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Merged
hernanmd merged 10 commits into from
Jan 18, 2024
Merged

Updated examples to plot PCA with Roassal 3 #321

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b8ffb91
Updated examples to plot PCA with Roassal 3.
May 25, 2023
ab0a10a
Merge branch 'master' into plot_pca
hernanmd May 25, 2023
264d746
Merge branch 'master' into plot_pca
Dec 27, 2023
f24cbfb
Add visualizations package with dependencies.
Dec 27, 2023
1cd367a
Add missing baseline reference to Roassal
Dec 27, 2023
f6ffd19
Repackage methods
Dec 27, 2023
c044efc
Remove Roassal reference in Baseline
Dec 28, 2023
bb48d99
AIDataInspector -> AIDataFrameInspector
Dec 28, 2023
cb9a018
Fix another reference: AIDataInspector -> AIDataFrameInspector
Dec 28, 2023
2c84554
Add compatibility method because Roassal chart class name changes bet…
Dec 28, 2023
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253 changes: 179 additions & 74 deletions src/BaselineOfPolyMath/BaselineOfPolyMath.class.st
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ Class {
#category : #BaselineOfPolyMath
}

{ #category : #baseline }
{ #category : #baselines }
BaselineOfPolyMath >> baseline: spec [

<baseline>
Expand All @@ -24,80 +24,14 @@ BaselineOfPolyMath >> baseline: spec [
sMark: spec;
xmlWriter: spec;
vectorMatrix: spec;
randomNumbers: spec.
randomNumbers: spec;
datasets: spec;
roassal: spec;
dataFrameInspector: spec.

