done part 3 and part 4
This commit is contained in:
parent
38704ac213
commit
703b77a39d
24 changed files with 1667 additions and 3 deletions
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@ -0,0 +1,118 @@
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118
clustering/org.apache.xerces.dom.CoreDocumentImpl_kmeans.csv
Normal file
118
clustering/org.apache.xerces.dom.CoreDocumentImpl_kmeans.csv
Normal file
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@ -0,0 +1,118 @@
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,cluster
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writeObject,0
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@ -0,0 +1,9 @@
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,k_means,hierarchical
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2,0.880893568779594,0.880893568779594
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3,0.865058028908998,0.8832576727129332
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4,0.8716739969277025,0.9044225339758202
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5,0.8801678593155939,0.9033046629733426
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6,0.9027364726730837,0.9090951948593619
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7,0.9172474681026531,0.9392626024065982
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8,0.9426743010154992,0.9453062501090475
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9,0.9512213095625077,0.9512213095625078
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@ -0,0 +1,92 @@
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,cluster
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getGrammarDescription,0
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getAttributeDeclIsExternal,0
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startDTD,0
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startExternalSubset,12
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endExternalSubset,12
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elementDecl,0
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attributeDecl,0
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externalEntityDecl,0
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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|
||||
getContentSpecIndex,10
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||||
getContentSpecAsString,10
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||||
printElements,0
|
||||
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|
||||
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|
||||
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|
||||
createElementDecl,1
|
||||
setElementDecl,0
|
||||
putElementNameMapping,0
|
||||
setFirstAttributeDeclIndex,0
|
||||
setContentSpecIndex,10
|
||||
createAttributeDecl,1
|
||||
setAttributeDecl,0
|
||||
createContentSpec,1
|
||||
setContentSpec,10
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
addUniqueLeafNode,0
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||||
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||||
isImmutable,0
|
||||
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|
||||
printAttribute,0
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||||
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|
||||
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|
||||
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|
||||
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||||
ensureNotationDeclCapacity,0
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||||
ensureContentSpecCapacity,10
|
||||
resize,0
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||||
isEntityDeclared,0
|
||||
isEntityUnparsed,0
|
||||
|
|
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@ -0,0 +1,92 @@
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|||
,cluster
|
||||
getGrammarDescription,4
|
||||
getElementDeclIsExternal,4
|
||||
getAttributeDeclIsExternal,4
|
||||
getAttributeDeclIndex,0
|
||||
startDTD,4
|
||||
startParameterEntity,15
|
||||
startExternalSubset,4
|
||||
endParameterEntity,4
|
||||
endExternalSubset,4
|
||||
elementDecl,14
|
||||
attributeDecl,13
|
||||
internalEntityDecl,4
|
||||
externalEntityDecl,4
|
||||
unparsedEntityDecl,4
|
||||
notationDecl,4
|
||||
endDTD,4
|
||||
setDTDSource,4
|
||||
getDTDSource,4
|
||||
textDecl,4
|
||||
comment,4
|
||||
processingInstruction,4
|
||||
startAttlist,4
|
||||
endAttlist,4
|
||||
startConditional,4
|
||||
ignoredCharacters,4
|
||||
endConditional,4
|
||||
setDTDContentModelSource,4
|
||||
getDTDContentModelSource,4
|
||||
startContentModel,4
|
||||
startGroup,4
|
||||
pcdata,4
|
||||
element,2
|
||||
separator,5
|
||||
occurrence,5
|
||||
endGroup,4
|
||||
any,4
|
||||
empty,4
|
||||
endContentModel,4
|
||||
isNamespaceAware,4
|
||||
getSymbolTable,4
|
||||
getFirstElementDeclIndex,4
|
||||
getNextElementDeclIndex,4
|
||||
getElementDeclIndex,4
|
||||
getContentSpecType,4
|
||||
getElementDecl,1
|
||||
getElementDeclName,4
|
||||
getFirstAttributeDeclIndex,4
