report almost done

clustering/org.apache.xerces.dom.CoreDocumentImpl_groundtruth.csv

@@ -0,0 +1,118 @@
+,cluster
+getOwnerDocument,0
+getNodeType,0
+getNodeName,0
+cloneNode,0
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+removeChild,0
+replaceChild,0
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+setTextContent,10
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+loadXML,0
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+writeObject,2

clustering/org.apache.xerces.dom.CoreDocumentImpl_hierarchical.csv

@@ -0,0 +1,118 @@
+,cluster
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+getXmlStandalone,14
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+readObject,5
+writeObject,5

clustering/org.apache.xerces.dom.CoreDocumentImpl_kmeans.csv

@@ -0,0 +1,118 @@
+,cluster
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clustering/org.apache.xerces.dom.CoreDocumentImpl_silhouette.csv

@@ -0,0 +1,45 @@
+,k_means,hierarchical
+2,0.3958383820498147,0.7008424223503156
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+45,0.7289990873402857,0.7289990873402858

clustering/org.apache.xerces.dom.CoreDocumentImpl_stats.csv

@@ -0,0 +1,89 @@
+,algorithm,k,min,mean,max
+0,hierarchical,2,1,58.5,116
+1,k_means,2,1,58.5,116
+2,hierarchical,3,1,39.0,113
+3,k_means,3,1,39.0,115
+4,hierarchical,4,1,29.25,113
+5,k_means,4,1,29.25,98
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+7,k_means,5,1,23.4,98
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+9,k_means,6,1,19.5,98
+10,hierarchical,7,1,16.714285714285715,97
+11,k_means,7,1,16.714285714285715,98
+12,hierarchical,8,1,14.625,97
+13,k_means,8,1,14.625,98
+14,hierarchical,9,1,13.0,96
+15,k_means,9,1,13.0,97
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+17,k_means,10,1,11.7,92
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+85,k_means,44,1,2.659090909090909,47
+86,hierarchical,45,1,2.6,46
+87,k_means,45,1,2.6,46

clustering/org.apache.xerces.impl.dtd.DTDGrammar_groundtruth.csv

@@ -0,0 +1,92 @@
+,cluster
+getGrammarDescription,0
+getElementDeclIsExternal,0
+getAttributeDeclIsExternal,0
+getAttributeDeclIndex,0
+startDTD,0
+startParameterEntity,11
+startExternalSubset,12
+endParameterEntity,11
+endExternalSubset,12
+elementDecl,0
+attributeDecl,0
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+unparsedEntityDecl,0
+notationDecl,0
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+setDTDSource,0
+getDTDSource,0
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+startConditional,0
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+setDTDContentModelSource,10
+getDTDContentModelSource,10
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+isImmutable,0
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+createChildModel,1
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+contentSpecTree,10
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+ensureAttributeDeclCapacity,0
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+ensureNotationDeclCapacity,0
+ensureContentSpecCapacity,10
+resize,0
+isEntityDeclared,0
+isEntityUnparsed,0

clustering/org.apache.xerces.impl.dtd.DTDGrammar_hierarchical.csv

@@ -0,0 +1,92 @@
+,cluster
+getGrammarDescription,0
+getElementDeclIsExternal,0
+getAttributeDeclIsExternal,0
+getAttributeDeclIndex,0
+startDTD,0
+startParameterEntity,0
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+elementDecl,1
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+unparsedEntityDecl,0
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+setDTDSource,0
+getDTDSource,0
+textDecl,0
+comment,0
+processingInstruction,0
+startAttlist,0
+endAttlist,0
+startConditional,0
+ignoredCharacters,0
+endConditional,0
+setDTDContentModelSource,0
+getDTDContentModelSource,0
+startContentModel,0
+startGroup,0
+pcdata,0
+element,0
+separator,0
+occurrence,0
+endGroup,0
+any,0
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+resize,0
+isEntityDeclared,0
+isEntityUnparsed,0

clustering/org.apache.xerces.impl.dtd.DTDGrammar_kmeans.csv

@@ -0,0 +1,92 @@
+,cluster
+getGrammarDescription,6
+getElementDeclIsExternal,50
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+startDTD,13
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+notationDecl,40
+endDTD,29
+setDTDSource,53
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+textDecl,6
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+setDTDContentModelSource,51
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+setFirstAttributeDeclIndex,3
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+createAttributeDecl,19
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+createContentSpec,41
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clustering/org.apache.xerces.impl.dtd.DTDGrammar_silhouette.csv