spec
package: 'ExtendedNumberParser';
package: 'Math-Accuracy-Core';
package: 'Math-Accuracy-ODE' with: [ spec requires: #( 'Math-ODE' 'XMLWriter' ) ];
package: 'Math-ArbitraryPrecisionFloat' with: [ spec requires: #( 'ExtendedNumberParser' ) ];
package: 'Math-AutomaticDifferenciation' with: [ spec requires: #( 'Math-Numerical' 'MathVectorMatrix' ) ];
package: 'Math-Benchmarks-KDTree' with: [ spec requires: #( 'Math-KDTree' 'SMark' ) ];
package: 'Math-Benchmarks-ODE' with: [ spec requires: #( 'Math-ODE' 'SMark' 'XMLWriter' ) ];
package: 'Math-Chromosome' with: [ spec requires: #( 'MathVectorMatrix' ) ];
package: 'Math-Clustering' with: [ spec requires: #( 'Math-Numerical' 'Math-Core-Process' 'MathVectorMatrix' ) ];
package: 'Math-Complex' with: [ spec requires: #( 'Math-Numerical' 'Math-Polynomials' ) ];
package: 'Math-Helpers';
package: 'Math-Distributions' with: [ spec requires: #( 'MathVectorMatrix' 'Math-Quantile' 'Math-Core-Process' ) ];
package: 'Math-Core-Process';
package: 'Math-Numerical'
with: [ spec requires: #( 'MathVectorMatrix' 'Math-Core-Process' 'Math-Distributions' 'Math-StatisticalMoments'
'Math-Series' ) ];
package: 'Math-Polynomials'
with: [ spec requires: #( 'MathVectorMatrix' 'Math-Core-Process' 'Math-Distributions' 'Math-StatisticalMoments'
'Math-Series' ) ];
package: 'Math-FastFourierTransform' with: [ spec requires: #( 'Math-Complex' ) ];
package: 'Math-FunctionFit'
with: [ spec requires: #( 'Math-Numerical' 'Math-Chromosome' 'Math-Accuracy-Core' 'MathVectorMatrix' 'Math-Helpers' 'Math-Polynomials' ) ];
package: 'Math-KDTree';
package: 'Math-Number-Extensions';
package: 'Math-ODE' with: [ spec requires: #( 'Math-Numerical' 'MathVectorMatrix' 'Math-Polynomials' ) ];
package: 'Math-Permutation' with: [ spec requires: #( 'MathVectorMatrix' 'Math-Core-Process' ) ];
package: 'Math-Physics-Constants';
package: 'Math-PrincipalComponentAnalysis' with: [ spec requires: #( 'Math-Numerical' 'MathVectorMatrix' 'Math-Polynomials' ) ];
package: 'Math-Quantile';
package: 'Math-Quaternion' with: [ spec requires: #( 'Math-Complex' 'Math-Numerical' 'Math-Polynomials' ) ];
package: 'Math-Series';
package: 'Math-StatisticalMoments' with: [ spec requires: #( 'Math-Helpers' 'Math-Distributions' ) ];
package: 'Math-TSNE';
package: 'Math-Tests-Accuracy' with: [ spec requires: #( 'Math-Accuracy-Core' ) ];
package: 'Math-Tests-ArbitraryPrecisionFloat' with: [ spec requires: #( 'Math-ArbitraryPrecisionFloat' ) ];
package: 'Math-Tests-AutomaticDifferenciation' with: [ spec requires: #( 'Math-AutomaticDifferenciation' 'MathVectorMatrix' ) ];
package: 'Math-Tests-Clustering' with: [ spec requires: #( 'Math-Clustering' 'Math-Distributions' 'Math-UtilsDataServer' ) ];
package: 'Math-Tests-Complex' with: [ spec requires: #( 'Math-Complex' ) ];
package: 'Math-Tests-Distributions' with: [ spec requires: #( 'Math-Distributions' ) ];
package: 'Math-Tests-Core-Process' with: [ spec requires: #( 'Math-Core-Process' ) ];
package: 'Math-Tests-Numerical' with: [ spec requires: #( 'Math-Numerical' 'Math-UtilsDataServer' ) ];
package: 'Math-Tests-FastFourierTransform' with: [ spec requires: #( 'Math-FastFourierTransform' 'Math-Numerical' 'Math-Polynomials' ) ];
package: 'Math-Tests-FunctionFit';
package: 'Math-Tests-KDTree' with: [ spec requires: #( 'Math-KDTree' ) ];
package: 'Math-Tests-Number-Extensions' with: [ spec requires: #( 'Math-Number-Extensions' ) ];
package: 'Math-Tests-ODE' with: [ spec requires: #( 'Math-ODE' ) ];
package: 'Math-Tests-Permutation' with: [ spec requires: #( 'Math-Permutation' ) ];
package: 'Math-Tests-PrincipalComponentAnalysis' with: [ spec requires: #( 'Math-PrincipalComponentAnalysis' ) ];
package: 'Math-Tests-Quantile' with: [ spec requires: #( 'Math-Quantile' ) ];
package: 'Math-Tests-Polynomials' with: [ spec requires: #( 'Math-Polynomials' ) ];
package: 'Math-Tests-Quaternion' with: [ spec requires: #( 'Math-Quaternion' ) ];
package: 'Math-Tests-TSNE' with: [ spec requires: #( 'Math-TSNE' ) ];
package: 'Math-UtilsDataServer'.
spec
group: 'Accuracy' with: #( 'Math-Accuracy-ODE' 'Math-Accuracy-Core' );
group: 'Benchmarks' with: #( 'Math-Benchmarks-ODE' 'Math-Benchmarks-KDTree' );
group: 'Core'
with:
#( 'Math-Complex' 'Math-Quaternion' 'Math-Numerical' 'MathRandomNumbers' 'Math-KDTree' 'Math-ODE' 'Math-ArbitraryPrecisionFloat'
'Math-FastFourierTransform' 'ExtendedNumberParser' 'Math-Quantile' 'Math-Physics-Constants' 'Math-Polynomials' 'Math-TSNE' 'Math-Core-Process'
'Math-Helpers' 'MathVectorMatrix' 'Math-Distributions' );
group: 'Extensions'
with: #( 'Math-Clustering' 'Math-Number-Extensions' 'Math-Chromosome' 'Math-PrincipalComponentAnalysis' 'Math-FunctionFit' 'Math-AutomaticDifferenciation'
'Math-Permutation' );
group: 'Tests'
with:
#( 'Math-Tests-Clustering' 'Math-Tests-Numerical' 'Math-Tests-Complex' 'Math-Tests-Quaternion' 'Math-Tests-ODE' 'Math-Tests-KDTree' 'Math-Tests-FunctionFit'
'Math-Tests-AutomaticDifferenciation' 'Math-Tests-FastFourierTransform' 'Math-Tests-Accuracy' 'Math-Tests-ArbitraryPrecisionFloat'
'Math-Tests-Quantile' 'Math-Tests-Polynomials' 'Math-Tests-PrincipalComponentAnalysis' 'Math-Tests-Number-Extensions' 'Math-Tests-Permutation'
'Math-Tests-TSNE' 'Math-Tests-Core-Process' 'Math-Tests-Distributions' );
group: 'default' with: #( 'Core' 'Extensions' 'Tests' 'Benchmarks' 'Accuracy' ) ].
self
packages: spec;
groups: spec ].