|
||||
getNextAttributeDeclIndex,4
|
||||
getAttributeDecl,4
|
||||
isCDATAAttribute,0
|
||||
getEntityDeclIndex,4
|
||||
getEntityDecl,4
|
||||
getNotationDeclIndex,4
|
||||
getNotationDecl,4
|
||||
getContentSpec,4
|
||||
getContentSpecIndex,4
|
||||
getContentSpecAsString,2
|
||||
printElements,4
|
||||
printAttributes,4
|
||||
addContentSpecToElement,11
|
||||
getElementContentModelValidator,1
|
||||
createElementDecl,4
|
||||
setElementDecl,4
|
||||
putElementNameMapping,4
|
||||
setFirstAttributeDeclIndex,4
|
||||
setContentSpecIndex,4
|
||||
createAttributeDecl,8
|
||||
setAttributeDecl,4
|
||||
createContentSpec,4
|
||||
setContentSpec,4
|
||||
createEntityDecl,4
|
||||
setEntityDecl,4
|
||||
createNotationDecl,4
|
||||
setNotationDecl,4
|
||||
addContentSpecNode,4
|
||||
addUniqueLeafNode,2
|
||||
initializeContentModelStack,10
|
||||
isImmutable,4
|
||||
appendContentSpec,2
|
||||
printAttribute,4
|
||||
createChildModel,2
|
||||
buildSyntaxTree,2
|
||||
contentSpecTree,2
|
||||
ensureElementDeclCapacity,7
|
||||
ensureAttributeDeclCapacity,9
|
||||
ensureEntityDeclCapacity,12
|
||||
ensureNotationDeclCapacity,3
|
||||
ensureContentSpecCapacity,6
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resize,4
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||||
isEntityDeclared,4
|
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isEntityUnparsed,4
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92
clustering/org.apache.xerces.impl.dtd.DTDGrammar_kmeans.csv
Normal file
92
clustering/org.apache.xerces.impl.dtd.DTDGrammar_kmeans.csv
Normal file
|
|
@ -0,0 +1,92 @@
|
|||
,cluster
|
||||
getGrammarDescription,1
|
||||
getElementDeclIsExternal,1
|
||||
getAttributeDeclIsExternal,1
|
||||
getAttributeDeclIndex,15
|
||||
startDTD,1
|
||||
startParameterEntity,12
|
||||
startExternalSubset,1
|
||||
endParameterEntity,1
|
||||
endExternalSubset,1
|
||||
elementDecl,9
|
||||
attributeDecl,13
|
||||
internalEntityDecl,1
|
||||
externalEntityDecl,1
|
||||
unparsedEntityDecl,1
|
||||
notationDecl,1
|
||||
endDTD,1
|
||||
setDTDSource,1
|
||||
getDTDSource,1
|
||||
textDecl,1
|
||||
comment,1
|
||||
processingInstruction,1
|
||||
startAttlist,1
|
||||
endAttlist,1
|
||||
startConditional,1
|
||||
ignoredCharacters,1
|
||||
endConditional,1
|
||||
setDTDContentModelSource,1
|
||||
getDTDContentModelSource,1
|
||||
startContentModel,1
|
||||
startGroup,1
|
||||
pcdata,1
|
||||
element,3
|
||||
separator,8
|
||||
occurrence,8
|
||||
endGroup,1
|
||||
any,1
|
||||
empty,1
|
||||
endContentModel,1
|
||||
isNamespaceAware,1
|
||||
getSymbolTable,1
|
||||
getFirstElementDeclIndex,1
|
||||
getNextElementDeclIndex,1
|
||||
getElementDeclIndex,1
|
||||
getContentSpecType,1
|
||||
getElementDecl,0
|
||||
getElementDeclName,1
|
||||
getFirstAttributeDeclIndex,1
|
||||
getNextAttributeDeclIndex,1
|
||||
getAttributeDecl,1
|
||||
isCDATAAttribute,7
|
||||
getEntityDeclIndex,1
|
||||
getEntityDecl,1
|
||||
getNotationDeclIndex,1
|
||||
getNotationDecl,1
|
||||
getContentSpec,1
|
||||
getContentSpecIndex,1
|
||||
getContentSpecAsString,3
|
||||
printElements,1
|
||||
printAttributes,1
|
||||
addContentSpecToElement,14
|
||||
getElementContentModelValidator,0
|
||||
createElementDecl,1
|
||||
setElementDecl,1
|
||||
putElementNameMapping,1
|
||||
setFirstAttributeDeclIndex,1
|
||||
setContentSpecIndex,1
|
||||
createAttributeDecl,7
|
||||
setAttributeDecl,1
|
||||
createContentSpec,1
|
||||
setContentSpec,1
|
||||
createEntityDecl,1
|
||||
setEntityDecl,1
|
||||
createNotationDecl,1
|
||||
setNotationDecl,1
|
||||
addContentSpecNode,1
|
||||
addUniqueLeafNode,3
|
||||
initializeContentModelStack,11
|
||||
isImmutable,1
|
||||
appendContentSpec,3
|
||||
printAttribute,1
|
||||
createChildModel,3
|
||||
buildSyntaxTree,3
|
||||
contentSpecTree,3
|
||||
ensureElementDeclCapacity,6
|
||||
ensureAttributeDeclCapacity,2
|
||||
ensureEntityDeclCapacity,4
|
||||
ensureNotationDeclCapacity,5
|
||||
ensureContentSpecCapacity,10
|
||||
resize,1
|
||||
isEntityDeclared,1
|
||||
isEntityUnparsed,1
|
||||
|
|
|
@ -0,0 +1,16 @@
|
|||
,k_means,hierarchical
|
||||
2,0.7973480585031026,0.5874087027846128
|
||||
3,0.7929515822141272,0.6083207410570212
|
||||
4,0.7875327826881011,0.692671697230321
|
||||
5,0.7432807419504763,0.7141629304171452
|
||||
6,0.7211961130227403,0.7297457578156361
|
||||
7,0.7108188520737106,0.7538651674386223
|
||||
8,0.7521496486020739,0.7823024861034127
|
||||
9,0.7975294826166544,0.8082189521577593
|
||||
10,0.8045822208703368,0.8104671295723321
|
||||
11,0.8091345582763917,0.826856236491233
|
||||
12,0.8140357581974259,0.834060274351163
|
||||
13,0.8468647347587057,0.8414782883217177
|
||||
14,0.8416685816849977,0.8402352442946155
|
||||
15,0.8494389858738608,0.8512242552836264
|
||||
16,0.8571428571428571,0.8571428571428571
|
||||
|
|
|
@ -0,0 +1,107 @@
|
|||
,cluster
|
||||
null2EmptyString,0
|
||||
emptyString2Null,0
|
||||
doc2SystemId,0
|
||||
parseSchema,0
|
||||
validateAnnotations,0
|
||||
createAnnotationValidator,1
|
||||
getGrammar,0
|
||||
findGrammar,0
|
||||
constructTrees,0