@@ -0,0 +1,64 @@
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clustering/org.apache.xerces.impl.dtd.DTDGrammar_stats.csv

@@ -0,0 +1,127 @@
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clustering/org.apache.xerces.impl.xs.traversers.XSDHandler_groundtruth.csv

@@ -0,0 +1,107 @@
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clustering/org.apache.xerces.impl.xs.traversers.XSDHandler_hierarchical.csv

@@ -0,0 +1,107 @@
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clustering/org.apache.xerces.impl.xs.traversers.XSDHandler_kmeans.csv

@@ -0,0 +1,107 @@
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clustering/org.apache.xerces.impl.xs.traversers.XSDHandler_silhouette.csv

@@ -0,0 +1,64 @@
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clustering/org.apache.xerces.impl.xs.traversers.XSDHandler_stats.csv

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clustering/org.apache.xerces.xinclude.XIncludeHandler_groundtruth.csv

@@ -0,0 +1,109 @@
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clustering/org.apache.xerces.xinclude.XIncludeHandler_hierarchical.csv

@@ -0,0 +1,109 @@
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clustering/org.apache.xerces.xinclude.XIncludeHandler_kmeans.csv

@@ -0,0 +1,109 @@
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clustering/org.apache.xerces.xinclude.XIncludeHandler_silhouette.csv

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+57,0.4522750157266781,0.44773608146478383
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+63,0.4775136217473302,0.49518159007961093
+64,0.4821848224907804,0.4872143751031807

clustering/org.apache.xerces.xinclude.XIncludeHandler_stats.csv

@@ -0,0 +1,127 @@
+,algorithm,k,min,mean,max
+0,hierarchical,2,2,54.0,106
+1,k_means,2,1,54.0,107
+2,hierarchical,3,1,36.0,106
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extract_feature_vectors.py

