fix: refactors knn and distance functions

benches/distance.rs

@@ -1,17 +1,14 @@
 #[macro_use]
 extern crate criterion;
 extern crate smartcore;
-extern crate ndarray;
-use ndarray::{Array, Array1};
-use smartcore::math::distance::Distance;
 
 use criterion::Criterion;
 use criterion::black_box;
 
 fn criterion_benchmark(c: &mut Criterion) {
-    let a = Array::from_vec(vec![1., 2., 3.]);
+    let a = vec![1., 2., 3.];
 
-    c.bench_function("Euclidean Distance", move |b| b.iter(|| Array1::distance(black_box(&a), black_box(&a))));
+    c.bench_function("Euclidean Distance", move |b| b.iter(|| smartcore::math::distance::euclidian::distance(black_box(&a), black_box(&a))));
 }
 
 criterion_group!(benches, criterion_benchmark);

src/algorithm/neighbour/bbd_tree.rs

@@ -1,6 +1,5 @@
-use std::collections::LinkedList;
-
 use crate::linalg::Matrix;
+use crate::math::distance::euclidian;
 
 #[derive(Debug)]
 pub struct BBDTree {    
@@ -77,10 +76,10 @@ impl BBDTree {
         let d = centroids[0].len();
 
         // Determine which mean the node mean is closest to
-        let mut min_dist = BBDTree::squared_distance(&self.nodes[node].center, &centroids[candidates[0]]);
+        let mut min_dist = euclidian::squared_distance(&self.nodes[node].center, &centroids[candidates[0]]);
         let mut closest = candidates[0];
         for i in 1..k {
-            let dist = BBDTree::squared_distance(&self.nodes[node].center, &centroids[candidates[i]]);
+            let dist = euclidian::squared_distance(&self.nodes[node].center, &centroids[candidates[i]]);
             if dist < min_dist {
                 min_dist = dist;
                 closest = candidates[i];
@@ -146,20 +145,7 @@ impl BBDTree {
         }
 
         return lhs >= 2f64 * rhs;
-    }
+    }    
-
-    fn squared_distance(x: &Vec<f64>,y: &Vec<f64>) -> f64 {
-        if x.len() != y.len() {
-            panic!("Input vector sizes are different.");
-        }
-
-        let mut sum = 0f64;
-        for i in 0..x.len() {
-            sum += (x[i] - y[i]).powf(2.);
-        }
-
-        return sum;
-    }
 
     fn build_node<M: Matrix>(&mut self, data: &M, begin: usize, end: usize) -> usize {
         let (_, d) = data.shape();

src/algorithm/neighbour/linear_search.rs

@@ -72,9 +72,8 @@ impl Eq for KNNPoint {}
 
 #[cfg(test)]
 mod tests {    
-    use super::*;          
+    use super::*;      
-    use crate::math::distance::Distance;
+    use crate::math::distance::euclidian;  
-    use ndarray::{arr1, Array1};
 
     struct SimpleDistance{}
 
@@ -92,11 +91,11 @@ mod tests {
 
         assert_eq!(vec!(1, 2, 0), algorithm1.find(&2, 3));
 
-        let data2 = vec!(arr1(&[1, 1]), arr1(&[2, 2]), arr1(&[3, 3]), arr1(&[4, 4]), arr1(&[5, 5]));
+        let data2 = vec!(vec![1., 1.], vec![2., 2.], vec![3., 3.], vec![4., 4.], vec![5., 5.]);
 
-        let algorithm2 = LinearKNNSearch::new(data2, &Array1::distance);
+        let algorithm2 = LinearKNNSearch::new(data2, &euclidian::distance);
 
-        assert_eq!(vec!(2, 3, 1), algorithm2.find(&arr1(&[3, 3]), 3));
+        assert_eq!(vec!(2, 3, 1), algorithm2.find(&vec![3., 3.], 3));
     }
 
     #[test]

src/classification/knn.rs

@@ -1,61 +1,67 @@
-use super::Classifier;
+use crate::linalg::Matrix;
-use std::collections::HashSet;
 use crate::algorithm::neighbour::{KNNAlgorithm, KNNAlgorithmName};
 use crate::algorithm::neighbour::linear_search::LinearKNNSearch;
 use crate::algorithm::neighbour::cover_tree::CoverTree;
 use crate::common::Nominal;
 use ndarray::{ArrayBase, Data, Ix1, Ix2};
-use std::fmt::Debug;
 