|
||||
isExistingGrammar,0
|
||||
updateImportListFor,0
|
||||
updateImportListWith,0
|
||||
buildGlobalNameRegistries,13
|
||||
traverseSchemas,0
|
||||
needReportTNSError,9
|
||||
addGlobalAttributeDecl,13
|
||||
addGlobalAttributeGroupDecl,13
|
||||
addGlobalElementDecl,13
|
||||
addGlobalGroupDecl,13
|
||||
addGlobalNotationDecl,13
|
||||
addGlobalTypeDecl,13
|
||||
addIDConstraintDecl,0
|
||||
getGlobalAttributeDecl,13
|
||||
getGlobalAttributeGroupDecl,13
|
||||
getGlobalElementDecl,13
|
||||
getGlobalGroupDecl,13
|
||||
getGlobalNotationDecl,13
|
||||
getGlobalTypeDecl,13
|
||||
getIDConstraintDecl,0
|
||||
getGlobalDecl,13
|
||||
getGlobalDeclFromGrammar,13
|
||||
traverseGlobalDecl,13
|
||||
schemaDocument2SystemId,0
|
||||
getGrpOrAttrGrpRedefinedByRestriction,0
|
||||
resolveKeyRefs,0
|
||||
getIDRegistry,0
|
||||
getIDRegistry_sub,0
|
||||
storeKeyRef,0
|
||||
resolveSchema,0
|
||||
resolveSchemaSource,0
|
||||
getSchemaDocument,0
|
||||
getSchemaDocument0,0
|
||||
getSchemaDocument1,0
|
||||
expandGrammars,0
|
||||
existingGrammars,0
|
||||
canAddComponents,14
|
||||
canAddComponent,14
|
||||
addGrammars,0
|
||||
addGrammarComponents,14
|
||||
createGrammarFrom,1
|
||||
addNewGrammarLocations,0
|
||||
addNewImportedGrammars,0
|
||||
updateImportList,0
|
||||
addNewGrammarComponents,14
|
||||
addGlobalElementDecls,13
|
||||
addGlobalAttributeDecls,13
|
||||
addGlobalAttributeGroupDecls,13
|
||||
addGlobalNotationDecls,13
|
||||
addGlobalGroupDecls,13
|
||||
addGlobalTypeDecls,13
|
||||
expandComponents,14
|
||||
expandRelatedComponents,14
|
||||
expandRelatedAttributeComponents,14
|
||||
expandRelatedElementComponents,14
|
||||
expandRelatedTypeComponents,14
|
||||
expandRelatedModelGroupDefinitionComponents,14
|
||||
expandRelatedAttributeGroupComponents,14
|
||||
expandRelatedComplexTypeComponents,14
|
||||
expandRelatedSimpleTypeComponents,14
|
||||
expandRelatedAttributeUsesComponents,14
|
||||
expandRelatedAttributeUseComponents,14
|
||||
expandRelatedParticleComponents,14
|
||||
expandRelatedModelGroupComponents,14
|
||||
addRelatedType,0
|
||||
addRelatedElement,0
|
||||
addRelatedAttribute,0
|
||||
addGlobalComponents,13
|
||||
addGlobalComponent,13
|
||||
updateImportDependencies,0
|
||||
expandImportList,0
|
||||
addImportList,0
|
||||
containedImportedGrammar,0
|
||||
getSchemaGrammar,0
|
||||
findDependentNamespaces,0
|
||||
addNamespaceDependency,0
|
||||
reportSharingError,9
|
||||
createTraversers,1
|
||||
prepareForParse,0
|
||||
prepareForTraverse,0
|
||||
setDeclPool,0
|
||||
setDVFactory,0
|
||||
reset,0
|
||||
traverseLocalElements,0
|
||||
removeParticle,0
|
||||
fillInLocalElemInfo,0
|
||||
checkForDuplicateNames,0
|
||||
renameRedefiningComponents,14
|
||||
findQName,0
|
||||
changeRedefineGroup,0
|
||||
findXSDocumentForDecl,0
|
||||
nonAnnotationContent,10
|
||||
setSchemasVisible,0
|
||||
element2Locator,0
|
||||
reportSchemaError,9
|
||||
reportSchemaWarning,0
|
||||
setGenerateSyntheticAnnotations,0
|
||||
|
|
|
@ -0,0 +1,107 @@
|
|||
,cluster
|
||||
null2EmptyString,6
|
||||
emptyString2Null,6
|
||||
doc2SystemId,3
|
||||
parseSchema,7
|
||||
validateAnnotations,3
|
||||
createAnnotationValidator,3
|
||||
getGrammar,3
|
||||
findGrammar,3
|
||||
constructTrees,2
|
||||
isExistingGrammar,3
|
||||
updateImportListFor,3
|
||||
updateImportListWith,3
|
||||
buildGlobalNameRegistries,0
|
||||
traverseSchemas,0
|
||||
needReportTNSError,3
|
||||
addGlobalAttributeDecl,3
|
||||
addGlobalAttributeGroupDecl,3
|
||||
addGlobalElementDecl,3
|
||||
addGlobalGroupDecl,3
|
||||
addGlobalNotationDecl,3
|
||||
addGlobalTypeDecl,3
|
||||
addIDConstraintDecl,3
|
||||
getGlobalAttributeDecl,3
|
||||
getGlobalAttributeGroupDecl,3
|
||||
getGlobalElementDecl,3
|
||||
getGlobalGroupDecl,3
|
||||
getGlobalNotationDecl,3
|
||||
getGlobalTypeDecl,3
|
||||
getIDConstraintDecl,3
|
||||
getGlobalDecl,3
|
||||
getGlobalDeclFromGrammar,3
|
||||
traverseGlobalDecl,0
|
||||
schemaDocument2SystemId,3
|
||||
getGrpOrAttrGrpRedefinedByRestriction,6
|
||||
resolveKeyRefs,3
|
||||
getIDRegistry,3
|
||||
getIDRegistry_sub,3
|
||||
storeKeyRef,0
|
||||
resolveSchema,3
|
||||
resolveSchemaSource,3
|
||||
getSchemaDocument,12
|
||||
getSchemaDocument0,3
|
||||
getSchemaDocument1,3
|
||||
expandGrammars,3
|
||||
existingGrammars,3
|
||||
canAddComponents,3
|
||||
canAddComponent,5
|
||||
addGrammars,3
|
||||
addGrammarComponents,3
|
||||
createGrammarFrom,3
|
||||
addNewGrammarLocations,3
|
||||
addNewImportedGrammars,3
|
||||
updateImportList,3
|
||||
addNewGrammarComponents,3
|
||||
addGlobalElementDecls,5
|
||||
addGlobalAttributeDecls,5
|
||||
addGlobalAttributeGroupDecls,5
|
||||
addGlobalNotationDecls,5
|
||||
addGlobalGroupDecls,5
|
||||
addGlobalTypeDecls,5
|
||||
expandComponents,3
|
||||
expandRelatedComponents,5
|
||||
expandRelatedAttributeComponents,3
|
||||
expandRelatedElementComponents,3
|
||||
expandRelatedTypeComponents,3
|
||||
expandRelatedModelGroupDefinitionComponents,3
|
||||
expandRelatedAttributeGroupComponents,3
|
||||
expandRelatedComplexTypeComponents,3
|
||||
