -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) +``` \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..7e4a9a6 --- /dev/null +++ b/pyproject.toml @@ -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", +] + + diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..6fdfcae --- /dev/null +++ b/requirements.txt @@ -0,0 +1 @@ +maturin==0.14.1 diff --git a/src/graph.rs b/src/graph.rs index 662a005..4649e5c 100644 --- a/src/graph.rs +++ b/src/graph.rs @@ -1,3 +1,4 @@ +use rand::Rng; use std::sync::{Arc, RwLock}; pub struct Node { pub x: f32, @@ -10,3 +11,26 @@ pub struct Edge { pub type EdgeMatrix = Arc>>>; pub type NodeVector = Arc>>; + +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) +} diff --git a/src/lib.rs b/src/lib.rs new file mode 100644 index 0000000..e6622dd --- /dev/null +++ b/src/lib.rs @@ -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> { + 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(()) +} diff --git a/src/main.rs b/src/main.rs deleted file mode 100644 index 1e74e23..0000000 --- a/src/main.rs +++ /dev/null @@ -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(()) -} diff --git a/src/my_model.rs b/src/my_model.rs deleted file mode 100644 index 23bfc3b..0000000 --- a/src/my_model.rs +++ /dev/null @@ -1,97 +0,0 @@ -use crate::graph::{EdgeMatrix, NodeVector, Node}; - -pub struct MyModel { - edges: EdgeMatrix, - ranks: Vec, - 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, - } - } -} diff --git a/src/reader.rs b/src/reader.rs new file mode 100644 index 0000000..e5d2f4d --- /dev/null +++ b/src/reader.rs @@ -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) +} diff --git a/src/runner.rs b/src/runner.rs new file mode 100644 index 0000000..3bd4062 --- /dev/null +++ b/src/runner.rs @@ -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 +} diff --git a/src/spring_model.rs b/src/spring_model.rs index 1ec293f..94168e1 100644 --- a/src/spring_model.rs +++ b/src/spring_model.rs @@ -1,38 +1,41 @@ -use crate::graph::{EdgeMatrix, NodeVector, Node}; +use crate::graph::{EdgeMatrix, Node, NodeVector}; - -const C_REP: f32 = 0.1; -const C_SPRING: f32 = 0.1; - -pub struct InitialModel { +pub struct MyModel { edges: EdgeMatrix, size: usize, 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 { - let opt_dist = 1.0 / (size as f32).sqrt(); - InitialModel{ edges, size, opt_dist, t: 0.1 } + MyModel { + edges, + size, + opt_dist, + c: c, + dc: c / ((iterations + 1) as f32), + } } - pub fn prepare(& mut self, nodes: &NodeVector) { - self.t = 0.1 * f32::max( - 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 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 mut node_x = node.x; - let mut node_y = node.y; + 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; @@ -47,30 +50,37 @@ impl InitialModel { 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().max(0.01); + 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 = (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_y = f_rep * unit_y; - node_x -= f_rep_x; - node_y -= f_rep_y; + sum_x -= f_rep_x; + sum_y -= f_rep_y; } 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_y = f_spring * unit_y; - node_x += f_spring_x; - node_y += f_spring_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, - y: node_y, - } + x: node_x + sum_x, + y: node_y + sum_y, + } } } diff --git a/src/utils.rs b/src/utils.rs index 2e2be32..7be8f55 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -15,7 +15,7 @@ pub fn gen_chunks(n: usize, chunks: usize) -> Vec> { borders } - +#[cfg(test)] mod test { use super::*; @@ -36,5 +36,4 @@ mod test { let borders = gen_chunks(10, 1); assert_eq!(borders, vec![(0..10)]); } - }