diff --git a/Cargo.lock b/Cargo.lock index 47df7de..ab2690a 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -33,7 +33,7 @@ dependencies = [ [[package]] name = "graph_force" -version = "0.1.3" +version = "0.2.0" dependencies = [ "pyo3", "rand", diff --git a/Cargo.toml b/Cargo.toml index a0515e9..d092abe 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "graph_force" -version = "0.1.3" +version = "0.2.0" edition = "2021" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html diff --git a/README.md b/README.md index 32db68e..fc75d0f 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,11 @@ pip install graph_force ``` ## Usage + +The first parameter defines the number of nodes in graph. +The second parameter is an iterable of edges, where each edge is a tuple of two integers representing the nodes it connects. Node ids start at 0. + + ```python import graph_force @@ -17,6 +22,9 @@ pos = graph_force.layout_from_edge_list(4, edges) ``` ### Example with networkx + +This library does not have a function to consume a networkx graph directly, but it is easy to convert it to an edge list. + ```python import networkx as nx import graph_force @@ -34,6 +42,47 @@ pos = graph_force.layout_from_edge_list(len(G.nodes), edges, iter=1000) nx.draw(G, {n: pos[i] for n, i in mapping.items()}, node_size=2, width=0.1) ``` +### Example with edge file + +This methods can be used with large graphs, where the edge list does not fit into memory. + +Format of the file: +- Little endian +- 4 bytes: number of nodes(int) +- 12 bytes: nodeA(int), nodeB(int), weight(float) + +```python +import graph_force +import struct + +with open("edges.bin", "rb") as f: + n = 10 + f.write(struct.pack("i", n)) + for x in range(n-1): + f.write(struct.pack("iif", x, x+1, 1)) + +pos = graph_force.layout_from_edge_file("edges.bin", iter=50) +``` + + +### Options + +`iter`, `threads` and `model` are optional parameters, supported by `layout_from_edge_list` and `layout_from_edge_file`. + +```python +pos = graph_force.layout_from_edge_list( + number_of_nodes, + edges, + iter=500, # number of iterations, default 500 + threads=0, # number of threads, default 0 (all available) + model="spring_model", # model to use, default "spring_model", other option is "networkx_model" +) +``` +#### Available models + +- `spring_model`: A simple spring model (my own implementation) +- `networkx_model`: Reimplementation of the [spring model from networkx](https://networkx.org/documentation/stable/reference/generated/networkx.drawing.layout.spring_layout.html) + ## Contributing - [Development](DEVELOPMENT.md) \ No newline at end of file diff --git a/src/lib.rs b/src/lib.rs index 7ec44ce..9b0140f 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,6 +1,7 @@ mod graph; mod model; mod networkx_model; +mod reader; mod runner; mod spring_model; mod utils; @@ -8,6 +9,32 @@ mod utils; use pyo3::exceptions; use pyo3::{prelude::*, types::PyIterator}; +fn pick_model(model: &str) -> Result, PyErr> { + match model { + "spring_model" => Ok(Box::new(spring_model::SimpleSpringModel::new(1.0))), + "networkx_model" => Ok(Box::new(networkx_model::NetworkXModel::new())), + _ => { + return Err(PyErr::new::( + "model must be either 'spring_model' or 'networkx_model'", + )) + } + } +} + +#[pyfunction(file_path, "*", iter = 500, threads = 0, model = "\"spring_model\"")] +fn layout_from_edge_file( + file_path: &str, + iter: usize, + threads: usize, + model: &str, +) -> PyResult> { + let (size, matrix) = reader::read_graph(file_path); + let model = pick_model(model)?; + + let r = runner::Runner::new(iter, threads); + Ok(r.layout(size, matrix, model)) +} + #[pyfunction( number_of_nodes, edges, @@ -23,15 +50,7 @@ fn layout_from_edge_list( threads: usize, model: &str, ) -> PyResult> { - let model: Box = match model { - "spring_model" => Box::new(spring_model::SimpleSpringModel::new(1.0)), - "networkx_model" => Box::new(networkx_model::NetworkXModel::new()), - _ => { - return Err(PyErr::new::( - "model must be either 'spring_model' or 'networkx_model'", - )) - } - }; + let model: Box = pick_model(model)?; let mut edge_matrix = graph::new_edge_matrix(number_of_nodes); match edges.extract::<&PyIterator>() { @@ -70,5 +89,6 @@ fn layout_from_edge_list( #[pymodule] fn graph_force(_py: Python, m: &PyModule) -> PyResult<()> { m.add_function(wrap_pyfunction!(layout_from_edge_list, m)?)?; + m.add_function(wrap_pyfunction!(layout_from_edge_file, m)?)?; Ok(()) } diff --git a/src/networkx_model.rs b/src/networkx_model.rs index ff5ad58..0c3ea54 100644 --- a/src/networkx_model.rs +++ b/src/networkx_model.rs @@ -3,6 +3,7 @@ use crate::model::ForceModel; /** * Translation of the NetworkX spring_layout function. + * https://networkx.org/documentation/stable/reference/generated/networkx.drawing.layout.spring_layout.html */ pub struct NetworkXModel { edges: EdgeMatrix, diff --git a/src/reader.rs b/src/reader.rs index e5d2f4d..dfec373 100644 --- a/src/reader.rs +++ b/src/reader.rs @@ -1,3 +1,7 @@ +use std::{fs::File, io::Read}; + +use crate::graph::{add_edge, new_edge_matrix, EdgeMatrix}; + /** * Read Graph data from file * Format: @@ -5,22 +9,20 @@ * - 4 bytes: number of nodes(int) * - 12 bytes: nodeA(int), nodeB(int), weight(float) */ -fn read_graph(file_name: &str) -> (usize, EdgeMatrix) { +pub 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 = new_edge_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; + let _weight = f32::from_le_bytes(buffer[8..12].try_into().unwrap()); + add_edge(&mut matrix, node_a, node_b); } } - (size, matrix_ptr) + (size, matrix) } diff --git a/tests/test_e2e.py b/tests/test_e2e.py index e3eba9c..84833dd 100644 --- a/tests/test_e2e.py +++ b/tests/test_e2e.py @@ -1,4 +1,5 @@ import graph_force +import struct def test_list_of_edges(): edges = [(1, 2), (2, 3), (3, 4), (4, 5), (5, 6)] @@ -28,3 +29,14 @@ def test_model_selection(): pos = graph_force.layout_from_edge_list(7, edges, model='networkx_model') assert pos is not None assert len(pos) == 7 + +def test_from_file(): + with open("/tmp/edges.bin", "wb") as f: + n = 10 + f.write(struct.pack("i", n)) + for x in range(n-1): + f.write(struct.pack("iif", x, x+1, 1)) + + pos = graph_force.layout_from_edge_file('/tmp/edges.bin') + assert pos is not None + assert len(pos) == 10 \ No newline at end of file