expandRelatedSimpleTypeComponents,3
|
||||
expandRelatedAttributeUsesComponents,3
|
||||
expandRelatedAttributeUseComponents,3
|
||||
expandRelatedParticleComponents,5
|
||||
expandRelatedModelGroupComponents,3
|
||||
addRelatedType,3
|
||||
addRelatedElement,5
|
||||
addRelatedAttribute,5
|
||||
addGlobalComponents,3
|
||||
addGlobalComponent,9
|
||||
updateImportDependencies,3
|
||||
expandImportList,3
|
||||
addImportList,3
|
||||
containedImportedGrammar,3
|
||||
getSchemaGrammar,3
|
||||
findDependentNamespaces,3
|
||||
addNamespaceDependency,3
|
||||
reportSharingError,3
|
||||
createTraversers,3
|
||||
prepareForParse,3
|
||||
prepareForTraverse,3
|
||||
setDeclPool,3
|
||||
setDVFactory,3
|
||||
reset,3
|
||||
traverseLocalElements,10
|
||||
removeParticle,4
|
||||
fillInLocalElemInfo,8
|
||||
checkForDuplicateNames,3
|
||||
renameRedefiningComponents,2
|
||||
findQName,6
|
||||
changeRedefineGroup,11
|
||||
findXSDocumentForDecl,3
|
||||
nonAnnotationContent,3
|
||||
setSchemasVisible,3
|
||||
element2Locator,3
|
||||
reportSchemaError,1
|
||||
reportSchemaWarning,1
|
||||
setGenerateSyntheticAnnotations,3
|
||||
|
|
|
@ -0,0 +1,107 @@
|
|||
,cluster
|
||||
null2EmptyString,8
|
||||
emptyString2Null,8
|
||||
doc2SystemId,0
|
||||
parseSchema,5
|
||||
validateAnnotations,0
|
||||
createAnnotationValidator,0
|
||||
getGrammar,0
|
||||
findGrammar,0
|
||||
constructTrees,3
|
||||
isExistingGrammar,0
|
||||
updateImportListFor,0
|
||||
updateImportListWith,0
|
||||
buildGlobalNameRegistries,2
|
||||
traverseSchemas,2
|
||||
needReportTNSError,0
|
||||
addGlobalAttributeDecl,0
|
||||
addGlobalAttributeGroupDecl,0
|
||||
addGlobalElementDecl,0
|
||||
addGlobalGroupDecl,0
|
||||
addGlobalNotationDecl,0
|
||||
addGlobalTypeDecl,0
|
||||
addIDConstraintDecl,0
|
||||
getGlobalAttributeDecl,0
|
||||
getGlobalAttributeGroupDecl,0
|
||||
getGlobalElementDecl,0
|
||||
getGlobalGroupDecl,0
|
||||
getGlobalNotationDecl,0
|
||||
getGlobalTypeDecl,0
|
||||
getIDConstraintDecl,0
|
||||
getGlobalDecl,0
|
||||
getGlobalDeclFromGrammar,0
|
||||
traverseGlobalDecl,2
|
||||
schemaDocument2SystemId,0
|
||||
getGrpOrAttrGrpRedefinedByRestriction,8
|
||||
resolveKeyRefs,0
|
||||
getIDRegistry,0
|
||||
getIDRegistry_sub,0
|
||||
storeKeyRef,9
|
||||
resolveSchema,0
|
||||
resolveSchemaSource,0
|
||||
getSchemaDocument,0
|
||||
getSchemaDocument0,0
|
||||
getSchemaDocument1,0
|
||||
expandGrammars,0
|
||||
existingGrammars,0
|
||||
canAddComponents,0
|
||||
canAddComponent,1
|
||||
addGrammars,0
|
||||
addGrammarComponents,0
|
||||
createGrammarFrom,0
|
||||
addNewGrammarLocations,0
|
||||
addNewImportedGrammars,0
|
||||
updateImportList,0
|
||||
addNewGrammarComponents,0
|
||||
addGlobalElementDecls,1
|
||||
addGlobalAttributeDecls,1
|
||||
addGlobalAttributeGroupDecls,1
|
||||
addGlobalNotationDecls,1
|
||||
addGlobalGroupDecls,1
|
||||
addGlobalTypeDecls,1
|
||||
expandComponents,0
|
||||
expandRelatedComponents,1
|
||||
expandRelatedAttributeComponents,0
|
||||
expandRelatedElementComponents,0
|
||||
expandRelatedTypeComponents,0
|
||||
expandRelatedModelGroupDefinitionComponents,0
|
||||
expandRelatedAttributeGroupComponents,0
|
||||
expandRelatedComplexTypeComponents,0
|
||||
expandRelatedSimpleTypeComponents,0
|
||||
expandRelatedAttributeUsesComponents,0
|
||||
expandRelatedAttributeUseComponents,0
|
||||
expandRelatedParticleComponents,1
|
||||
expandRelatedModelGroupComponents,0
|
||||
addRelatedType,0
|
||||
addRelatedElement,1
|
||||
addRelatedAttribute,1
|
||||
addGlobalComponents,0
|
||||
addGlobalComponent,6
|
||||
updateImportDependencies,0
|
||||
expandImportList,0
|
||||
addImportList,0
|
||||
containedImportedGrammar,0
|
||||
getSchemaGrammar,0
|
||||
findDependentNamespaces,0
|
||||
addNamespaceDependency,0
|
||||
reportSharingError,0
|
||||
createTraversers,0
|
||||
prepareForParse,0
|
||||
prepareForTraverse,0
|
||||
setDeclPool,0
|
||||
setDVFactory,0
|
||||
reset,0
|
||||
traverseLocalElements,7
|
||||
removeParticle,10
|
||||
fillInLocalElemInfo,12
|
||||
checkForDuplicateNames,0
|
||||
renameRedefiningComponents,13
|
||||
findQName,8
|
||||
changeRedefineGroup,11
|
||||
findXSDocumentForDecl,0
|
||||
nonAnnotationContent,0
|
||||
setSchemasVisible,0
|
||||
element2Locator,0
|
||||
reportSchemaError,4
|
||||
reportSchemaWarning,4
|
||||
setGenerateSyntheticAnnotations,0
|
||||
|
|
|
@ -0,0 +1,14 @@
|
|||
,k_means,hierarchical
|
||||
2,0.653710343152024,0.6897290995261953
|
||||
3,0.7619679813132313,0.739093871180792
|
||||
4,0.7984312146893348,0.8064687623601431
|
||||
5,0.8435547562272465,0.8435547562272465
|
||||
6,0.8611535046317008,0.842649115950788
|
||||
7,0.8678669375642456,0.8504397238719222
|
||||
8,0.8739125874487823,0.8174948896615486
|
||||
9,0.8788481792716016,0.8747912741464551
|
||||
10,0.8903718217266576,0.8775840532668583
|
||||
11,0.8875387867792598,0.8867064376197864
|
||||
12,0.8959671318660039,0.8952551515692575
|
||||
13,0.902637950556443,0.9017527022417632
|
||||
14,0.9084235209322024,0.8989895586680513
|
||||
|
|
|
@ -0,0 +1,109 @@
|
|||
,cluster
|
||||
reset,0