spec for: #( #'pharo6.x' #'pharo7.x' #'pharo8.x' #'pharo9.x' #'pharo10.x' ) do: [
spec
Expand All @@ -107,6 +41,169 @@ BaselineOfPolyMath >> baseline: spec [
package: 'Math-CompatibilityUpToPharo11' ]
]

{ #category : #dependencies }
BaselineOfPolyMath >> dataFrameInspector: spec [

spec
baseline: 'AIDataFrameInspector'
with: [ spec repository: 'github://pharo-ai/data-inspector/src' ]
]

{ #category : #dependencies }
BaselineOfPolyMath >> datasets: spec [

spec
baseline: 'AIDatasets'
with: [ spec repository: 'github://pharo-ai/datasets' ].
]

{ #category : #baselines }
BaselineOfPolyMath >> groups: spec [

spec
group: 'Accuracy'
with: #( 'Math-Accuracy-ODE' 'Math-Accuracy-Core' );
group: 'Benchmarks'
with: #( 'Math-Benchmarks-ODE' 'Math-Benchmarks-KDTree' );
group: 'Core'
with:
#( 'Math-Complex' 'Math-Quaternion' 'Math-Numerical'
'MathRandomNumbers' 'Math-KDTree' 'Math-ODE' 'Math-ArbitraryPrecisionFloat'
'Math-FastFourierTransform' 'ExtendedNumberParser'
'Math-Quantile' 'Math-Physics-Constants'
'Math-Polynomials' 'Math-TSNE' 'Math-Core-Process'
'Math-Helpers' 'MathVectorMatrix' 'Math-Distributions' );
group: 'Extensions'
with:
#( 'Math-Clustering' 'Math-Number-Extensions'
'Math-Chromosome' 'Math-PrincipalComponentAnalysis'
'Math-FunctionFit' 'Math-AutomaticDifferenciation'
'Math-Permutation' );
group: 'Tests'
with: #( 'Math-Tests-Clustering' 'Math-Tests-Numerical'
'Math-Tests-Complex' 'Math-Tests-Quaternion'
'Math-Tests-ODE' 'Math-Tests-KDTree' 'Math-Tests-FunctionFit'
'Math-Tests-AutomaticDifferenciation'
'Math-Tests-FastFourierTransform'
'Math-Tests-Accuracy' 'Math-Tests-ArbitraryPrecisionFloat'
'Math-Tests-Quantile' 'Math-Tests-Polynomials'
'Math-Tests-PrincipalComponentAnalysis'
'Math-Tests-Number-Extensions' 'Math-Tests-Permutation'
'Math-Tests-TSNE' 'Math-Tests-Core-Process'
'Math-Tests-Distributions' );
group: 'visualizations'
with:
#( 'Core' 'Extensions' 'Tests' 'Benchmarks' 'Accuracy' 'Math-Visualizations' );
group: 'default'
with: #( 'Core' 'Extensions' 'Tests' 'Benchmarks' 'Accuracy' )
]