@@ -0,0 +1,143 @@
+#!/usr/bin/env python3
+import javalang
+import os
+import pandas as pd
+import glob
+import warnings
+import tabulate
+
+DIR: str = os.path.dirname(os.path.realpath(__file__))
+SOURCES: str = DIR + '/resources/xerces2-j-src'
+OUT_DIR: str = DIR + '/feature_vectors'
+IN_DIR: str = DIR + '/god_classes'
+
+
+def clean_output():
+    filelist = glob.glob(OUT_DIR + '/*.csv')
+    for f in filelist:
+        os.remove(f)
+        
+
+def get_fields(java_class: javalang.tree.ClassDeclaration) -> set[str]:
+    names = set()
+    for f in java_class.fields:
+        names.add(f.declarators[0].name)
+    return names
+
+
+def get_methods(java_class: javalang.tree.ClassDeclaration) -> set[str]:
+    names = set()
+    for f in java_class.methods:
+        names.add(f.name)
+    return names
+
+
+def empty_qualifier(node: any) -> bool:
+    return node.qualifier is None or node.qualifier == '' or node.qualifier == 'this'
+
+
+def get_fields_accessed_by_method(method: javalang.tree.MethodDeclaration, fields: set[str]) -> set[str]:
+    # Ignore formal parameters and local variable declarations
+    local_variables = set()
+    for _, node in method.filter(javalang.tree.LocalVariableDeclaration):
+        local_variables.add(node.declarators[0].name)
+    for _, node in method.filter(javalang.tree.FormalParameter):
+        local_variables.add(node.name)
+
+    nodes = set()
+    for _, node in method.filter(javalang.tree.MemberReference):
+        if empty_qualifier(node):
+            name = node.member
+            if name in fields:
+                nodes.add(name)
+        else:
+            # qualifier of 'a.b.c.x' is 'a.b.c', we only care about 'a'
+            name = node.qualifier.split('.', maxsplit=1)[0] 
+
+            # cannot use field set here, since a class may be referenced (through a static property)
+            # hence we fetch the local variables (and parameters) in the method and we explicitly avoid them
+            if not name in local_variables:
+                
+                # if a MemberReference includes a non empty qualifier (e.g., a.x),
+                # consider the qualifier (a), not the member (x)˝
+                nodes.add(name)
+    return nodes
+
+
+def get_methods_accessed_by_method(method: javalang.tree.MethodDeclaration, methods: set[str]) -> set[str]:
+    nodes = set()
+    for _, node in method.filter(javalang.tree.MethodInvocation):
+        name: str = node.member
+        if empty_qualifier(node) and name in methods:
+            nodes.add(name)
+    return nodes
+
+
+def parse(path: str, name: str, df_table):
+    # Get the AST of the file
+    with open(path) as file:
+        data = file.read()
+    tree = javalang.parse.parse(data)
+
+    # Fetch package name from package declaration
+    # if node is missing, assuming default package ('')
+    package_name = ''
+    for _, node in tree.filter(javalang.tree.PackageDeclaration):
+        package_name = node.name
+        break
+
+    for _, node in tree.filter(javalang.tree.ClassDeclaration):
+
+        # consider only the class matching the input file name, to skip inner classes
+        if path.endswith(node.name + '.java'):
+            fqdn = package_name + '.' + node.name
+            
+            fields = get_fields(node)
+            methods = get_methods(node)
+
+            cols = sorted(fields.union(methods))
+
+            df = pd.DataFrame(columns=cols, dtype=int)
+            for m in node.methods:
+                # make sure method is included in csv file
+                df.loc[m.name, :] = 0
+
+                m_fields = get_fields_accessed_by_method(m, fields)
+                m_methods = get_methods_accessed_by_method(m, methods)
+
+                for member in m_fields.union(m_methods):
+                    if member not in df:
+                        df[member] = 0
+                    df.loc[m.name, member] = 1
+            df = df.fillna(0)
+
+            for i in df.columns:
+                df[[i]] = df[[i]].astype(int)
+
+            df = df.loc[:, (df != 0).any(axis=0)]
+
+            df_table.loc[name, '# Feature Vectors'] = df.shape[0]
+            df_table.loc[name, '# Attributes'] = df.shape[1]
+            
+            df.to_csv(OUT_DIR + '/' + fqdn + '.csv')
+            break
+
+
+def main():
+    warnings.simplefilter(action='ignore', category=pd.errors.PerformanceWarning)
+    clean_output()
+
+    df = pd.read_csv(IN_DIR + '/god_classes.csv')
+
+    df_table = pd.DataFrame(columns=['# Feature Vectors', '# Attributes'])
+
+    for clazz in df['class_name'].to_list():
+        clazz_path = SOURCES + '/' + clazz.replace('.', '/') + '.java'
+        print(clazz_path)
+        parse(clazz_path, clazz, df_table)
+
+    df_table.index.name = "Class Name"
+    print(df_table.to_markdown())
+
+if __name__ == '__main__':
+    main()

feature_vectors/org.apache.xerces.dom.CoreDocumentImpl.csv

@@ -0,0 +1,118 @@
+,actualEncoding,allowGrammarAccess,callUserDataHandlers,canRenameElements,changes,copyEventListeners,createAttribute,createAttributeNS,createCDATASection,createComment,createDocumentFragment,createDocumentType,createElement,createElementNS,createEntity,createEntityReference,createNotation,createProcessingInstruction,createTextNode,docElement,docType,domNormalizer,encoding,errorChecking,fConfiguration,fDocumentURI,fFreeNLCache,fXPathEvaluator,getIdentifier,getImplementation,getUserData,getXmlEncoding,getXmlStandalone,getXmlVersion,identifiers,importNode,isNormalizeDocRequired,isXMLName,kidOK,nodeCounter,nodeTable,removeIdentifier,removeUserDataTable,renamedAttrNode,renamedElement,replaceRenameElement,setUserData,setUserDataTable,setXmlEncoding,setXmlStandalone,setXmlVersion,standalone,undeferChildren,userData,version,xml11Version,xmlVersionChanged,Node,UserDataHandler,kid,DOMMessageFormatter,DOMException,NamespaceContext
+getOwnerDocument,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+getNodeType,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0
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+getTextContent,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+setTextContent,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+getFeature,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0
+createAttribute,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,1,0
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+createComment,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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feature_vectors/org.apache.xerces.impl.dtd.DTDGrammar.csv

@@ -0,0 +1,92 @@
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feature_vectors/org.apache.xerces.impl.xs.traversers.XSDHandler.csv

@@ -0,0 +1,107 @@
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feature_vectors/org.apache.xerces.xinclude.XIncludeHandler.csv

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find_god_classes.py

@@ -3,6 +3,7 @@ import javalang
 import os
 import pandas as pd
 import glob
+import tabulate
 