|
||||
getRecognizedFeatures,0
|
||||
setFeature,0
|
||||
getRecognizedProperties,0
|
||||
setProperty,0
|
||||
getFeatureDefault,0
|
||||
getPropertyDefault,0
|
||||
setDocumentHandler,0
|
||||
getDocumentHandler,0
|
||||
startDocument,0
|
||||
xmlDecl,0
|
||||
doctypeDecl,0
|
||||
comment,0
|
||||
processingInstruction,0
|
||||
startElement,0
|
||||
emptyElement,0
|
||||
endElement,0
|
||||
startGeneralEntity,0
|
||||
textDecl,0
|
||||
endGeneralEntity,0
|
||||
characters,0
|
||||
ignorableWhitespace,0
|
||||
startCDATA,0
|
||||
endCDATA,0
|
||||
endDocument,0
|
||||
setDocumentSource,0
|
||||
getDocumentSource,0
|
||||
attributeDecl,0
|
||||
elementDecl,0
|
||||
endAttlist,0
|
||||
endConditional,0
|
||||
endDTD,0
|
||||
endExternalSubset,12
|
||||
endParameterEntity,11
|
||||
externalEntityDecl,0
|
||||
getDTDSource,0
|
||||
ignoredCharacters,0
|
||||
internalEntityDecl,0
|
||||
notationDecl,0
|
||||
setDTDSource,0
|
||||
startAttlist,0
|
||||
startConditional,0
|
||||
startDTD,0
|
||||
startExternalSubset,12
|
||||
startParameterEntity,11
|
||||
unparsedEntityDecl,0
|
||||
getDTDHandler,0
|
||||
setDTDHandler,0
|
||||
setErrorReporter,9
|
||||
handleFallbackElement,0
|
||||
handleIncludeElement,0
|
||||
hasXIncludeNamespace,0
|
||||
isIncludeElement,0
|
||||
isFallbackElement,0
|
||||
sameBaseURIAsIncludeParent,4
|
||||
sameLanguageAsIncludeParent,0
|
||||
setupCurrentBaseURI,4
|
||||
searchForRecursiveIncludes,0
|
||||
isTopLevelIncludedItem,0
|
||||
isTopLevelIncludedItemViaInclude,0
|
||||
isTopLevelIncludedItemViaFallback,0
|
||||
processAttributes,0
|
||||
getRelativeBaseURI,4
|
||||
getIncludeParentBaseURI,4
|
||||
getIncludeParentLanguage,0
|
||||
getIncludeParentDepth,0
|
||||
getResultDepth,0
|
||||
modifyAugmentations,0
|
||||
getState,0
|
||||
setState,0
|
||||
setSawFallback,0
|
||||
getSawFallback,0
|
||||
setSawInclude,0
|
||||
getSawInclude,0
|
||||
reportResourceError,9
|
||||
reportFatalError,9
|
||||
reportError,9
|
||||
setParent,0
|
||||
setHref,0
|
||||
setXIncludeLocator,0
|
||||
isRootDocument,0
|
||||
addUnparsedEntity,0
|
||||
addNotation,0
|
||||
checkUnparsedEntity,0
|
||||
checkNotation,0
|
||||
checkAndSendUnparsedEntity,0
|
||||
checkAndSendNotation,0
|
||||
checkWhitespace,0
|
||||
checkMultipleRootElements,0
|
||||
setRootElementProcessed,0
|
||||
getRootElementProcessed,0
|
||||
copyFeatures,0
|
||||
copyFeatures1,0
|
||||
saveBaseURI,4
|
||||
restoreBaseURI,4
|
||||
saveLanguage,0
|
||||
restoreLanguage,0
|
||||
getBaseURI,4
|
||||
getLanguage,0
|
||||
getRelativeURI,4
|
||||
scopeOfBaseURI,4
|
||||
scopeOfLanguage,0
|
||||
processXMLBaseAttributes,0
|
||||
processXMLLangAttributes,0
|
||||
isValidInHTTPHeader,0
|
||||
createInputSource,1
|
||||
isEqual,0
|
||||
escapeHref,0
|
||||
|
|
|
@ -0,0 +1,109 @@
|
|||
,cluster
|
||||
reset,13
|
||||
getRecognizedFeatures,0
|
||||
setFeature,0
|
||||
getRecognizedProperties,0
|
||||
setProperty,0
|
||||
getFeatureDefault,12
|
||||
getPropertyDefault,8
|
||||
setDocumentHandler,0
|
||||
getDocumentHandler,0
|
||||
startDocument,9
|
||||
xmlDecl,0
|
||||
doctypeDecl,0
|
||||
comment,0
|
||||
processingInstruction,0
|
||||
startElement,0
|
||||
emptyElement,0
|
||||
endElement,0
|
||||
startGeneralEntity,7
|
||||
textDecl,0
|
||||
endGeneralEntity,0
|
||||
characters,0
|
||||
ignorableWhitespace,0
|
||||
startCDATA,0
|
||||
endCDATA,0
|
||||
endDocument,0
|
||||
setDocumentSource,0
|
||||
getDocumentSource,0
|
||||
attributeDecl,0
|
||||
elementDecl,0
|
||||
endAttlist,0
|
||||
endConditional,0
|
||||
endDTD,0
|
||||
endExternalSubset,0
|
||||
endParameterEntity,0
|
||||
externalEntityDecl,0
|
||||
getDTDSource,0
|
||||
ignoredCharacters,0
|
||||
internalEntityDecl,0
|
||||
notationDecl,0
|
||||
setDTDSource,0
|
||||
startAttlist,0
|
||||
startConditional,0
|
||||
startDTD,0
|
||||
startExternalSubset,0
|
||||
startParameterEntity,0
|
||||
unparsedEntityDecl,0
|
||||
getDTDHandler,0
|
||||
setDTDHandler,0
|
||||
setErrorReporter,3
|
||||
handleFallbackElement,0
|
||||
handleIncludeElement,11
|
||||
hasXIncludeNamespace,0
|
||||
isIncludeElement,0
|
||||
isFallbackElement,0
|
||||
sameBaseURIAsIncludeParent,0
|
||||
sameLanguageAsIncludeParent,0
|
||||
setupCurrentBaseURI,0
|
||||
searchForRecursiveIncludes,0
|
||||
isTopLevelIncludedItem,0
|
||||
isTopLevelIncludedItemViaInclude,0
|
||||
isTopLevelIncludedItemViaFallback,0
|
||||
processAttributes,14
|
||||
getRelativeBaseURI,0
|
||||
getIncludeParentBaseURI,0
|
||||
getIncludeParentLanguage,0
|
||||
getIncludeParentDepth,0
|
||||
getResultDepth,0
|
||||
modifyAugmentations,5
|
||||
getState,0
|
||||
setState,0
|
||||
setSawFallback,10
|
||||
getSawFallback,10
|
||||
setSawInclude,4
|
||||
getSawInclude,4
|
||||
reportResourceError,1
|
||||
reportFatalError,1
|
||||
reportError,3
|
||||
setParent,0
|
||||
setHref,0
|
||||
setXIncludeLocator,0
|
||||
isRootDocument,0
|
||||
addUnparsedEntity,0
|
||||
addNotation,0
|
||||
checkUnparsedEntity,0
|
||||
checkNotation,0
|
||||
checkAndSendUnparsedEntity,0
|
||||
checkAndSendNotation,0
|
||||
checkWhitespace,0
|
||||