 
-type F<X> = dyn Fn(&X, &X) -> f64;
+type F = dyn Fn(&Vec<f64>, &Vec<f64>) -> f64;
 
-pub struct KNNClassifier<'a, X, Y> 
+pub struct KNNClassifier<'a> {     
-where
+    classes: Vec<f64>,
-    Y: Nominal,
-    X: Debug
-{     
-    classes: Vec<Y>,
     y: Vec<usize>,    
-    knn_algorithm: Box<dyn KNNAlgorithm<X> + 'a>,
+    knn_algorithm: Box<dyn KNNAlgorithm<Vec<f64>> + 'a>,
     k: usize,        
 }
 
-impl<'a, X, Y> KNNClassifier<'a, X, Y> 
+impl<'a> KNNClassifier<'a> {
-where
-    Y: Nominal,
-    X: Debug
-{
 
-    pub fn fit(x: Vec<X>, y: Vec<Y>, k: usize, distance: &'a F<X>, algorithm: KNNAlgorithmName) -> KNNClassifier<X, Y> {
+    pub fn fit<M: Matrix>(x: &M, y: &M::RowVector, k: usize, distance: &'a F, algorithm: KNNAlgorithmName) -> KNNClassifier<'a> {
 
-        assert!(Vec::len(&x) == Vec::len(&y), format!("Size of x should equal size of y; |x|=[{}], |y|=[{}]", Vec::len(&x), Vec::len(&y)));
+        let y_m = M::from_row_vector(y.clone());
 
-        assert!(k > 1, format!("k should be > 1, k=[{}]", k));      
+        let (_, y_n) = y_m.shape();
-        
+        let (x_n, _) = x.shape();
-        let c_hash: HashSet<Y> = y.clone().into_iter().collect(); 
-        let classes: Vec<Y> = c_hash.into_iter().collect();
-        let y_i:Vec<usize> = y.into_iter().map(|y| classes.iter().position(|yy| yy == &y).unwrap()).collect();    
 
-        let knn_algorithm: Box<dyn KNNAlgorithm<X> + 'a> = match algorithm {
+        let data = x.to_vector();
-            KNNAlgorithmName::CoverTree => Box::new(CoverTree::<X>::new(x, distance)),
+
-            KNNAlgorithmName::LinearSearch => Box::new(LinearKNNSearch::<X>::new(x, distance))
+        let mut yi: Vec<usize> = vec![0; y_n];
+        let classes = y_m.unique();                
+
+        for i in 0..y_n {
+            let yc = y_m.get(0, i);                        
+            yi[i] = classes.iter().position(|c| yc == *c).unwrap();            
+        }
+
+        assert!(x_n == y_n, format!("Size of x should equal size of y; |x|=[{}], |y|=[{}]", x_n, y_n));
+
+        assert!(k > 1, format!("k should be > 1, k=[{}]", k));                  
+
+        let knn_algorithm: Box<dyn KNNAlgorithm<Vec<f64>> + 'a> = match algorithm {
+            KNNAlgorithmName::CoverTree => Box::new(CoverTree::<Vec<f64>>::new(data, distance)),
+            KNNAlgorithmName::LinearSearch => Box::new(LinearKNNSearch::<Vec<f64>>::new(data, distance))
         };
 
-        KNNClassifier{classes:classes, y: y_i, k: k, knn_algorithm: knn_algorithm}
+        KNNClassifier{classes:classes, y: yi, k: k, knn_algorithm: knn_algorithm}
 
     }
-    
-}
 
-impl<'a, X, Y> Classifier<X, Y> for KNNClassifier<'a, X, Y> 
+    pub fn predict<M: Matrix>(&self, x: &M) -> M::RowVector {    
-where    
+        let mut result = M::zeros(1, x.shape().0);
-    Y: Nominal,
-    X: Debug
- {    
 
-    fn predict(&self, x: &X) -> Y {                       
+        let (n, _) = x.shape();                               
-        let idxs = self.knn_algorithm.find(x, self.k);        
+        
+        for i in 0..n {
+            result.set(0, i, self.classes[self.predict_for_row(x, i)]);
+        }
+
+        result.to_row_vector()
+    }
+
+    pub(in crate) fn predict_for_row<M: Matrix>(&self, x: &M, row: usize) -> usize {
+
+        let idxs = self.knn_algorithm.find(&x.get_row_as_vec(row), self.k);        
         let mut c = vec![0; self.classes.len()];
         let mut max_c = 0;
         let mut max_i = 0;
@@ -65,41 +71,31 @@ where
                 max_c = c[self.y[i]];
                 max_i = self.y[i];
             }          
-        }                    
+        }   
+
+        max_i
 
-        self.classes[max_i].clone()
-    }
-
-}
-
-pub struct NDArrayUtils {
-
-}
-
-impl NDArrayUtils {
-
-    pub fn array2_to_vec<E, S>(x: &ArrayBase<S, Ix2>) -> Vec<ArrayBase<S, Ix1>> 
-    where
-        E: Nominal,
-        S: Data<Elem = E>,
-        std::vec::Vec<ArrayBase<S, Ix1>>: std::iter::FromIterator<ndarray::ArrayBase<ndarray::OwnedRepr<E>, Ix1>>{            
-            let x_vec: Vec<ArrayBase<S, Ix1>> = x.outer_iter().map(|x| x.to_owned()).collect();            
-            x_vec
     }
+    
 }
 
 #[cfg(test)]
 mod tests {    
-    use super::*;          
+    use super::*;    
-    use crate::math::distance::Distance;
+    use crate::math::distance::euclidian; 
-    use ndarray::{arr1, arr2, Array1}; 
+    use crate::linalg::naive::dense_matrix::DenseMatrix;   
 
     #[test]
     fn knn_fit_predict() {                
-        let x = arr2(&[[1, 2], [3, 4], [5, 6], [7, 8], [9, 10]]); 
+        let x = DenseMatrix::from_array(&[
-        let y = arr1(&[2, 2, 2, 3, 3]);        
+            &[1., 2.],
-        let knn = KNNClassifier::fit(NDArrayUtils::array2_to_vec(&x), y.to_vec(), 3, &Array1::distance, KNNAlgorithmName::LinearSearch);        
+            &[3., 4.],
-        let r = knn.predict_vec(&NDArrayUtils::array2_to_vec(&x));
+            &[5., 6.], 
+            &[7., 8.], 
+            &[9., 10.]]); 
+        let y = vec![2., 2., 2., 3., 3.];        
+        let knn = KNNClassifier::fit(&x, &y, 3, &euclidian::distance, KNNAlgorithmName::LinearSearch);        
+        let r = knn.predict(&x);
         assert_eq!(5, Vec::len(&r));
         assert_eq!(y.to_vec(), r);
     }

src/cluster/kmeans.rs

@@ -3,6 +3,7 @@ extern crate rand;
 use rand::Rng;
 
 use crate::linalg::Matrix;
+use crate::math::distance::euclidian;
 use crate::algorithm::neighbour::bbd_tree::BBDTree;
 
 #[derive(Debug)]
@@ -101,7 +102,7 @@ impl KMeans{
             let mut best_cluster = 0;
 
             for j in 0..self.k {
-                let dist = KMeans::squared_distance(&x.get_row_as_vec(i), &self.centroids[j]);                
+                let dist = euclidian::squared_distance(&x.get_row_as_vec(i), &self.centroids[j]);                
                 if dist < min_dist {
                     min_dist = dist;
                     best_cluster = j;
@@ -127,7 +128,7 @@ impl KMeans{
             // the distance from each sample to its closest center in scores.
             for i in 0..n {
                 // compute the distance between this sample and the current center
-                let dist = KMeans::squared_distance(&data.get_row_as_vec(i), &centroid);
+                let dist = euclidian::squared_distance(&data.get_row_as_vec(i), &centroid);
                 
                 if dist < d[i] {
                     d[i] = dist;
@@ -151,7 +152,7 @@ impl KMeans{
 
         for i in 0..n {
             // compute the distance between this sample and the current center
-            let dist = KMeans::squared_distance(&data.get_row_as_vec(i), &centroid);            
+            let dist = euclidian::squared_distance(&data.get_row_as_vec(i), &centroid);            
             
             if dist < d[i] {
                 d[i] = dist;
@@ -161,19 +162,6 @@ impl KMeans{
 
         y
     }
-
-    fn squared_distance(x: &Vec<f64>,y: &Vec<f64>) -> f64 {
-        if x.len() != y.len() {
-            panic!("Input vector sizes are different.");
-        }
-
-        let mut sum = 0f64;
-        for i in 0..x.len() {
-            sum += (x[i] - y[i]).powf(2.);
-        }
-
-        return sum;
-    }
     