{ #category : #baselines }
BaselineOfPolyMath >> packages: spec [

spec
package: 'ExtendedNumberParser';
package: 'Math-Accuracy-Core';
package: 'Math-Accuracy-ODE'
with: [ spec requires: #( 'Math-ODE' 'XMLWriter' ) ];
package: 'Math-ArbitraryPrecisionFloat'
with: [ spec requires: #( 'ExtendedNumberParser' ) ];
package: 'Math-AutomaticDifferenciation'
with: [ spec requires: #( 'Math-Numerical' 'MathVectorMatrix' ) ];
package: 'Math-Benchmarks-KDTree'
with: [ spec requires: #( 'Math-KDTree' 'SMark' ) ];
package: 'Math-Benchmarks-ODE'
with: [ spec requires: #( 'Math-ODE' 'SMark' 'XMLWriter' ) ];
package: 'Math-Chromosome'
with: [ spec requires: #( 'MathVectorMatrix' ) ];
package: 'Math-Clustering' with: [
spec requires:
#( 'Math-Numerical' 'Math-Core-Process' 'MathVectorMatrix' ) ];
package: 'Math-Complex'
with: [ spec requires: #( 'Math-Numerical' 'Math-Polynomials' ) ];
package: 'Math-Helpers';
package: 'Math-Distributions' with: [
spec requires:
#( 'MathVectorMatrix' 'Math-Quantile' 'Math-Core-Process' ) ];
package: 'Math-Core-Process';
package: 'Math-Numerical' with: [
spec requires:
#( 'MathVectorMatrix' 'Math-Core-Process' 'Math-Distributions'
'Math-StatisticalMoments' 'Math-Series' ) ];
package: 'Math-Polynomials' with: [
spec requires:
#( 'MathVectorMatrix' 'Math-Core-Process' 'Math-Distributions'
'Math-StatisticalMoments' 'Math-Series' ) ];
package: 'Math-FastFourierTransform'
with: [ spec requires: #( 'Math-Complex' ) ];
package: 'Math-FunctionFit' with: [
spec requires:
#( 'Math-Numerical' 'Math-Chromosome' 'Math-Accuracy-Core'
'MathVectorMatrix' 'Math-Helpers' 'Math-Polynomials' ) ];
package: 'Math-KDTree';
package: 'Math-Number-Extensions';
package: 'Math-ODE' with: [
spec requires:
#( 'Math-Numerical' 'MathVectorMatrix' 'Math-Polynomials' ) ];
package: 'Math-Permutation'
with: [ spec requires: #( 'MathVectorMatrix' 'Math-Core-Process' ) ];
package: 'Math-Physics-Constants';
package: 'Math-PrincipalComponentAnalysis' with: [
spec requires:
#( 'Math-Numerical' 'MathVectorMatrix' 'Math-Polynomials' ) ];
package: 'Math-Quantile';
package: 'Math-Quaternion' with: [
spec requires:
#( 'Math-Complex' 'Math-Numerical' 'Math-Polynomials' ) ];
package: 'Math-Series';
package: 'Math-StatisticalMoments'
with: [ spec requires: #( 'Math-Helpers' 'Math-Distributions' ) ];
package: 'Math-TSNE';
package: 'Math-Tests-Accuracy'
with: [ spec requires: #( 'Math-Accuracy-Core' ) ];
package: 'Math-Tests-ArbitraryPrecisionFloat'
with: [ spec requires: #( 'Math-ArbitraryPrecisionFloat' ) ];
package: 'Math-Tests-AutomaticDifferenciation' with: [
spec requires:
#( 'Math-AutomaticDifferenciation'
'MathVectorMatrix' ) ];
package: 'Math-Tests-Clustering' with: [
spec requires:
#( 'Math-Clustering' 'Math-Distributions' 'Math-UtilsDataServer' ) ];
package: 'Math-Tests-Complex'
with: [ spec requires: #( 'Math-Complex' ) ];
package: 'Math-Tests-Distributions'
with: [ spec requires: #( 'Math-Distributions' ) ];
package: 'Math-Tests-Core-Process'
with: [ spec requires: #( 'Math-Core-Process' ) ];
package: 'Math-Tests-Numerical'
with: [ spec requires: #( 'Math-Numerical' 'Math-UtilsDataServer' ) ];
package: 'Math-Tests-FastFourierTransform' with: [
spec requires:
#( 'Math-FastFourierTransform' 'Math-Numerical' 'Math-Polynomials' ) ];
package: 'Math-Tests-FunctionFit';
package: 'Math-Tests-KDTree'
with: [ spec requires: #( 'Math-KDTree' ) ];
package: 'Math-Tests-Number-Extensions'
with: [ spec requires: #( 'Math-Number-Extensions' ) ];
package: 'Math-Tests-ODE' with: [ spec requires: #( 'Math-ODE' ) ];
package: 'Math-Tests-Permutation'
with: [ spec requires: #( 'Math-Permutation' ) ];
package: 'Math-Tests-PrincipalComponentAnalysis'
with: [ spec requires: #( 'Math-PrincipalComponentAnalysis' ) ];
package: 'Math-Tests-Quantile'
with: [ spec requires: #( 'Math-Quantile' ) ];
package: 'Math-Tests-Polynomials'
with: [ spec requires: #( 'Math-Polynomials' ) ];
package: 'Math-Tests-Quaternion'
with: [ spec requires: #( 'Math-Quaternion' ) ];
package: 'Math-Tests-TSNE'
with: [ spec requires: #( 'Math-TSNE' ) ];
package: 'Math-UtilsDataServer';
package: 'Math-Visualizations'
with: [ spec requires: #( 'AIDatasets' 'AIDataFrameInspector') ]
]