 # God class if:
 # |M(C)| > E(M) + 6*V(M)
@@ -69,6 +70,10 @@ def main():
     god_classes_df = df[df['method_num'] > threshold]
     god_classes_df.to_csv(OUT_DIR + '/god_classes.csv')
 
+    god_classes_df.columns = ['Class Name', '# Methods']
+    god_classes_df = god_classes_df.set_index('Class Name', drop=True)
+    print(god_classes_df.to_markdown())
+
 
 if __name__ == '__main__':
     main()

ground_truth.py

@@ -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()

hierarchical.py

@@ -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()

k_means.py

@@ -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()

keyword_list.txt

@@ -0,0 +1,14 @@
+create
+object
+cache
+uri
+standalone
+encoding
+identifier
+user
+error
+content
+parameter
+subset
+global
+component

prec_recall.py

@@ -0,0 +1,60 @@
+#!/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')
+    df_table = pd.DataFrame(columns=pd.MultiIndex.from_tuples([
+        ('KMeans', 'Precision'),
+        ('KMeans', 'Recall'),
+        ('Agglomerative', 'Precision'),
+        ('Agglomerative', 'Recall')]))
+    df_table.index.name = 'Class Name'
+
+    for f in filelist:
+        clazz_name = os.path.basename(f)
+        clazz_name = clazz_name[:clazz_name.rfind('_groundtruth.csv')]
+
+        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)
+
+            algo = 'KMeans' if method == 'kmeans' else 'Agglomerative'
+            
+            df_table.loc[clazz_name, [(algo, 'Precision'), (algo, 'Recall')]] = [
+                str(round(precision * 100, 2)) + '%', 
+                str(round(recall * 100, 2)) + '%'
+            ]
+
+    df_table.columns = [x[0] + ' ' + x[1] for x in df_table.columns]
+    print(df_table.to_markdown())
+
+
+if __name__ == '__main__':
+    main()

readme.md

@@ -1,4 +1,4 @@
-### Information Modelling & Analysis: Project 1
+# Information Modelling & Analysis: Project 1
 
 Student: *enter your name here*
 
@@ -10,3 +10,52 @@ For your convenience, the source code to be analyzed (xerces2)
 **Attention**: Please consider the submission instructions available on iCorsi.
 
 **Report**: You may want to use the template distributed on iCorsi.
+
+## Install dependencies
+
+```shell
+# create venv
+python -m venv env
+source env/bin/activate
+
+pip3 install -r requirements.txt
+```
+
+## Running part 1: find god classes
+
+```shell
+./find_god_classes.py
+```
+
+The resulting CSV file containing a list of God classes is generated in the `god_classes/god_classes.csv` path.
+
+## Running part 3: clustering and silhouette metric
+
+To compute optimal k-means and agglomerative clusterings using silhouette 
+validation for all classes run:
+
+```shell
+./silhouette.py --validate --autorun
+```
+
+To compute k-means or agglomerative clustering for a specific number of 
+clusters `K` and a specific class `KLASS` run respectively:
+
+```shell
+./k_means.py KLASS K
+```
+
+```shell
+./hierarchical.py KLASS K
+```
+
+Then, to check their silhouette metric run:
+
+```shell
+./silhouette.py
+```
+
+## Compile report
+
+- Install [Pandoc](https://pandoc.org/);
+- Run `pandoc main.md -o main.pdf` in `report` directory.

report/build.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+set -e
+
+SCRIPT_DIR=$(cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd)
+
+cd "$SCRIPT_DIR"
+pandoc main.md -o main.pdf  

