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More functions for working with clusters and display of cluster and k-means centroids

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This commit is contained in:
Antonio Garrote 2010-03-02 09:41:25 +01:00
parent 5d6d85fc0e
commit fba9f97845
4 changed files with 154 additions and 15 deletions
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97
src/clj_ml/clusterers.clj
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@ -4,9 +4,10 @@
;;
(ns clj-ml.clusterers
(:use [clj-ml utils data])
(:use [clj-ml utils data ui]
[incanter charts])
(:import (java.util Date Random)
(weka.clusterers SimpleKMeans)))
(weka.clusterers ClusterEvaluation SimpleKMeans)))
;; Setting up clusterer options
@ -54,3 +55,95 @@
"Applies a clustering algorithm to a set of data"
([clusterer dataset]
(.buildClusterer clusterer dataset)))
;; Retrieving information from a clusterer
(defmulti clusterer-info
"Retrieves the data from a cluster, these data are clustering-algorithm dependent"
(fn [clusterer] (class clusterer)))
(defmethod clusterer-info SimpleKMeans
([clusterer]
"Accepts a k-means clusterer
Returns a map with:
:number-clusters The number of clusters in the clusterer
:centroids Map with the identifier and the centroid values for each cluster"
{:number-clusters (.numberOfClusters clusterer)
:centroids (second
(reduce (fn [acum item]
(let [counter (first acum)
map (second acum)]
(list (+ counter 1)
(conj map {counter item}))))
(list 0 {})
(dataset-seq (.getClusterCentroids clusterer))))
:cluster-sizes (let [sizes (.getClusterSizes clusterer)]
(reduce (fn [acum item]
(conj acum {item (aget sizes item)}))
{}
(range 0 (.numberOfClusters clusterer))))
:squared-error (.getSquaredError clusterer)}))
;; Evaluating clusterers
(defmulti clusterer-evaluate
"Evaluetes a trained clusterer using the provided dataset or cross-validation"
(fn [clusterer mode & evaluation-data] mode))
(defmethod clusterer-evaluate :dataset
([clusterer mode & evaluation-data]
(let [test-data (nth evaluation-data 0)
evaluation (do (let [evl (new ClusterEvaluation)]
(.setClusterer evl clusterer)
evl))]
(.evaluateClusterer evaluation test-data)
(println (.clusterResultsToString evaluation))
evaluation)))
;; Clustering collections
(defn clusterer-cluster
"Add a class to each instance according to the provided clusterer"
([clusterer dataset]
(let [attributes (conj (clj-ml.data/dataset-attributes-definition dataset)
{:class (map #(keyword (str %1)) (range 0 (.numberOfClusters clusterer)))})
clustered (map (fn [i] (conj (instance-to-vector i)
(keyword (str (.clusterInstance clusterer i)))))
(dataset-seq dataset))
nds (make-dataset (keyword (str "clustered " (dataset-name dataset)))
attributes
clustered)]
(dataset-set-class nds (- (count attributes) 1))
nds)))
;; visualization
(defmulti clusterer-display-for-attributes
(fn [clusterer dataset attribute-x attribute-y] (class clusterer)))
(defmethod clusterer-display-for-attributes SimpleKMeans
([clusterer dataset attribute-x attribute-y & visualization-options]
(let [attr-x (if (keyword? attribute-x) (instance-index-attr dataset attribute-x) attribute-x)
attr-y (if (keyword? attribute-y) (instance-index-attr dataset attribute-y) attribute-y)
opts (first-or-default visualization-options {})
display? (if (= (get visualization-options :visualize) false)
false
true)
true-opts (conj opts {:visualize false})
plot (dataset-display-class-for-attributes dataset attribute-x attribute-y true-opts)
info (clusterer-info clusterer)
centroids (:centroids info)]
(do
(loop [ks (keys centroids)]
(if (empty? ks)
(if display?
(visualize-plot plot)
plot)
(let [k (first ks)
centroid (get centroids k)
val-x (instance-value-at centroid attr-x)
val-y (instance-value-at centroid attr-y)]
(add-pointer plot val-x val-y :text (str "centroid " k " (" (float val-x) "," (float val-y) ")"))
(recur (rest ks)))))))))