{ #category : #accessing }
BaselineOfPolyMath >> projectClass [
^ [ self class environment at: #MetacelloCypressBaselineProject ]
Expand All @@ -120,6 +217,14 @@ BaselineOfPolyMath >> randomNumbers: spec [
spec baseline: 'MathRandomNumbers' with: [ spec repository: 'github://PolyMathOrg/random-numbers:v1.x.x/src' ]
]

{ #category : #dependencies }
BaselineOfPolyMath >> roassal: spec [

spec
baseline: 'Roassal'
with: [ spec repository: 'github://pharo-graphics/Roassal' ].
]

{ #category : #dependencies }
BaselineOfPolyMath >> sMark: spec [

Expand Down
13 changes: 7 additions & 6 deletions src/Math-PrincipalComponentAnalysis/PMDataTransformer.class.st
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Original file line number Diff line number Diff line change
Expand Up @@ -3,22 +3,23 @@ PMDataTransformer is the abstract root class of transformers. All data transform

"
Class {
#name : #PMDataTransformer,
#superclass : #Object,
#category : #'Math-PrincipalComponentAnalysis'
#name : 'PMDataTransformer',
#superclass : 'Object',
#category : 'Math-PrincipalComponentAnalysis',
#package : 'Math-PrincipalComponentAnalysis'
}

{ #category : #accessing }
{ #category : 'accessing' }
PMDataTransformer >> fit: aPMMatrix [
^ self subclassResponsibility
]

{ #category : #accessing }
{ #category : 'accessing' }
PMDataTransformer >> fitAndTransform: aPMMatrix [
^ (self fit: aPMMatrix) transform: aPMMatrix
]

{ #category : #transforming }
{ #category : 'transforming' }
PMDataTransformer >> transform: aPMMatrix [
^ self subclassResponsibility
]
17 changes: 9 additions & 8 deletions src/Math-PrincipalComponentAnalysis/PMPrincipalComponentAnalyser.class.st
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Original file line number Diff line number Diff line change
@@ -1,33 +1,34 @@
Class {
#name : #PMPrincipalComponentAnalyser,
#superclass : #Object,
#name : 'PMPrincipalComponentAnalyser',
#superclass : 'Object',
#instVars : [
'componentsNumber'
],
#category : #'Math-PrincipalComponentAnalysis'
#category : 'Math-PrincipalComponentAnalysis',
#package : 'Math-PrincipalComponentAnalysis'
}

{ #category : #accessing }
{ #category : 'accessing' }
PMPrincipalComponentAnalyser >> componentsNumber [
^ componentsNumber
]

{ #category : #accessing }
{ #category : 'accessing' }
PMPrincipalComponentAnalyser >> componentsNumber: anInteger [
componentsNumber := anInteger
]

{ #category : #accessing }
{ #category : 'accessing' }
PMPrincipalComponentAnalyser >> fit: aPMMatrix [
^ self subclassResponsibility
]

{ #category : #accessing }
{ #category : 'accessing' }
PMPrincipalComponentAnalyser >> fitAndTransform: aPMMatrix [
^ (self fit: aPMMatrix) transform: aPMMatrix
]

{ #category : #accessing }
{ #category : 'accessing' }
PMPrincipalComponentAnalyser >> transform: aPMMatrix [
^ self subclassResponsibility
]
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