checkMultipleRootElements,0
|
||||
setRootElementProcessed,0
|
||||
getRootElementProcessed,0
|
||||
copyFeatures,7
|
||||
copyFeatures1,0
|
||||
saveBaseURI,0
|
||||
restoreBaseURI,0
|
||||
saveLanguage,0
|
||||
restoreLanguage,0
|
||||
getBaseURI,0
|
||||
getLanguage,0
|
||||
getRelativeURI,0
|
||||
scopeOfBaseURI,0
|
||||
scopeOfLanguage,0
|
||||
processXMLBaseAttributes,2
|
||||
processXMLLangAttributes,2
|
||||
isValidInHTTPHeader,0
|
||||
createInputSource,6
|
||||
isEqual,0
|
||||
escapeHref,0
|
||||
|
109
clustering/org.apache.xerces.xinclude.XIncludeHandler_kmeans.csv
Normal file
109
clustering/org.apache.xerces.xinclude.XIncludeHandler_kmeans.csv
Normal file
|
|
@ -0,0 +1,109 @@
|
|||
,cluster
|
||||
reset,2
|
||||
getRecognizedFeatures,0
|
||||
setFeature,0
|
||||
getRecognizedProperties,0
|
||||
setProperty,0
|
||||
getFeatureDefault,0
|
||||
getPropertyDefault,13
|
||||
setDocumentHandler,0
|
||||
getDocumentHandler,0
|
||||
startDocument,9
|
||||
xmlDecl,0
|
||||
doctypeDecl,0
|
||||
comment,0
|
||||
processingInstruction,0
|
||||
startElement,0
|
||||
emptyElement,0
|
||||
endElement,0
|
||||
startGeneralEntity,1
|
||||
textDecl,0
|
||||
endGeneralEntity,0
|
||||
characters,0
|
||||
ignorableWhitespace,0
|
||||
startCDATA,0
|
||||
endCDATA,0
|
||||
endDocument,0
|
||||
setDocumentSource,0
|
||||
getDocumentSource,0
|
||||
attributeDecl,0
|
||||
elementDecl,0
|
||||
endAttlist,0
|
||||
endConditional,0
|
||||
endDTD,0
|
||||
endExternalSubset,0
|
||||
endParameterEntity,0
|
||||
externalEntityDecl,0
|
||||
getDTDSource,0
|
||||
ignoredCharacters,0
|
||||
internalEntityDecl,0
|
||||
notationDecl,0
|
||||
setDTDSource,0
|
||||
startAttlist,0
|
||||
startConditional,0
|
||||
startDTD,0
|
||||
startExternalSubset,0
|
||||
startParameterEntity,0
|
||||
unparsedEntityDecl,0
|
||||
getDTDHandler,0
|
||||
setDTDHandler,0
|
||||
setErrorReporter,4
|
||||
handleFallbackElement,0
|
||||
handleIncludeElement,3
|
||||
hasXIncludeNamespace,0
|
||||
isIncludeElement,0
|
||||
isFallbackElement,0
|
||||
sameBaseURIAsIncludeParent,0
|
||||
sameLanguageAsIncludeParent,0
|
||||
setupCurrentBaseURI,0
|
||||
searchForRecursiveIncludes,0
|
||||
isTopLevelIncludedItem,0
|
||||
isTopLevelIncludedItemViaInclude,0
|
||||
isTopLevelIncludedItemViaFallback,0
|
||||
processAttributes,12
|
||||
getRelativeBaseURI,0
|
||||
getIncludeParentBaseURI,0
|
||||
getIncludeParentLanguage,0
|
||||
getIncludeParentDepth,0
|
||||
getResultDepth,0
|
||||
modifyAugmentations,11
|
||||
getState,0
|
||||
setState,14
|
||||
setSawFallback,8
|
||||
getSawFallback,8
|
||||
setSawInclude,7
|
||||
getSawInclude,7
|
||||
reportResourceError,6
|
||||
reportFatalError,6
|
||||
reportError,4
|
||||
setParent,0
|
||||
setHref,0
|
||||
setXIncludeLocator,0
|
||||
isRootDocument,0
|
||||
addUnparsedEntity,0
|
||||
addNotation,0
|
||||
checkUnparsedEntity,0
|
||||
checkNotation,0
|
||||
checkAndSendUnparsedEntity,0
|
||||
checkAndSendNotation,0
|
||||
checkWhitespace,0
|
||||
checkMultipleRootElements,0
|
||||
setRootElementProcessed,0
|
||||
getRootElementProcessed,0
|
||||
copyFeatures,1
|
||||
copyFeatures1,0
|
||||
saveBaseURI,0
|
||||
restoreBaseURI,0
|
||||
saveLanguage,0
|
||||
restoreLanguage,0
|
||||
getBaseURI,0
|
||||
getLanguage,0
|
||||
getRelativeURI,0
|
||||
scopeOfBaseURI,0
|
||||
scopeOfLanguage,0
|
||||
processXMLBaseAttributes,5
|
||||
processXMLLangAttributes,5
|
||||
isValidInHTTPHeader,0
|
||||
createInputSource,10
|
||||
isEqual,0
|
||||
escapeHref,0
|
||||
|
|
|
@ -0,0 +1,15 @@
|
|||
,k_means,hierarchical
|
||||
2,0.7400737900068505,0.7450255723178434
|
||||
3,0.750834341421787,0.7590675173051686
|
||||
4,0.7679751766235376,0.7537209967731088
|
||||
5,0.7694034011467328,0.7857193607872571
|
||||
6,0.7912800923302977,0.7998705023701569
|
||||
7,0.7945459689471787,0.8089785658259816
|
||||
8,0.8182179715203751,0.8386247544828634
|
||||
9,0.8417229111627736,0.8681233694906747
|
||||
10,0.8647266620127783,0.879025772110854
|
||||
11,0.8825387834587034,0.8849687834612566
|
||||
12,0.8852199398177911,0.891045019202272
|
||||
13,0.8905822525359668,0.8974662016344479
|
||||
14,0.9036154755382922,0.9037208985767615
|
||||
15,0.9101193816556802,0.9101193816556802
|
||||
|
47
ground_truth.py
Executable file
47
ground_truth.py
Executable file
|
|
@ -0,0 +1,47 @@
|
|||
#!/usr/bin/env python3
|
||||
import os
|
||||
import pandas as pd
|
||||
import glob
|
||||
|
||||
|
||||
DIR: str = os.path.dirname(os.path.realpath(__file__))
|
||||
IN_DIR: str = DIR + '/feature_vectors'
|
||||
OUT_DIR: str = DIR + '/clustering'
|
||||
|
||||
|
||||
def clean_output():
|
||||
filelist = glob.glob(OUT_DIR + '/*_groundtruth.csv')
|
||||
for f in filelist:
|
||||
os.remove(f)
|
||||
|
||||
|
||||
def ground_truth(method_name: str, keywords: list[str]):
|
||||
for i, key in enumerate(keywords):
|
||||
if method_name.find(key) != -1:
|
||||
return i + 1
|
||||
|
||||
return 0
|
||||
|
||||
|
||||
def create_ground_truth(path: str, keywords: list[str]):
|
||||
clazz_name = os.path.basename(path)
|
||||
clazz_name = clazz_name[:clazz_name.rfind('.')]