report/main.md

@@ -0,0 +1,270 @@
+---
+author: Claudio Maggioni
+title: Information Modelling & Analysis -- Project 1
+geometry: margin=2cm,bottom=3cm
+---
+
+<!--
+The following shows a minimal submission report for project 1. If you
+choose to use this template, replace all template instructions (the
+yellow bits) with your own values. In addition, for any section, if
+**and only if** anything was unclear or warnings were raised by the
+code, and you had to take assumptions about the correct implementation (e.g.,
+about details of a metric), describe your assumptions in one or two sentences.
+
+You may - at your own risk - also choose not to use this template. As long as
+your submission is a latex-generated, English PDF containing all expected info,
+you'll be fine.  -->
+
+# Code Repository
+
+The code and result files part of this submission can be found at:
+
+::: center Repository:
+\url{https://github.com/infoMA2023/project-01-god-classes-maggicl}
+
+Commit ID: **TBD** :::
+
+# Data Pre-Processing
+
+## God Classes
+
+The first part of the project requires to label some classes of the _Xerces_
+project as "God classes" based on the number of methods each class has. From
+here onwards the Java package prefix `org.apache.xerces` is omitted when discussing 
+fully qualified domain names of classes for sake of brevity.
+
+Specifically, I label "God classes" the classes that have a number of methods
+six times the standard deviation above the the mean number of methods, i.e.
+where the condition
+
+$$|M(C)| > \mu(M) + 6\sigma(M)$$
+
+holds.
+
+To scan and compute the number of methods of each class I use the Python library
+`javalang`, which implements the Java AST and parser. The Python script
+`./find_god_classes.py` uses this library to parse each file in the project and
+compute the number of methods of each class. Note that only non-constructor
+methods are counted (specifically the code counts the number of `method` nodes
+in each `ClassDeclaration` node).
+
+Then, the script computes mean and standard deviation of the number of methods
+and filters the list of classes according to the condition described above. The
+file `god_classes/god_classes.csv` then is outputted listing all the god classes
+found.
+
+The god classes I identified, and their corresponding number of methods can be
+found in Table [1](#tab:god_classes){reference-type="ref"
+reference="tab:god_classes"}. 
+
+::: {#tab:god_classes}
+| **Class Name**                                 | **# Methods** |
+|:------------------------------------------------|------------:|
+| impl.xs.traversers.XSDHandler |         118 |
+| impl.dtd.DTDGrammar           |         101 |
+| xinclude.XIncludeHandler      |         116 |
+| dom.CoreDocumentImpl          |         125 |
+
+  : Identified God Classes
+:::
+
+
+## Feature Vectors
+
+In this part of the project we produce the feature vectors used to later cluster
+the methods of each God class into separate clusters. We produce one feature
+method per non-constructor Java method in each god class.
+
+The columns of each vector represent fields and methods referenced by each
+method, i.e. fields and methods actively used by the method in their method's
+body.
+
+When analyzing references to fields, additional constraints need to be specified
+to handle edge cases.  Namely, a field's property may be referenced (e.g. an
+access to array `a` may fetch its `length` property, i.e. `a.length`). In this
+cases I consider the qualifier (i.e. the field itself, `a`) itself and not its
+property. When the qualifier is a class (i.e.  the code references a property of
+another class, e.g. `Integer.MAX_VALUE`) we consider the class name itself (i.e.
+`Integer`) and not the name of the property. Should the qualifier be a
+subproperty itself (e.g. in `a.b.c`, where `a.b` would be the qualifier
+according to `javalang`)
+
+For methods, I only consider calls to methods of the class itself where the
+qualifier is unspecified or `this`. Calls to parent methods (i.e. calls like
+`super.something()`) are not considered.
+
+The feature vector extraction phase is performed by the Python script
+`extract_feature_vectors.py`. The script takes `god_classes/god_classes.csv` as
+input and loads the AST of each class listed in it. Then, a list of all the
+fields and methods in the class is built, and each method is scanned to see
+which fields and methods it references in its body according to the previously
+described rules. Then, a CSV per class is built storing all feature vectors.
+Each file has a name matching to the FQDN (Fully-qualified domain name) of the
+class. Each CSV row refers to a method in the class, and each CSV column refers
+to a field, method or referenced class. A cell has the value of 1 when the
+method of that row references the field, method or class marked by that column,
+and it has the value 0 otherwise. Columns with only zeros are omitted.