 }
 

src/linalg/mod.rs

@@ -18,6 +18,18 @@ pub trait Matrix: Clone + Debug {
 
     fn get_col_as_vec(&self, col: usize) -> Vec<f64>;
 
+    fn to_vector(&self) -> Vec<Vec<f64>> {
+
+        let (n, _) = self.shape();
+        let mut data = Vec::new();
+
+        for i in 0..n {
+            data.push(self.get_row_as_vec(i));
+        }
+
+        data
+    }
+
     fn set(&mut self, row: usize, col: usize, x: f64);
 
     fn qr_solve_mut(&mut self, b: Self) -> Self;

src/math/distance/euclidian.rs

@@ -1,56 +1,33 @@
-use crate::math::distance::Distance;
+pub fn distance(x: &Vec<f64>, y: &Vec<f64>) -> f64 {    
-use ndarray::{ArrayBase, Data, Dimension};
+    return squared_distance(x, y).sqrt();
-use crate::common::AnyNumber;
+}
 
-impl<A, S1, S2, D> Distance<ArrayBase<S2, D>> for ArrayBase<S1, D>
+pub fn squared_distance(x: &Vec<f64>,y: &Vec<f64>) -> f64 {
-where
+    if x.len() != y.len() {
-        A: AnyNumber,
+        panic!("Input vector sizes are different.");
-        S1: Data<Elem = A>,        
-        S2: Data<Elem = A>,        
-        D: Dimension
-{
-    fn distance_to(&self, other: &Self) -> f64 
-    {
-        Self::distance(self, other)
     }
 
-    fn distance(a: &Self, b: &ArrayBase<S2, D>) -> f64 
+    let mut sum = 0f64;
-    {
+    for i in 0..x.len() {
-        if a.len() != b.len() {
+        sum += (x[i] - y[i]).powf(2.);
-            panic!("vectors a and b have different length");
-        } else {     
-            ((a - b)*(a - b)).sum().to_f64().unwrap().sqrt()            
-        }
     }
 
-
+    return sum;
 }
 
 
 #[cfg(test)]
 mod tests {
-    use super::*;
+    use super::*;    
-    use ndarray::{Array1, ArrayView1, arr1};    
 
     #[test]
     fn measure_simple_euclidian_distance() {
-        let a = arr1(&[1, 2, 3]);
+        let a = vec![1., 2., 3.];
-        let b = arr1(&[4, 5, 6]);             
+        let b = vec![4., 5., 6.];             
         
-        let d_arr = Array1::distance(&a, &b);
+        let d_arr = distance(&a, &b);        
-        let d_view = ArrayView1::distance(&a.view(), &b.view());
 
-        assert!((d_arr - 5.19615242).abs() < 1e-8);
+        assert!((d_arr - 5.19615242).abs() < 1e-8);        
-        assert!((d_view - 5.19615242).abs() < 1e-8);
     }    
 
-    #[test]
-    fn measure_simple_euclidian_distance_static() {
-        let a = arr1(&[-2.1968219, -0.9559913, -0.0431738,  1.0567679,  0.3853515]);
-        let b = arr1(&[-1.7781325, -0.6659839,  0.9526148, -0.9460919, -0.3925300]);    
-
-        let d = Array1::distance(&a, &b);
-
-        assert!((d - 2.422302).abs() < 1e-6);
-    }
 }

src/math/distance/mod.rs

@@ -1,9 +1 @@
-pub mod euclidian;
+pub mod euclidian;
-
-pub trait Distance<T> {
-
-    fn distance_to(&self, other: &Self) -> f64;
-
-    fn distance(a: &Self, b: &T) -> f64;     
-
-}