From 164d15c6e7917eef108272f327a9fd6deae1f77e Mon Sep 17 00:00:00 2001 From: Thomas Forgione Date: Tue, 20 Feb 2018 14:54:40 +0100 Subject: [PATCH] Cleaning --- .gitignore | 1 + plot/centers.dat | 3 - plot/dat.dat | 300 --------------------------------------------- plot/diagram.png | Bin 9805 -> 0 bytes plot/plot.gpi | 11 -- plot/regen.sh | 5 - src/cluster.rs | 38 ------ src/clusterable.rs | 43 +++++++ src/example.rs | 45 +++---- src/kmeans.rs | 90 +++++++++----- src/kmeansdata.rs | 168 ------------------------- src/lib.rs | 12 +- src/test.rs | 44 ------- 13 files changed, 134 insertions(+), 626 deletions(-) delete mode 100644 plot/centers.dat delete mode 100644 plot/dat.dat delete mode 100644 plot/diagram.png delete mode 100644 plot/plot.gpi delete mode 100755 plot/regen.sh delete mode 100644 src/cluster.rs create mode 100644 src/clusterable.rs delete mode 100644 src/kmeansdata.rs delete mode 100644 src/test.rs diff --git a/.gitignore b/.gitignore index 143b1ca..3328184 100644 --- 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centers.dat" u 1:2 t "blue" pt 7 diff --git a/plot/regen.sh b/plot/regen.sh deleted file mode 100755 index 1636408..0000000 --- a/plot/regen.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env bash -cd .. -cargo run --release --bin example -cd plot -gnuplot plot.gpi diff --git a/src/cluster.rs b/src/cluster.rs deleted file mode 100644 index 7b0e8ae..0000000 --- a/src/cluster.rs +++ /dev/null @@ -1,38 +0,0 @@ -pub type Cluster = Vec; - -pub trait Clusterable where Self: Sized + Clone + PartialEq { - fn distance(&self, rhs: &Self) -> f64; - fn get_centroid(elements: &Vec) -> Option; -} - -macro_rules! impl_clusterable { - ( $type: ty) => { - impl Clusterable for $type { - fn distance(&self, rhs: &Self) -> f64 { - if self > rhs { - *self as f64 - *rhs as f64 - } else { - *rhs as f64 - *self as f64 - } - } - - fn get_centroid(elements: &Vec) -> Option { - - if elements.len() == 0 { - return None; - } - - let mut tmp = 0.0 as Self; - for element in elements { - tmp += *element as Self; - } - Some(tmp / elements.len() as Self) - - } - } - } -} - -impl_clusterable!(f32); -impl_clusterable!(f64); - diff --git a/src/clusterable.rs b/src/clusterable.rs new file mode 100644 index 0000000..f685424 --- /dev/null +++ b/src/clusterable.rs @@ -0,0 +1,43 @@ +use std::fmt::Debug; + +pub trait Clusterable where Self: Sized + Clone + PartialEq + Debug { + fn distance(&self, rhs: &Self) -> f64; + fn get_centroid<'a, I>(elements: I) -> Option + where I: Iterator, Self: 'a; +} + +macro_rules! impl_clusterable { + ( $type: ty) => { + impl Clusterable for $type { + fn distance(&self, rhs: &Self) -> f64 { + if self > rhs { + *self as f64 - *rhs as f64 + } else { + *rhs as f64 - *self as f64 + } + } + + fn get_centroid<'a, I>(elements: I) -> Option + where I: Iterator, Self: 'a { + + let mut tmp = 0.0; + let mut count = 0.0; + for element in elements { + tmp += element; + count += 1.0; + } + + if count > 0.0 { + Some(tmp / count) + } else { + None + } + + } + } + } +} + +impl_clusterable!(f32); +impl_clusterable!(f64); + diff --git a/src/example.rs b/src/example.rs index a2ad4c4..79c5668 100644 --- a/src/example.rs +++ b/src/example.rs @@ -7,7 +7,7 @@ use rand::distributions::Range; use rand::distributions::normal::Normal; use generic_kmeans::{kmeans, Clusterable}; -#[derive(PartialEq, Copy, Clone)] +#[derive(PartialEq, Copy, Clone, Debug)] struct Vector2 { pub x: T, pub y: T, @@ -30,28 +30,28 @@ impl Display for Vector2 { impl Clusterable for Vector2 { fn distance(&self, other: &Self) -> f64 { - (self.x - other.x) * (self.x - other.y) + (self.y - other.y) * (self.y - other.y) + (self.x - other.x) * (self.x - other.x) + (self.y - other.y) * (self.y - other.y) } - fn get_centroid(cluster: &Vec>) -> Option> { - - let len = cluster.len(); - - if len == 0 { - return None; - } + fn get_centroid<'a, I>(cluster: I) -> Option + where I: Iterator, Self: 'a { let mut centroid = Vector2::new(0.0, 0.0); + let mut count = 0.0; for i in cluster { centroid.x += i.x; centroid.y += i.y; + count += 1.0; } - centroid.x /= len as f64; - centroid.y /= len as f64; - - Some(centroid) + if count > 0.0 { + centroid.x /= count as f64; + centroid.y /= count as f64; + Some(centroid) + } else { + None + } } } @@ -85,21 +85,24 @@ fn main() { } + let initialization = vec![ + Vector2::new(0.0,0.0), + Vector2::new(10.0,0.0), + Vector2::new(0.0,10.0), + ]; - let (clusters, nb_iterations) = kmeans( - centers.iter().map(|x| x.clone().0).collect::>(), elements, 100000).ok().unwrap(); - println!("{}", nb_iterations); + let (clusters, nb_iterations) = kmeans(initialization, elements, 100000).ok().unwrap(); let mut output = File::create("plot/dat.dat").unwrap(); - for (cluster, color) in clusters.iter().zip(&colors) { - for element in cluster { - use std::io::Write; - writeln!(output, "{} {} {}", element.x, element.y, color).unwrap(); - } + for (element, &label) in clusters.iter() { + use std::io::Write; + writeln!(output, "{} {} {}", element.x, element.y, colors[label]).unwrap(); } + println!("Finished in {} iterations", nb_iterations); + let mut center_file = File::create("plot/centers.dat").unwrap(); for (&(center, _, _), color) in centers.iter().zip(&colors) { use std::io::Write; diff --git a/src/kmeans.rs b/src/kmeans.rs index 29a3c8d..a245dc2 100644 --- a/src/kmeans.rs +++ b/src/kmeans.rs @@ -1,48 +1,82 @@ -use std; - -use kmeansdata::KmeansData; -use cluster::{Cluster, Clusterable}; +use std::slice::Iter; +use std::iter::Zip; +use clusterable::Clusterable; pub struct Kmeans { - pub centroids: Vec, - pub data: KmeansData, + centroids: Vec, + elements: Vec, + labels: Vec, + cluster_number: usize, } impl Kmeans { - pub fn new(centroids: Vec, data: Vec>) -> Kmeans { + pub fn new(centroids: Vec, data: Vec) -> Kmeans { + let labels = Kmeans::build_labels(¢roids, &data); + let cluster_number = centroids.len(); Kmeans { centroids: centroids, - data: KmeansData::from_clusters(data), + elements: data, + labels: labels, + cluster_number: cluster_number } } - pub fn guess_centroids(data: Vec>) -> Kmeans { + /// \returns True if converged + pub fn iterate(&mut self) -> bool { + // Update the centroids + let centroids = Kmeans::build_centroids(&self.elements, &self.labels, self.cluster_number); + + if self.centroids == centroids { + true + } else { + self.centroids = centroids; + Kmeans::update_labels(&self.centroids, &self.elements, &mut self.labels); + false + } + } + + pub fn build_labels(centroids: &Vec, data: &Vec) -> Vec { + debug_assert_ne!