+
+Table [2](#tab:feat_vec){reference-type="ref" reference="tab:feat_vec"} shows
+aggregate numbers regarding the extracted feature vectors for the god classes.
+Note that the number of attributes refers to the number of fields, methods or
+classes actually references (i.e. the number of columns after omission of 0s).
+
+::: {#tab:feat_vec}
+| **Class Name**                                  | **# Feature Vectors** | **# Attributes\*** |
+|:------------------------------------------------|----------------------:|-----------------:|
+| impl.xs.traversers.XSDHandler |                 106 |            183 |
+| impl.dtd.DTDGrammar           |                  91 |            106 |
+| xinclude.XIncludeHandler      |                 108 |            143 |
+| dom.CoreDocumentImpl          |                 117 |             63 |
+
+  : Feature vector summary (\*= used at least once)
+:::
+
+# Clustering {#sec:clustering}
+
+In this section I covering the techniques to cluster the methods of each god
+class. The project aims to use KMeans clustering and agglomerative hierarchical
+clustering to group these methods toghether in cohesive units which could be
+potentially refactored out of the god class they belong to.
+
+## Algorithm Configurations
+
+To perform KMeans clustering, I use the `cluster.KMeans` Scikit-Learn
+implementation of the algorithm.  I use the default parameters: feature vectors
+are compared with euclidian distance, centroids are used instead of medioids,
+and the initial centroids are computed with the greedy algorithm `kmeans++`. The
+random seed is fixed to $0$ to allow for reproducibility between executions of
+the clustering script.
+
+To perform Hierarchical clustering, I use the `cluster.AgglomerativeClustering`
+Scikit-Learn implementation of the algorithm.  Again feature vectors are
+compared with euclidian distance, but as a linkage metric I choose to use
+complete linkage.  As agglomerative clustering is deternministic, no random seed
+is needed for this algorithm.
+
+I run the two algorithms for all $k \in [2,65]$, or if less than 65 feature
+vectors with distinct values are assigned to the god class, the upper bound of
+$k$ is such value.
+
+## Testing Various K & Silhouette Scores
+
+To find the optimal value of $k$ for both algorithms, the distribution of
+cluster sizes and silhouette across values of $k$, and to apply the optimal
+clustering for each god class I run the command:
+
+```shell
+./silhouette.py --validate --autorun
+```
+
+Feature vectors are read from the `feature_vectors` directory and all the
+results are stored in the `clustering` directory.
+
+Figures [1](#fig:xsd){reference-type="ref" reference="fig:xsd"},
+[2](#fig:dtd){reference-type="ref" reference="fig:dtd"},
+[3](#fig:xinc){reference-type="ref" reference="fig:xinc"}, and
+[4](#fig:cimpl){reference-type="ref" reference="fig:cimpl"} show the
+distributions of cluster sizes for each god class obtained by running the KMeans
+and agglomerative clustering algorithm as described in the previous sections.
+
+For all god classes, the mean of number of elements in each cluster
+exponentially decreases as $k$ increases. Aside the first values of $k$ for
+class `DTDGrammar` (where it was 2), the minimum cluster size was 1 for all
+analyzed clusterings.  Conversely, the maximum cluster size varies a lot, almost
+always being monotonically non increasing as $k$ increases, occasionally forming
+wide plateaus. The silhouette metric distribution instead generally follows a
+dogleg-like path, sharply decreasing for the first values of $k$ and slowly
+increasing afterwards $k$. This leads the choice of the optimal $k$ number of
+clusters for each algorithm to be between really low and really high values.
+
+The figures also show the distribution of the silhouette metric per algorithm
+and per value of $k$. The optimal values of $k$ and the respective silhouette
+values for each implementation are reported in Table
+[3](#tab:sumup){reference-type="ref" reference="tab:sumup"}.
+
+From the values we can gather that agglomerative clustering performs overall
+better than KMeans for the god classes in the project.  Almost god classes are
+optimally clustered with few clusters, with the exception of `CoreDocumentImpl`
+being optimally clustered with unit clusters. This could indicate higher
+cohesion between implementation details of the other classes, and lower cohesion
+in `CoreDocumentImpl` (given the name it would not be surprising if this class
+plays the role of an utility class of sort, combining lots of implementation
+details affecting different areas of the code).
+
+Agglomerative clustering with complete linkage could perform better than KMeans
+due to a more urgent need for separation rather than cohesion in the classes
+that were analyzed. Given the high dimensionality of the feature vectures used,