|
||||
|
||||
df = pd.read_csv(path, index_col=0).filter([])
|
||||
df['cluster'] = df.index.map(lambda m: ground_truth(m.lower(), keywords))
|
||||
df.to_csv(OUT_DIR + '/' + clazz_name + '_groundtruth.csv')
|
||||
|
||||
|
||||
def main():
|
||||
with open(DIR + '/keyword_list.txt', 'r') as f:
|
||||
keywords: list[str] = [x.strip().strip('\n').lower() for x in f.readlines()]
|
||||
|
||||
clean_output()
|
||||
|
||||
filelist = glob.glob(IN_DIR + '/*.csv')
|
||||
for f in filelist:
|
||||
create_ground_truth(f, keywords)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
49
hierarchical.py
Executable file
49
hierarchical.py
Executable file
|
|
@ -0,0 +1,49 @@
|
|||
#!/usr/bin/env python3
|
||||
from sklearn.cluster import AgglomerativeClustering
|
||||
import numpy as np
|
||||
import glob
|
||||
import os
|
||||
import pandas as pd
|
||||
import argparse
|
||||
|
||||
DIR: str = os.path.dirname(os.path.realpath(__file__))
|
||||
OUT_DIR: str = DIR + '/clustering'
|
||||
IN_DIR: str = DIR + '/feature_vectors'
|
||||
|
||||
|
||||
def cluster_hierarchical(path: str, n_clusters: int, save_to_disk: bool = True) -> tuple[any, any]:
|
||||
clazz_name = os.path.basename(path)
|
||||
clazz_name = clazz_name[:clazz_name.rfind('.')]
|
||||
|
||||
df = pd.read_csv(path)
|
||||
X = df.drop(df.columns[0], axis=1).to_numpy()
|
||||
kmeans = AgglomerativeClustering(
|
||||
n_clusters=n_clusters, linkage='complete').fit(X)
|
||||
|
||||
Y = kmeans.labels_ # array of cluster # assigned to each method
|
||||
|
||||
# combine cluster labels with method name
|
||||
assigned = pd.DataFrame(Y, columns=['cluster']).set_axis(
|
||||
df.iloc[:, 0].values)
|
||||
|
||||
if save_to_disk:
|
||||
assigned.to_csv(OUT_DIR + '/' + clazz_name + '_hierarchical.csv')
|
||||
|
||||
return (X, Y,)
|
||||
|
||||
|
||||
def main():
|
||||
parser = argparse.ArgumentParser(
|
||||
description='Compute agglomerative clustering')
|
||||
parser.add_argument('class_name', type=str, help='name of the god class')
|
||||
parser.add_argument('n_clusters', type=int, help='number of clusters')
|
||||
|
||||
args = parser.parse_args()
|
||||
path = IN_DIR + '/' + args.class_name + '.csv'
|
||||
|
||||
os.remove(OUT_DIR + '/' + args.class_name + '_hierarchical.csv')
|
||||
cluster_hierarchical(path, args.n_clusters)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
52
k_means.py
Executable file
52
k_means.py
Executable file
|
|
@ -0,0 +1,52 @@
|
|||
#!/usr/bin/env python3
|
||||
from sklearn.cluster import KMeans
|
||||
import numpy as np
|
||||
import glob
|
||||
import os
|
||||
import pandas as pd
|
||||
import argparse
|
||||
|
||||
DIR: str = os.path.dirname(os.path.realpath(__file__))
|
||||
OUT_DIR: str = DIR + '/clustering'
|
||||
IN_DIR: str = DIR + '/feature_vectors'
|
||||
|
||||
RAND_SEED: int = 0
|
||||
|
||||
|
||||
def cluster_kmeans(path: str, n_clusters: int, save_to_disk: bool = True) -> tuple[any, any]:
|
||||
clazz_name = os.path.basename(path)
|
||||
clazz_name = clazz_name[:clazz_name.rfind('.')]
|
||||
|
||||
df = pd.read_csv(path, index_col=0)
|
||||
X = df.to_numpy()
|
||||
|
||||
kmeans = KMeans(n_clusters=n_clusters,
|
||||
random_state=RAND_SEED, n_init='auto').fit(X)
|
||||
|
||||
Y = kmeans.labels_ # array of cluster # assigned to each method
|
||||
|
||||
# combine cluster labels with method name
|
||||
assigned = pd.DataFrame(Y, columns=['cluster']).set_axis(
|
||||
df.index.values)
|
||||
|
||||
if save_to_disk:
|
||||
assigned.to_csv(OUT_DIR + '/' + clazz_name + '_kmeans.csv')
|
||||
|
||||
return (X, Y,)
|
||||
|
||||
|
||||
def main():
|
||||
parser = argparse.ArgumentParser(
|
||||
description='Compute k-means clustering')
|
||||
parser.add_argument('class_name', type=str, help='name of the god class')
|
||||
parser.add_argument('n_clusters', type=int, help='number of clusters')
|
||||
|
||||
args = parser.parse_args()
|
||||
path = IN_DIR + '/' + args.class_name + '.csv'
|
||||
|
||||
os.remove(OUT_DIR + '/' + args.class_name + '_kmeans.csv')
|
||||
cluster_kmeans(path, args.n_clusters)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
14
keyword_list.txt
Normal file
14
keyword_list.txt
Normal file
|
|
@ -0,0 +1,14 @@
|
|||
create
|
||||
object
|
||||
cache
|
||||
uri
|
||||
standalone
|
||||
encoding
|
||||
identifier
|
||||
user
|
||||
error
|
||||
content
|
||||
parameter
|
||||
subset
|
||||
global
|
||||
component
|
||||
49
prec_recall.py
Executable file
49
prec_recall.py
Executable file
|
|
@ -0,0 +1,49 @@
|
|||
#!/usr/bin/env python3
|
||||
import numpy as np
|
||||
import glob
|
||||
import os
|
||||
import pandas as pd
|
||||
|
||||
DIR: str = os.path.dirname(os.path.realpath(__file__))
|
||||
IN_DIR: str = DIR + '/clustering'
|
||||
OUT_DIR: str = DIR + ''
|
||||
|
||||
|
||||
def intrapairs(path: str) -> set[set[str, str]]:
|
||||
df = pd.read_csv(path)
|
||||
clusters: list[list[str]] = df.groupby(
|
||||
'cluster').agg(list).iloc[:, 0].values
|
||||
|
||||
intrapairs: set[set[str]] = set() # inner sets always contain 2 elements
|
||||
for cluster in clusters:
|
||||
for i, e1 in enumerate(cluster):
|
||||
for j in range(i + 1, len(cluster)):
|
||||
e2 = cluster[j]
|
||||
intrapairs.add(frozenset((e1, e2,)))
|
||||
return intrapairs
|
||||
|
||||
|
||||
def main():
|
||||
filelist = glob.glob(IN_DIR + '/*_groundtruth.csv')
|
||||
for f in filelist:
|
||||
clazz_name = os.path.basename(f)
|
||||
clazz_name = clazz_name[:clazz_name.rfind('_groundtruth.csv')]
|
||||
print(clazz_name)
|
||||
|
||||
ground_pairs = intrapairs(f)
|
||||
for method in ['kmeans', 'hierarchical']:
|
||||
cluster_pairs = intrapairs(
|
||||
IN_DIR + '/' + clazz_name + '_' + method + '.csv')
|
||||
|
||||
n_common = len(ground_pairs.intersection(cluster_pairs))
|
||||
precision = n_common / len(cluster_pairs)
|
||||
recall = n_common / len(ground_pairs)
|
||||
|
||||
print(method + " precision: " + str(precision))
|
||||
print(method + " recall: " + str(recall))
|
||||
|
||||
print()
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
28
readme.md
28
readme.md
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@ -21,7 +21,7 @@ source env/bin/activate
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pip3 install -r requirements.txt
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```
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## Run *find god classes*
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## Running part 1: find god classes
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```shell
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./find_god_classes.py
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@ -29,6 +29,32 @@ pip3 install -r requirements.txt
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The resulting CSV file containing a list of God classes is generated in the `god_classes/god_classes.csv` path.
