Merge pull request #332 from DurieuxPol/fix/jacobi

Adjustments following changes made to JacobiTransformation

Author: jordanmontt

src/BaselineOfPolyMath/BaselineOfPolyMath.class.st

@@ -10,12 +10,13 @@ PolyMath is a Smalltalk project, similar to existing scientific libraries like N
 
 "
 Class {
-	#name : #BaselineOfPolyMath,
-	#superclass : #BaselineOf,
-	#category : #BaselineOfPolyMath
+	#name : 'BaselineOfPolyMath',
+	#superclass : 'BaselineOf',
+	#category : 'BaselineOfPolyMath',
+	#package : 'BaselineOfPolyMath'
 }
 
-{ #category : #baselines }
+{ #category : 'baselines' }
 BaselineOfPolyMath >> baseline: spec [
 
 	<baseline>
@@ -41,23 +42,23 @@ BaselineOfPolyMath >> baseline: spec [
 			package: 'Math-CompatibilityUpToPharo11' ]
 ]
 
-{ #category : #dependencies }
+{ #category : 'dependencies' }
 BaselineOfPolyMath >> dataFrameInspector: spec [
 
 	spec
 		baseline: 'AIDataFrameInspector'
 		with: [ spec repository: 'github://pharo-ai/data-inspector/src' ]
 ]
 
-{ #category : #dependencies }
+{ #category : 'dependencies' }
 BaselineOfPolyMath >> datasets: spec [
 
 	spec 
 		baseline: 'AIDatasets' 
 		with: [ spec repository: 'github://pharo-ai/datasets' ].
 ]
 
-{ #category : #baselines }
+{ #category : 'baselines' }
 BaselineOfPolyMath >> groups: spec [
 
 	spec
@@ -98,7 +99,7 @@ BaselineOfPolyMath >> groups: spec [
 		with: #( 'Core' 'Extensions' 'Tests' 'Benchmarks' 'Accuracy' )
 ]
 
-{ #category : #baselines }
+{ #category : 'baselines' }
 BaselineOfPolyMath >> packages: spec [
 
 	spec
@@ -204,40 +205,40 @@ BaselineOfPolyMath >> packages: spec [
 		with: [ spec requires: #( 'AIDatasets' 'AIDataFrameInspector') ]
 ]
 
-{ #category : #accessing }
+{ #category : 'accessing' }
 BaselineOfPolyMath >> projectClass [
 	^ [ self class environment at: #MetacelloCypressBaselineProject ]
 		on: NotFound
 		do: [ super projectClass ]
 ]
 
-{ #category : #dependencies }
+{ #category : 'dependencies' }
 BaselineOfPolyMath >> randomNumbers: spec [
 
 	spec baseline: 'MathRandomNumbers' with: [ spec repository: 'github://PolyMathOrg/random-numbers:v1.x.x/src' ]
 ]
 
-{ #category : #dependencies }
+{ #category : 'dependencies' }
 BaselineOfPolyMath >> roassal: spec [
 
 	spec 
 		baseline: 'Roassal' 
 		with: [ spec repository: 'github://pharo-graphics/Roassal' ].
 ]
 
-{ #category : #dependencies }
+{ #category : 'dependencies' }
 BaselineOfPolyMath >> sMark: spec [
 
 	spec baseline: 'SMark' with: [ spec repository: 'github://smarr/SMark:v1.0.4' ]
 ]
 
-{ #category : #dependencies }
+{ #category : 'dependencies' }
 BaselineOfPolyMath >> vectorMatrix: spec [
 
-	spec baseline: 'MathVectorMatrix' with: [ spec repository: 'github://PolyMathOrg/vector-matrix:v1.x.x/src' ]
+	spec baseline: 'MathVectorMatrix' with: [ spec repository: 'github://PolyMathOrg/vector-matrix/src' ]
 ]
 
-{ #category : #dependencies }
+{ #category : 'dependencies' }
 BaselineOfPolyMath >> xmlWriter: spec [
 
 	spec baseline: 'XMLWriter' with: [ spec repository: 'github://pharo-contributions/XML-XMLWriter:2.9.x/src' ]

src/BaselineOfPolyMath/package.st

@@ -1 +1 @@
-Package { #name : #BaselineOfPolyMath }
+Package { #name : 'BaselineOfPolyMath' }

src/Math-PrincipalComponentAnalysis/PMPrincipalComponentAnalyserJacobiTransformation.class.st

@@ -33,7 +33,7 @@ PMPrincipalComponentAnalyserJacobiTransformation >> accumulate: aPMVectorOrArray
 PMPrincipalComponentAnalyserJacobiTransformation >> components [
 	"Precondition: accumulate: should have been used."
 
-	^ self jacobiTransform evaluate copyFrom: 1 to: componentsNumber
+	^ self jacobiTransform eigenValues copyFrom: 1 to: componentsNumber
 ]
 
 { #category : 'accessing' }
@@ -59,5 +59,5 @@ PMPrincipalComponentAnalyserJacobiTransformation >> transform: aPMMatrix [
 PMPrincipalComponentAnalyserJacobiTransformation >> transformMatrix [
 	"Return a matrix that can be applied to any data vector to extract the relevant component of the data vector"
 
-	^ PMMatrix rows: (self jacobiTransform transform rows copyFrom:1 to: componentsNumber )
+	^ PMMatrix rows: (self jacobiTransform eigenVectors rows copyFrom:1 to: componentsNumber )
 ]

src/Math-Tests-Numerical/PMNumericalMethodsTestCase.class.st

@@ -63,8 +63,7 @@ PMNumericalMethodsTestCase >> testEigenvalues [
 	charPol := PMPolynomial coefficients: #(82 -66 15 -1).
 	roots := charPol roots asSortedCollection asArray reverse.
 	finder := PMJacobiTransformation matrix: m.
-	finder desiredPrecision: 1.0e-09.
-	eigenvalues := finder evaluate.
+	eigenvalues := finder eigenValues.
 	self assert: eigenvalues size equals: 3.
 	self assert: ((roots at: 1) - (eigenvalues at: 1)) abs < 1.0e-09.
 	self assert: ((roots at: 2) - (eigenvalues at: 2)) abs < 1.0e-09.

src/Math-Tests-TSNE/PMTSNETest.class.st

@@ -82,5 +82,5 @@ PMTSNETest >> testreduceXToInputDimsUsing [
 	t := (PMTSNE new)
 			x: (PMMatrix rows: #(#(0 0) #(2 2) #(2 0))).
 	t reduceXToInputDimsUsing: PMPrincipalComponentAnalyserJacobiTransformation.
-	self assert: (t x) closeTo: (PMMatrix rows: #(#(-0.5 -1.5) #(-0.5 1.5) #(1 0)))
+	self assert: (t x) closeTo: (PMMatrix rows: #(#(-1.5 -0.5) #(1.5 -0.5) #(0 1)))
 ]