(0, centroids.len()); + + let mut output = vec![0; data.len()]; + Kmeans::update_labels(centroids, data, &mut output); + output + } + + pub fn update_labels(centroids: &Vec, data: &Vec, labels: &mut Vec) { + for (element, new_label) in data.iter().zip(labels.iter_mut()) { + *new_label = centroids + .iter() + .enumerate() + .min_by(|&(_, c1), &(_, c2)| { + c1.distance(element).partial_cmp(&c2.distance(element)).unwrap() + }).unwrap().0; + } + } + + pub fn build_centroids(data: &Vec, labels: &Vec, cluster_number: usize) -> Vec { + let mut centroids = vec![]; - for cluster in &data { - if let Some(centroid) = T::get_centroid(cluster) { - centroids.push(centroid); + for label in 0..cluster_number { + + let to_consider = data + .iter() + .enumerate() + .filter(|&(index, _)| labels[index] == label) + .map(|(_, element)| element); + + if let Some(centroid) = T::get_centroid(to_consider) { + centroids.push(centroid); } } - Kmeans::new(centroids, data) - + centroids } - fn from_data(centroids: Vec, data: KmeansData) -> Kmeans { - Kmeans { - centroids: centroids, - data: data, - } + pub fn iter(&self) -> Zip, Iter> { + debug_assert_eq!(self.elements.len(), self.labels.len()); + return self.elements.iter().zip(self.labels.iter()); } - pub fn next_iteration(self) -> (Kmeans, bool) { - let (new_centroids, data) = self.data.iterate(&self.centroids); - let stable = new_centroids == self.centroids; - (Kmeans::from_data(new_centroids, data), stable) - } - - pub fn iter(&self) -> std::slice::Iter> { - self.data.clusters() - } } diff --git a/src/kmeansdata.rs b/src/kmeansdata.rs deleted file mode 100644 index aca75ce..0000000 --- a/src/kmeansdata.rs +++ /dev/null @@ -1,168 +0,0 @@ -use std; -use std::marker::PhantomData; - -use cluster::{Clusterable, Cluster}; - - -pub struct KmeansData { - clusters: Vec>, -} - -impl KmeansData { - - pub fn from_clusters(data: Vec>) -> KmeansData { - KmeansData { - clusters: data, - } - } - - pub fn new(centroids: &Vec, data: KmeansDataIntoIter) -> KmeansData { - - let mut clusters = vec![]; - - for _ in centroids { - clusters.push(Cluster::new()); - } - - let mut new_kmeans: KmeansData = KmeansData { - clusters: clusters, - }; - - for element in data { - - // Compute the distance - let mut distance = std::f64::MAX; - let mut index = 0; - - for (new_index, centroid) in centroids.iter().enumerate() { - let new_distance = element.distance(centroid); - - if new_distance < distance { - distance = new_distance; - index = new_index; - } - } - - // Add element to the new kmeans - new_kmeans.clusters[index].push(element) - - } - - new_kmeans - } - - pub fn add_cluster(&mut self) { - self.clusters.push(Cluster::new()); - } - - pub fn iterate(self, centroids: &Vec) -> (Vec, KmeansData) { - // Compute the result with the given centroids - let result = KmeansData::new(¢roids, self.into_iter()); - - // Compute the new centroids - let mut new_centroids = vec![]; - - for cluster in &result.clusters { - - if let Some(centroid) = T::get_centroid(cluster) { - new_centroids.push(centroid); - } - - } - - (new_centroids, result) - } - - pub fn iter(&self) -> KmeansDataIter { - KmeansDataIter { - global_iter: self.clusters.iter(), - local_iter: None, - _phantom: PhantomData, - } - } - - pub fn clusters(&self) -> std::slice::Iter> { - self.clusters.iter() - } - -} - -pub struct KmeansDataIter<'a, T> where T:'a, T: Clusterable { - global_iter: std::slice::Iter<'a, std::vec::Vec>, - local_iter: Option>, - _phantom: PhantomData, -} - -impl<'a, T: 'a + Clusterable> Iterator for KmeansDataIter<'a, T> { - type Item = &'a T; - fn next(&mut self) -> Option<&'a T> { - if let Some(ref mut local_iter) = self.local_iter { - match local_iter.next() { - Some(t) => Some(t), - None => { - if let Some(next) = self.global_iter.next() { - *local_iter = next.iter(); - match local_iter.next() { - Some(t) => Some(t), - None => None, - } - } else { - None - } - } - } - } else { - self.local_iter = match self.global_iter.next() { - None => None, - Some(t) => Some(t.iter()), - }; - self.next() - } - } -} - -pub struct KmeansDataIntoIter where T: Clusterable { - global_iter: std::vec::IntoIter>, - local_iter: Option>, - _phantom: PhantomData, -} - -impl Iterator for KmeansDataIntoIter { - type Item = T; - fn next(&mut self) -> Option { - if let Some(ref mut local_iter) = self.local_iter { - match local_iter.next() { - Some(t) => Some(t), - None => { - if let Some(next) = self.global_iter.next() { - *local_iter = next.into_iter(); - match local_iter.next() { - Some(t) => Some(t), - None => None, - } - } else { - None - } - } - } - } else { - self.local_iter = match self.global_iter.next() { - None => None, - Some(t) => Some(t.into_iter()), - }; - self.next() - } - } -} - -impl IntoIterator for KmeansData { - type Item = T; - type IntoIter = KmeansDataIntoIter; - fn into_iter(self) -> Self::IntoIter { - Self::IntoIter { - global_iter: self.clusters.into_iter(), - local_iter: None, - _phantom: PhantomData, - } - } -} diff --git a/src/lib.rs b/src/lib.rs index 84dd9d6..dcc08ff 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,11 +1,8 @@ pub mod kmeans; -pub mod kmeansdata; -pub mod cluster; -pub mod test; +pub mod clusterable; pub use kmeans::Kmeans; -pub use kmeansdata::KmeansData; -pub use cluster::{Cluster, Clusterable}; +pub use clusterable::Clusterable; pub enum Error { IterationsLimitExceeded, @@ -14,12 +11,11 @@ pub enum Error { pub fn kmeans(centroids: Vec, data: Vec, max_iterations: usize) -> Result<(Kmeans, usize), Error> { - let mut kmeans = Kmeans::new(centroids, vec![data]); + let mut kmeans = Kmeans::new(centroids, data); for nb_iterations in 0..max_iterations { - let (new_kmeans, stable) = kmeans.next_iteration(); - kmeans = new_kmeans; + let stable = kmeans.iterate(); if stable { return Ok((kmeans, nb_iterations)); diff --git a/src/test.rs b/src/test.rs deleted file mode 100644 index e78028a..0000000 --- a/src/test.rs +++ /dev/null @@ -1,44 +0,0 @@ -#[cfg(test)] -mod test { - #[test] - fn iterators() { - use kmeansdata::KmeansData; - let data = vec![4.0, 5.0, 11.0, 12.0, 13.0]; - let kmeans = KmeansData::from_clusters(vec![ - vec![4.0, 5.0], - vec![11.0, 12.0, 13.0], - ]); - - for (val1, val2) in kmeans.into_iter().zip(data) { - assert_eq!(val1, val2); - } - } - - #[test] - fn iterate() { - use kmeans::Kmeans; - - let data = vec![ - vec![4.0, 5.0, 11.0, 12.0], - vec![13.0], - ]; - - let solution = vec![ - vec![4.0, 5.0], - vec![11.0, 12.0, 13.0], - ]; - - let mut kmeans = Kmeans::guess_centroids(data.clone()); - - for _ in 0..4 { - let (new_kmeans, stable) = kmeans.next_iteration(); - kmeans = new_kmeans; - } - - for (k1, k2) in kmeans.iter().zip(solution) { - for (i, j) in k1.iter().zip(&k2) { - assert_eq!(i, j); - } - } - } -}