Python package #1
|
|
@ -1,2 +1,4 @@
|
|||
/target
|
||||
result/
|
||||
|
||||
venv/
|
||||
|
|
@ -0,0 +1,3 @@
|
|||
{
|
||||
"editor.formatOnSave": true,
|
||||
}
|
||||
|
|
@ -2,6 +2,18 @@
|
|||
# It is not intended for manual editing.
|
||||
version = 3
|
||||
|
||||
[[package]]
|
||||
name = "autocfg"
|
||||
version = "1.1.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
|
||||
|
||||
[[package]]
|
||||
name = "bitflags"
|
||||
version = "1.3.2"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
|
||||
|
||||
[[package]]
|
||||
name = "cfg-if"
|
||||
version = "1.0.0"
|
||||
|
|
@ -20,24 +32,157 @@ dependencies = [
|
|||
]
|
||||
|
||||
[[package]]
|
||||
name = "graph"
|
||||
name = "graph_force"
|
||||
version = "0.1.0"
|
||||
dependencies = [
|
||||
"pyo3",
|
||||
"rand",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "indoc"
|
||||
version = "1.0.7"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "adab1eaa3408fb7f0c777a73e7465fd5656136fc93b670eb6df3c88c2c1344e3"
|
||||
|
||||
[[package]]
|
||||
name = "libc"
|
||||
version = "0.2.137"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "fc7fcc620a3bff7cdd7a365be3376c97191aeaccc2a603e600951e452615bf89"
|
||||
|
||||
[[package]]
|
||||
name = "lock_api"
|
||||
version = "0.4.9"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "435011366fe56583b16cf956f9df0095b405b82d76425bc8981c0e22e60ec4df"
|
||||
dependencies = [
|
||||
"autocfg",
|
||||
"scopeguard",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "memoffset"
|
||||
version = "0.6.5"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "5aa361d4faea93603064a027415f07bd8e1d5c88c9fbf68bf56a285428fd79ce"
|
||||
dependencies = [
|
||||
"autocfg",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "once_cell"
|
||||
version = "1.16.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "86f0b0d4bf799edbc74508c1e8bf170ff5f41238e5f8225603ca7caaae2b7860"
|
||||
|
||||
[[package]]
|
||||
name = "parking_lot"
|
||||
version = "0.12.1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f"
|
||||
dependencies = [
|
||||
"lock_api",
|
||||
"parking_lot_core",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "parking_lot_core"
|
||||
version = "0.9.4"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "4dc9e0dc2adc1c69d09143aff38d3d30c5c3f0df0dad82e6d25547af174ebec0"
|
||||
dependencies = [
|
||||
"cfg-if",
|
||||
"libc",
|
||||
"redox_syscall",
|
||||
"smallvec",
|
||||
"windows-sys",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "ppv-lite86"
|
||||
version = "0.2.17"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
|
||||
|
||||
[[package]]
|
||||
name = "proc-macro2"
|
||||
version = "1.0.47"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "5ea3d908b0e36316caf9e9e2c4625cdde190a7e6f440d794667ed17a1855e725"
|
||||
dependencies = [
|
||||
"unicode-ident",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "pyo3"
|
||||
version = "0.17.3"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "268be0c73583c183f2b14052337465768c07726936a260f480f0857cb95ba543"
|
||||
dependencies = [
|
||||
"cfg-if",
|
||||
"indoc",
|
||||
"libc",
|
||||
"memoffset",
|
||||
"parking_lot",
|
||||
"pyo3-build-config",
|
||||
"pyo3-ffi",
|
||||
"pyo3-macros",
|
||||
"unindent",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "pyo3-build-config"
|
||||
version = "0.17.3"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "28fcd1e73f06ec85bf3280c48c67e731d8290ad3d730f8be9dc07946923005c8"
|
||||
dependencies = [
|
||||
"once_cell",
|
||||
"target-lexicon",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "pyo3-ffi"
|
||||
version = "0.17.3"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "0f6cb136e222e49115b3c51c32792886defbfb0adead26a688142b346a0b9ffc"
|
||||
dependencies = [
|
||||
"libc",
|
||||
"pyo3-build-config",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "pyo3-macros"
|
||||
version = "0.17.3"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "94144a1266e236b1c932682136dc35a9dee8d3589728f68130c7c3861ef96b28"
|
||||
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]]
|
||||
name = "rand"
|
||||
version = "0.8.5"
|
||||
|
|
@ -68,8 +213,115 @@ dependencies = [
|
|||
"getrandom",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "redox_syscall"
|
||||
version = "0.2.16"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a"
|
||||
dependencies = [
|
||||
"bitflags",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "scopeguard"
|
||||
version = "1.1.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd"
|
||||
|
||||
[[package]]
|
||||
name = "smallvec"
|
||||
version = "1.10.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0"
|
||||
|
||||
[[package]]
|
||||
name = "syn"
|
||||
version = "1.0.103"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "a864042229133ada95abf3b54fdc62ef5ccabe9515b64717bcb9a1919e59445d"
|
||||
dependencies = [
|
||||
"proc-macro2",
|
||||
"quote",
|
||||
"unicode-ident",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "target-lexicon"
|
||||
version = "0.12.5"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "9410d0f6853b1d94f0e519fb95df60f29d2c1eff2d921ffdf01a4c8a3b54f12d"
|
||||
|
||||
[[package]]
|
||||
name = "unicode-ident"
|
||||
version = "1.0.5"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "6ceab39d59e4c9499d4e5a8ee0e2735b891bb7308ac83dfb4e80cad195c9f6f3"
|
||||
|
||||
[[package]]
|
||||
name = "unindent"
|
||||
version = "0.1.10"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "58ee9362deb4a96cef4d437d1ad49cffc9b9e92d202b6995674e928ce684f112"
|
||||
|
||||
[[package]]
|
||||
name = "wasi"
|
||||
version = "0.11.0+wasi-snapshot-preview1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
|
||||
|
||||
[[package]]
|
||||
name = "windows-sys"
|
||||
version = "0.42.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "5a3e1820f08b8513f676f7ab6c1f99ff312fb97b553d30ff4dd86f9f15728aa7"
|
||||
dependencies = [
|
||||
"windows_aarch64_gnullvm",
|
||||
"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"
|
||||
|
|
|
|||
|
|
@ -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"] }
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
```
|
||||
|
|
@ -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",
|
||||
]
|
||||
|
||||
|
||||
|
|
@ -0,0 +1 @@
|
|||
maturin==0.14.1
|
||||
24
src/graph.rs
24
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<RwLock<Vec<Vec<Edge>>>>;
|
||||
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)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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(())
|
||||
}
|
||||
116
src/main.rs
116
src/main.rs
|
|
@ -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(())
|
||||
}
|
||||
|
|
@ -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,
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -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)
|
||||
}
|
||||
|
|
@ -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
|
||||
}
|
||||
|
|
@ -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,
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ pub fn gen_chunks(n: usize, chunks: usize) -> Vec<Range<usize>> {
|
|||
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)]);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue