[Issue 81] Refactoring/Clean Up

src/Math-Tests-PrincipalComponentAnalysis/PMPCAJacobiTransformationTest.class.st

@@ -0,0 +1,14 @@
+"
+This test checks that the Jacobi transform based PCA meets the acceptance requirements defined in PMPrincipalComponentAnalysisTest
+"
+Class {
+	#name : #PMPCAJacobiTransformationTest,
+	#superclass : #PMPrincipalComponentAnalyserTest,
+	#category : #'Math-Tests-PrincipalComponentAnalysis'
+}
+
+{ #category : #running }
+PMPCAJacobiTransformationTest >> setUp [
+	pca := PMPrincipalComponentAnalyserJacobiTransformation new
+		componentsNumber: 2
+]

src/Math-Tests-PrincipalComponentAnalysis/PMPCASingularValueDecompositionTest.class.st

@@ -0,0 +1,25 @@
+"
+This test checks that the SVD transform based PCA meets the acceptance requirements defined in PMPrincipalComponentAnalysisTest
+"
+Class {
+	#name : #PMPCASingularValueDecompositionTest,
+	#superclass : #PMPrincipalComponentAnalyserTest,
+	#category : #'Math-Tests-PrincipalComponentAnalysis'
+}
+
+{ #category : #running }
+PMPCASingularValueDecompositionTest >> setUp [
+	pca := PMPrincipalComponentAnalyserSVD new componentsNumber: 2
+]
+
+{ #category : #'scikit-learn-example' }
+PMPCASingularValueDecompositionTest >> testPCAwithPCAandJacobiTransformationReturnSame [
+	| m pca1 pca2 |
+	m := PMMatrix rows: #(#(-1 -1) #(-2 -1) #(-3 -2) #(1 1) #(2 1) #(3 2)).
+	pca1 := PMPrincipalComponentAnalyserSVD new componentsNumber: 2.
+	pca1 fit: m.
+	pca2 := PMPrincipalComponentAnalyserJacobiTransformation new componentsNumber: 2.
+	pca2 fit: m.
+
+	self assert: pca1 transformMatrix abs closeTo: pca2 transformMatrix abs
+]

src/Math-Tests-PrincipalComponentAnalysis/PMPrincipalComponentAnalyserTest.class.st

@@ -8,67 +8,33 @@ Class {
 	#name : #PMPrincipalComponentAnalyserTest,
 	#superclass : #TestCase,
 	#instVars : [
-		'average',
-		'covarianceMatrix',
-		'accumulator',
-		'server'
+		'pca'
 	],
 	#category : #'Math-Tests-PrincipalComponentAnalysis'
 }
 
-{ #category : #'pca tutorial' }
-PMPrincipalComponentAnalyserTest >> testJacobiBasedTransformWithMeanCentredMeasurements [
-	"As acceptance tests we use the worked example of the PCA tutorial of Lindsay Smith"
-	| m pca transformedData expected |
-	m := PMMatrix rows: #(
-			#(0.69 0.49) 
-			#(-1.31 -1.21) 
-			#(0.39 0.99) 
-			#(0.09  0.29) 
-			#(1.29 1.09) 
-			#(0.49 0.79) 
-			#(0.19 -0.31) 
-			#(-0.81 -0.81) 
-			#(-0.31 -0.31) 
-			#(-0.71 -1.01)
-		  ).
-	pca := PMPrincipalComponentAnalyserJacobiTransformation new componentsNumber: 2.
-
-	pca fit: m.	
-	transformedData := pca transform: m.
-
-	expected := PMMatrix rows: #(
-						#(-0.827970186 -0.175115307) 
-						#(1.77758033 0.142857227) 
-						#(-0.992197494 0.384374989) 
-						#(-0.274210416 0.130417207) 
-						#(-1.67580142 -0.209498461) 
-						#(-0.912949103 0.175282444) 
-						#(0.0991094375 -0.349824698) 
-						#(1.14457216 0.0464172582) 
-						#(0.438046137 0.0177646297) 
-						#(1.22382056 -0.162675287)).
-	self assert: (transformedData abs) closeTo: expected abs.
+{ #category : #testing }
+PMPrincipalComponentAnalyserTest class >> isAbstract [ 
+	^ self name = #PMPrincipalComponentAnalyserTest
 ]
 
-{ #category : #tests }
-PMPrincipalComponentAnalyserTest >> testPCAwithPCAandJacobiTransformationReturnSame [
-	| m pca1 pca2 |
-	m := PMMatrix rows: #(#(-1 -1) #(-2 -1) #(-3 -2) #(1 1) #(2 1) #(3 2)).
-	pca1 := PMPrincipalComponentAnalyserSVD new componentsNumber: 2.
-	pca1 fit: m.
-	pca2 := PMPrincipalComponentAnalyserJacobiTransformation new componentsNumber: 2.
-	pca2 fit: m.
+{ #category : #'scikit-learn-example' }
+PMPrincipalComponentAnalyserTest >> testTransformMatrix [
+	| m expected |
+	m := PMMatrix
+		rows: #(#(-1 -1) #(-2 -1) #(-3 -2) #(1 1) #(2 1) #(3 2)).
 
-	self assert: pca1 transformMatrix abs closeTo: pca2 transformMatrix abs
+	pca fit: m.
+
+	expected := (PMMatrix
+		rows: #(#(-0.83849224 -0.54491354) #(0.54491354 -0.83849224))) abs.
+	self assert: pca transformMatrix abs closeTo: expected
 ]
 
-{ #category : #'pca tutorial' }
-PMPrincipalComponentAnalyserTest >> testSVDBasedTransformWithMeanCentredMeasurements [
-	"As acceptance tests we use the worked example of the PCA tutorial of Lindsay Smith"
-
-	| m pca transformedData expected |
-	m := PMMatrix rows: #(
+{ #category : #'lindsay-smith-pca-tutorial' }
+PMPrincipalComponentAnalyserTest >> testTransformWithMeanCentredMeasurements [
+	| meanCentredData transformedData expected |
+	meanCentredData := PMMatrix rows: #(
 			#(0.69 0.49) 
 			#(-1.31 -1.21) 
 			#(0.39 0.99) 
@@ -80,10 +46,8 @@ PMPrincipalComponentAnalyserTest >> testSVDBasedTransformWithMeanCentredMeasurem
 			#(-0.31 -0.31) 
 			#(-0.71 -1.01)
 		  ).
-	pca := PMPrincipalComponentAnalyserSVD new componentsNumber: 2.
 
-	pca fit: m.	
-	transformedData := pca transform: m.
+	transformedData := pca fitAndTransform: meanCentredData.
 
 	expected := PMMatrix rows: #(
 						#(-0.827970186 -0.175115307) 
@@ -98,32 +62,3 @@ PMPrincipalComponentAnalyserTest >> testSVDBasedTransformWithMeanCentredMeasurem
 						#(1.22382056 -0.162675287)).
 	self assert: (transformedData abs) closeTo: expected abs.
 ]
-
-{ #category : #tests }
-PMPrincipalComponentAnalyserTest >> testTransformMatrixWithJacobiTransformation [
-	| m pca expected |
-	m := PMMatrix
-		rows: #(#(-1 -1) #(-2 -1) #(-3 -2) #(1 1) #(2 1) #(3 2)).
-	pca := PMPrincipalComponentAnalyserJacobiTransformation new
-		componentsNumber: 2.
-
-	pca fit: m.
-
-	expected := (PMMatrix
-		rows: #(#(-0.83849224 -0.54491354) #(0.54491354 -0.83849224))) abs.
-	self assert: pca transformMatrix abs closeTo: expected
-]
-
-{ #category : #tests }
-PMPrincipalComponentAnalyserTest >> testTransformMatrixWithSVD [
-	| m pca expected |
-	m := PMMatrix
-		rows: #(#(-1 -1) #(-2 -1) #(-3 -2) #(1 1) #(2 1) #(3 2)).
-	pca := PMPrincipalComponentAnalyserSVD new componentsNumber: 2.
-
-	pca fit: m.
-
-	expected := (PMMatrix
-		rows: #(#(-0.83849224 -0.54491354) #(0.54491354 -0.83849224))) abs.
-	self assert: pca transformMatrix abs closeTo: expected
-]