initial version of the gradient filter
This commit is contained in:
Radovan Bast
1
.gitignore
vendored
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1
.gitignore
vendored
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@@ -0,0 +1 @@
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/target
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898
Cargo.lock
generated
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898
Cargo.lock
generated
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@@ -0,0 +1,898 @@
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name = "windows-numerics"
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||||
version = "0.2.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "9150af68066c4c5c07ddc0ce30421554771e528bde427614c61038bc2c92c2b1"
|
||||
dependencies = [
|
||||
"windows-core",
|
||||
"windows-link 0.1.3",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "windows-result"
|
||||
version = "0.3.4"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "56f42bd332cc6c8eac5af113fc0c1fd6a8fd2aa08a0119358686e5160d0586c6"
|
||||
dependencies = [
|
||||
"windows-link 0.1.3",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "windows-strings"
|
||||
version = "0.4.2"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "56e6c93f3a0c3b36176cb1327a4958a0353d5d166c2a35cb268ace15e91d3b57"
|
||||
dependencies = [
|
||||
"windows-link 0.1.3",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "windows-sys"
|
||||
version = "0.61.2"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "ae137229bcbd6cdf0f7b80a31df61766145077ddf49416a728b02cb3921ff3fc"
|
||||
dependencies = [
|
||||
"windows-link 0.2.1",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "windows-threading"
|
||||
version = "0.1.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "b66463ad2e0ea3bbf808b7f1d371311c80e115c0b71d60efc142cafbcfb057a6"
|
||||
dependencies = [
|
||||
"windows-link 0.1.3",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "wit-bindgen"
|
||||
version = "0.46.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "f17a85883d4e6d00e8a97c586de764dabcc06133f7f1d55dce5cdc070ad7fe59"
|
||||
|
||||
[[package]]
|
||||
name = "zerocopy"
|
||||
version = "0.8.27"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "0894878a5fa3edfd6da3f88c4805f4c8558e2b996227a3d864f47fe11e38282c"
|
||||
dependencies = [
|
||||
"zerocopy-derive",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "zerocopy-derive"
|
||||
version = "0.8.27"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "88d2b8d9c68ad2b9e4340d7832716a4d21a22a1154777ad56ea55c51a9cf3831"
|
||||
dependencies = [
|
||||
"proc-macro2",
|
||||
"quote",
|
||||
"syn",
|
||||
]
|
||||
12
Cargo.toml
Normal file
12
Cargo.toml
Normal file
@@ -0,0 +1,12 @@
|
||||
[package]
|
||||
name = "gradient-filter"
|
||||
version = "0.1.0"
|
||||
edition = "2024"
|
||||
|
||||
[dependencies]
|
||||
anyhow = "1.0.100"
|
||||
clap = { version = "4.5.53", features = ["derive"] }
|
||||
indicatif = {version = "0.18.3", features = ["rayon"]}
|
||||
kiddo = "5.2.2"
|
||||
rand = "0.9.2"
|
||||
rayon = "1.11.0"
|
||||
9
README.md
Normal file
9
README.md
Normal file
@@ -0,0 +1,9 @@
|
||||
Build the code:
|
||||
```bash
|
||||
$ cargo build --release
|
||||
```
|
||||
|
||||
Example run:
|
||||
```bash
|
||||
$ ./target/release/gradient-filter --input examples/small.txt --output output.txt
|
||||
```
|
||||
176
src/main.rs
Normal file
176
src/main.rs
Normal file
@@ -0,0 +1,176 @@
|
||||
use std::fs::File;
|
||||
use std::io::{BufRead, BufReader, BufWriter, Write};
|
||||
use std::time::Instant;
|
||||
|
||||
use anyhow::Result;
|
||||
use clap::Parser;
|
||||
use indicatif::ParallelProgressIterator;
|
||||
use kiddo::{KdTree, SquaredEuclidean};
|
||||
use rand::Rng;
|
||||
use rayon::prelude::*;
|
||||
|
||||
#[derive(Parser, Debug)]
|
||||
#[command(name = "Gradient filter", version)]
|
||||
struct Args {
|
||||
/// Path to input file
|
||||
#[arg(short, long)]
|
||||
input: String,
|
||||
|
||||
/// Path to output file
|
||||
#[arg(short, long)]
|
||||
output: String,
|
||||
|
||||
/// Number of neighbors to compute gradient
|
||||
#[arg(long, default_value_t = 10)]
|
||||
k: usize,
|
||||
|
||||
/// Epsilon value to jitter points
|
||||
#[arg(long, default_value_t = 1.0e-3)]
|
||||
eps: f64,
|
||||
|
||||
/// Gradient norm threshold
|
||||
#[arg(short, long, default_value_t = 0.09)]
|
||||
gradient: f64,
|
||||
}
|
||||
|
||||
fn main() -> Result<()> {
|
||||
let args = Args::parse();
|
||||
|
||||
let points = read_data(&args.input)?;
|
||||
|
||||
let points: Vec<_> = points
|
||||
.into_par_iter()
|
||||
.map(|p| jitter_point(&p, args.eps))
|
||||
.collect();
|
||||
|
||||
let start = Instant::now();
|
||||
let mut tree: KdTree<f64, 2> = KdTree::new();
|
||||
for (i, p) in points.iter().enumerate() {
|
||||
tree.add(&[p[0], p[1]], i as u64);
|
||||
}
|
||||
println!("time spent building KD-tree: {:?}", start.elapsed());
|
||||
|
||||
let start = Instant::now();
|
||||
let gradient_magnitudes: Vec<f64> = points
|
||||
.par_iter()
|
||||
.progress_count(points.len() as u64)
|
||||
.map(|&p| {
|
||||
let neighbors: Vec<_> = tree
|
||||
.nearest_n::<SquaredEuclidean>(&[p[0], p[1]], args.k)
|
||||
.into_iter()
|
||||
.filter(|c| c.distance > 0.0)
|
||||
.map(|c| (c.item as usize, c.distance))
|
||||
.collect();
|
||||
|
||||
gradient2(&p, &neighbors, &points)
|
||||
})
|
||||
.collect();
|
||||
println!("time spent computing gradients: {:?}", start.elapsed());
|
||||
|
||||
let threshold2 = args.gradient * args.gradient;
|
||||
|
||||
let mut writer = BufWriter::new(File::create(&args.output)?);
|
||||
let mut num_output_points = 0;
|
||||
for (i, &g) in gradient_magnitudes.iter().enumerate() {
|
||||
if g > threshold2 {
|
||||
writeln!(
|
||||
writer,
|
||||
"{:.6};{:.6};{:.6}",
|
||||
points[i][0],
|
||||
points[i][1],
|
||||
g.sqrt()
|
||||
)?;
|
||||
num_output_points += 1;
|
||||
}
|
||||
}
|
||||
writer.flush()?;
|
||||
|
||||
println!(
|
||||
"reduction: {:.2}%",
|
||||
100.0 * (1.0 - (num_output_points as f64) / (points.len() as f64))
|
||||
);
|
||||
|
||||
Ok(())
|
||||
}
|
||||
|
||||
fn parse_point(line: &str) -> Option<[f64; 3]> {
|
||||
// parse "x;y;z"
|
||||
let parts: Vec<_> = line.trim().split(';').collect();
|
||||
if parts.len() != 3 {
|
||||
return None;
|
||||
}
|
||||
|
||||
let x = parts[0].trim().parse::<f64>().ok()?;
|
||||
let y = parts[1].trim().parse::<f64>().ok()?;
|
||||
let z = parts[2].trim().parse::<f64>().ok()?;
|
||||
|
||||
Some([x, y, z])
|
||||
}
|
||||
|
||||
fn read_data(input_path: &str) -> Result<Vec<[f64; 3]>> {
|
||||
let reader = BufReader::new(File::open(input_path)?);
|
||||
let mut points = Vec::new();
|
||||
for line in reader.lines() {
|
||||
let line = line?;
|
||||
if let Some(p) = parse_point(&line) {
|
||||
points.push(p);
|
||||
}
|
||||
}
|
||||
Ok(points)
|
||||
}
|
||||
|
||||
fn jitter_point(p: &[f64; 3], eps: f64) -> [f64; 3] {
|
||||
let mut rng = rand::rng();
|
||||
[
|
||||
p[0] + rng.random_range(-eps..eps),
|
||||
p[1] + rng.random_range(-eps..eps),
|
||||
p[2],
|
||||
]
|
||||
}
|
||||
|
||||
fn gradient2(reference_point: &[f64; 3], neighbors: &[(usize, f64)], points: &[[f64; 3]]) -> f64 {
|
||||
if neighbors.len() < 3 {
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
let mut m00 = 0.0;
|
||||
let mut m01 = 0.0;
|
||||
let mut m11 = 0.0;
|
||||
let mut b0 = 0.0;
|
||||
let mut b1 = 0.0;
|
||||
|
||||
// use squared distance to farthest neighbor as scale
|
||||
let h2 = neighbors.last().unwrap().1;
|
||||
|
||||
for (i, d2) in neighbors {
|
||||
let p = points[*i];
|
||||
|
||||
let dx = p[0] - reference_point[0];
|
||||
let dy = p[1] - reference_point[1];
|
||||
let dz = p[2] - reference_point[2];
|
||||
|
||||
let w = (-d2 / h2).exp();
|
||||
|
||||
m00 += w * dx * dx;
|
||||
m01 += w * dx * dy;
|
||||
m11 += w * dy * dy;
|
||||
|
||||
b0 += w * dx * dz;
|
||||
b1 += w * dy * dz;
|
||||
}
|
||||
|
||||
// small ridge term to stabilize M
|
||||
let regularization = 1e-6;
|
||||
m00 += regularization;
|
||||
m11 += regularization;
|
||||
|
||||
let det = m00 * m11 - m01 * m01;
|
||||
if det.abs() < 1e-12 {
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
let gx = (m11 * b0 - m01 * b1) / det;
|
||||
let gy = (-m01 * b0 + m00 * b1) / det;
|
||||
|
||||
gx * gx + gy * gy
|
||||
}
|
||||
Reference in New Issue
Block a user