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## Running part 3: clustering and silhouette metric
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To compute optimal k-means and agglomerative clusterings using silhouette
|
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validation for all classes run:
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```shell
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||||
./silhouette.py --validate --autorun
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```
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To compute k-means or agglomerative clustering for a specific number of
|
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clusters `K` and a specific class `KLASS` run respectively:
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|
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```shell
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./k_means.py KLASS K
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```
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```shell
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./hierarchical.py KLASS K
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```
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||||
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Then, to check their silhouette metric run:
|
||||
|
||||
```shell
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||||
./silhouette.py
|
||||
```
|
||||
|
||||
## Compile report
|
||||
|
||||
- Install [Pandoc](https://pandoc.org/);
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||||
|
|
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|
|
@ -1,4 +1,4 @@
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|||
javalang==0.13.0
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numpy==1.23.5
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||||
pandas==1.5.2
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||||
scikit_learn==1.2.1
|
||||
shrek==0.0.2
|
||||
scikit_learn==1.2.2
|
||||
|
|
|
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95
silhouette.py
Executable file
95
silhouette.py
Executable file
|
|
@ -0,0 +1,95 @@
|
|||
#!/usr/bin/env python3
|
||||
from sklearn.cluster import AgglomerativeClustering
|
||||
from sklearn.metrics import silhouette_score
|
||||
import numpy as np
|
||||
import glob
|
||||
import os
|
||||
import pandas as pd
|
||||
import argparse
|
||||
from k_means import cluster_kmeans
|
||||
from hierarchical import cluster_hierarchical
|
||||
|
||||
DIR: str = os.path.dirname(os.path.realpath(__file__))
|
||||
OUT_DIR: str = DIR + '/clustering'
|
||||
IN_DIR: str = DIR + '/feature_vectors'
|
||||
|
||||
K_MAX: int = 65
|
||||
|
||||
|
||||
def clean_output():
|
||||
filelist = glob.glob(OUT_DIR + '/*_silhouette.csv')
|
||||
for f in filelist:
|
||||
os.remove(f)
|
||||
|
||||
|
||||
def validate(path: str, clazz_name: str, autorun: bool):
|
||||
df = pd.DataFrame(columns=['k_means', 'hierarchical'], dtype=float)
|
||||
|
||||
# We bound the number of clusters by the number of distinct points in our dataset.
|
||||
# To count them, we compute the number of "distinct" feature vectors and we
|
||||
# bound to the minimum of K_MAX and this number.
|
||||
nodup = pd.read_csv(path, index_col=0).drop_duplicates()
|
||||
max_distinct = len(nodup)
|
||||
|
||||
for n in range(2, min(K_MAX, max_distinct)):
|
||||
X_h, Y_h = cluster_hierarchical(path, n, save_to_disk=False)
|
||||
df.loc[n, 'k_means'] = silhouette_score(X_h, Y_h)
|
||||
|
||||
X_k, Y_k = cluster_kmeans(path, n, save_to_disk=False)
|
||||
df.loc[n, 'hierarchical'] = silhouette_score(X_k, Y_k)
|
||||
|
||||
k_kmeans = df[['k_means']].idxmax()[0]
|
||||
k_hierarchical = df[['hierarchical']].idxmax()[0]
|
||||
|
||||
print("K_means optimal value: " + str(k_kmeans))
|
||||
print("Hierarchical optimal value: " + str(k_hierarchical))
|
||||
|
||||
df.to_csv(OUT_DIR + '/' + clazz_name + '_silhouette.csv')
|
||||
|
||||
if autorun:
|
||||
cluster_hierarchical(path, k_hierarchical)
|
||||
cluster_kmeans(path, k_kmeans)
|
||||
|
||||
|
||||
|
||||
def compute_silhouette(path: str, clazz_name: str, suffix: str):
|
||||
df_y = pd.read_csv(OUT_DIR + '/' + clazz_name + '_' + suffix + '.csv')
|
||||
Y = df_y.iloc[:, 1].values
|
||||
|
||||
df = pd.read_csv(path)
|
||||
X = df.drop(df.columns[0], axis=1).to_numpy()
|
||||
|
||||
print("Silhouette for " + suffix + ": " + str(silhouette_score(X, Y)))
|
||||
|
||||
|
||||
def main():
|
||||
parser = argparse.ArgumentParser(description='Compute silhouette metric.')
|
||||
parser.add_argument('--validate', action='store_true',
|
||||
help='compute optimal k for each algorithm')
|
||||
parser.add_argument('--autorun', action='store_true',
|
||||
help='if validating, computes CSV for optimal clustering automatically')
|
||||
|
||||
|
||||
args = parser.parse_args()
|
||||
|
||||
if args.validate:
|
||||
clean_output()
|
||||
|
||||
filelist = glob.glob(IN_DIR + '/*.csv')
|
||||
for f in filelist:
|
||||
clazz_name = os.path.basename(f)
|
||||
clazz_name = clazz_name[:clazz_name.rfind('.')]
|
||||
|
||||
print(clazz_name)
|
||||
|
||||
if args.validate:
|
||||
validate(f, clazz_name, args.autorun)
|
||||
|
||||
compute_silhouette(f, clazz_name, 'kmeans')
|
||||
compute_silhouette(f, clazz_name, 'hierarchical')
|
||||
|
||||
print()
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
Reference in a new issue