33
src/clj_ml/data.clj
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@ -4,14 +4,14 @@
;;
(ns clj-ml.data
(:use [clj-ml utils])
(:use [clj-ml utils ui])
(:import (weka.core Instance Instances FastVector Attribute)
(cljml ClojureInstances)))
;; Construction of individual data and datasets
(defn attribute-name-at- [dataset-or-instance pos]
(defn attribute-name-at [dataset-or-instance pos]
(let [class-attr (.attribute dataset-or-instance pos)]
(.name class-attr)))
@ -21,10 +21,17 @@
(loop [c 0]
(if (= c max)
(throw (.Exception (str "Attribute " attrs " not found")))
(if (= attrs (attribute-name-at- dataset-or-instance c))
(if (= attrs (attribute-name-at dataset-or-instance c))
c
(recur (+ c 1 )))))))
(defn dataset-index-attr [dataset attr]
(index-attr dataset attr))
(defn instance-index-attr [instance attr]
(index-attr instance attr))
(defn make-instance
"Creates a new dataset instance from a vector"
([dataset vector]
@ -153,6 +160,10 @@
(+ c 1)))
acum))))
(defn dataset-get-class [dataset]
"Returns the index of the class attribute for this dataset"
(.classIndex dataset))
;; manipulation of instances
(defn instance-set-class [instance pos]
@ -256,3 +267,19 @@
"Removes and returns the first instance in the dataset"
[dataset]
(dataset-extract-at dataset 0))
;; visualization
(defn dataset-display-numeric-attributes [dataset attributes & visualization-options]
"Displays the provided attributes into a box plot"
(let [attr (map #(if (keyword? %1) (index-attr dataset %1) %1) attributes)
options (first-or-default visualization-options {})]
(display-object :dataset :boxplot {:dataset dataset :cols attr} options)))
(defn dataset-display-class-for-attributes [dataset attribute-x attribute-y & visualization-options]
"Displays how a pair of attributes are distributed for each class"
(let [attr-x (if (keyword? attribute-x) (index-attr dataset attribute-x) attribute-x)
attr-y (if (keyword? attribute-y) (index-attr dataset attribute-y) attribute-y)
opts (first-or-default visualization-options {})
class-index (dataset-get-class dataset)]
(display-object :dataset :scatter-plot {:dataset dataset :cols [attr-x attr-y] :group-by class-index} opts)))

32
src/clj_ml/ui.clj
View file

@ -7,6 +7,12 @@
(:use (incanter core stats charts)
(clj-ml data utils)))
(defn visualize-plot [plot]
"Prepare a plot to be displayed"
(do (clear-background plot)
(view plot)
plot))
(defmulti display-object
"Displays some kind of clj-ml object"
(fn [kind chart data opts] [kind chart]))
@ -24,17 +30,18 @@
{}
cols)
title (or (get display-opts :title) (str "Dataset '" (dataset-name dataset) "' Box Plot"))
legend (or (get display-opts :legend) true)]
legend (if (nil? (get display-opts :legend)) true (get display-opts :legend))
should-display (get display-opts :visualize)]
(loop [plot nil
ks (keys vals-map)]
(if (empty? ks)
(do
(view plot)
(if should-display
(visualize-plot plot)
plot)
(let [this-val (get vals-map (first ks))
the-plot (if (nil? plot)
(box-plot this-val :title title)
(do (add-box-plot plot this-val)
(box-plot this-val :title title :legend legend :series-label (key-to-str (first ks)))
(do (add-box-plot plot this-val :series-label (key-to-str (first ks)))
plot))]
(recur the-plot (rest ks))))))))
@ -73,12 +80,13 @@
title (or (get display-opts :title) (str "Dataset '" (dataset-name dataset) "' Scatter Plot ("
(key-to-str (nth cols-names col-0)) " vs "
(key-to-str (nth cols-names col-1)) ")"))
legend (or (get display-opts :legend) true)]
legend (if (nil? (get display-opts :legend)) true (get display-opts :legend))
should-display (get display-opts :visualize)]
(loop [plot nil
ks (keys folded-points)]
(if (empty? ks)
(do
(view plot)
(if should-display
(visualize-plot plot)
plot)
(let [this-vals (get folded-points (first ks))
this-val-0 (get this-vals col-0)
@ -87,8 +95,10 @@
(scatter-plot this-val-0 this-val-1
:title title
:x-label (key-to-str (nth cols-names col-0))
:y-label (key-to-str (nth cols-names col-1)))
(do (add-points plot this-val-0 this-val-1)
:y-label (key-to-str (nth cols-names col-1))
:series-label (key-to-str (first ks))
:legend legend)
(do (add-points plot this-val-0 this-val-1 :series-label (key-to-str (first ks)))
plot))]
(recur the-plot (rest ks))))))))
@ -97,6 +107,8 @@
;(defn load-test-from-slime []
; (do
; (add-classpath "file:///Users/antonio.garrote/Development/old/clj-ml/lib/joda-time-1.6.jar")
; (add-classpath "file:///Users/antonio.garrote/Development/old/clj-ml/lib/opencsv-2.0.1.jar")
; (add-classpath "file:///Users/antonio.garrote/Development/old/clj-ml/classes/")
; (add-classpath "file:///Applications/weka-3-6-2/weka.jar")
; (add-classpath "file:///Users/antonio.garrote/Development/old/clj-ml/src/")

7
src/clj_ml/utils.clj
View file

@ -17,6 +17,13 @@
(let [sk (str k)]
(.substring sk 1)))))
(defn first-or-default
"Returns the first element in the collection or the default value"
([col default]
(if (empty? col)
default
(first col))))
;; Manipulation of array of options
(defn check-option [opts val flag map]