+and the fact that eucledian distance is used to compare feature vectors, the
+hyper-space of method features for each god class is likely sparse, with
+occasional clusters of tightly-knit features.  Given the prevailing sparsity,
+complete linkage could be suitable here since it avoids to agglomerate distant
+clusters above all.
+
+![Clustering metrics for class impl.xs.traversers.XSDHandler](../clustering/org.apache.xerces.impl.xs.traversers.XSDHandler_stats.png){#fig:xsd}
+
+![Clustering metrics for class impl.dtd.DTDGrammar](../clustering/org.apache.xerces.impl.dtd.DTDGrammar_stats.png){#fig:dtd}
+
+![Clustering metrics for class xinclude.XIncludeHandler](../clustering/org.apache.xerces.xinclude.XIncludeHandler_stats.png){#fig:xinc}
+
+![Clustering metrics for class dom.CoreDocumentImpl](../clustering/org.apache.xerces.dom.CoreDocumentImpl_stats.png){#fig:cimpl}
+
+::: {#tab:sumup}
+| **Class Name**            | **KMeans K** |   **KMeans silhouette** |   **Hierarchical K** |   **Hierarchical silhouette** |
+|:------------- --------------|-----------:|--------------------:|-----------------:|--------------------------:|
+| dom.CoreDocumentImpl        |         45 |0.7290 |               45 |                    0.7290 | 
+| impl.xs.traversers.XSDHandler |          2 |0.5986 |                3 |                    0.5989 | 
+| impl.dtd.DTDGrammar           |         58 |0.3980 |                2 |                    0.4355 | 
+| xinclude.XIncludeHandler      |          2 |0.6980 |                2 |                    0.6856 |
+
+  : Optimal hyperparameters and corresponding silhouette metrics for KMeans and
+Hierarchical clustering algorithm. 
+:::
+
+# Evaluation
+
+## Ground Truth
+
+I computed the ground truth using the Python script `./ground_truth.py` The
+generated files are checked into the repository with the names
+`clustering/{className}_groundtruth.csv` where `{className}` is the FQDN of each
+god class.
+
+The ground truth in this project is not given but generated according to simple
+heuristics. Since no inherent structure or labelling from experts exists to
+group the methods in each god class, the project requires to label methods based
+on keyword matching whitin each method name. The list of keywords used can be
+found in `keyword_list.txt`. This approach allows to have a ground truth at all
+with little computational cost and labelling effort, but it assumes the method
+name and the chosen keywords are indeed of enough significance to form a
+meaningful clustering of methods that form refactorable cohesive units of
+functionality. 
+
+## Precision and Recall
+
+::: {#tab:eval}
+| **Class Name**                                      | **KMeans Precision**   | **KMeans Recall**   | **Agglomerative Precision**   | **Agglomerative Recall**   |
+|:------------------------------------------------|-------------------:|----------------:|--------------------------:|-----------------------:|
+| xinclude.XIncludeHandler      | 69.83%             | 97.80%           | 69.58%                    | 95.65%                 |
+| dom.CoreDocumentImpl          | 64.80%              | 28.26%          | 68.11%                    | 29.70%                  |
+| impl.xs.traversers.XSDHandler | 36.17%             | 97.24%          | 36.45%                    | 96.11%                 |
+| impl.dtd.DTDGrammar           | 87.65%             | 6.87%           | 52.21%                    | 94.28%                 |
+
+  : Evaluation Summary
+:::
+
+Precision and Recall, for the optimal configurations found in Section
+[3](#sec:clustering){reference-type="ref" reference="sec:clustering"}, are
+reported in Table [4](#tab:eval){reference-type="ref" reference="tab:eval"}.
+
+\begin{center}
+\color{red} comment precision and recall values
+\end{center}
+
+## Practical Usefulness
+
+\begin{center}
+\color{red}Discuss the practical usefulness of the obtained code refactoring assistant in a
+realistic setting (1 paragraph).
+\end{center}
+

requirements.txt

@@ -1,4 +1,5 @@
 javalang==0.13.0
-pandas==1.5.2
-scikit_learn==1.2.1
-shrek==0.0.2
+numpy==1.24.2
+pandas==2.0.0
+scikit_learn==1.2.2
+tabulate==0.9.0

silhouette.py

@@ -0,0 +1,147 @@
+#!/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
+from collections import Counter
+import seaborn as sns
+import matplotlib.pyplot as plt
+
+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)
+    filelist = glob.glob(OUT_DIR + '/*.png')
+    for f in filelist:
+        os.remove(f)
+
+
+def validate(path: str, clazz_name: str, autorun: bool, df_table):
+    df = pd.DataFrame(columns=['k_means', 'hierarchical'], dtype=float)
+    df_stats = pd.DataFrame(columns=['algorithm', 'k', 'min', 'mean', 'max'])
+    
+    def add_stat(algo: str, k: int, Y: any, i: int):
+        y_occurs = list(Counter(Y).values()) # count number of elements in each cluster
+        df_stats.loc[i, :] = [algo, k, np.min(y_occurs), np.mean(y_occurs), np.max(y_occurs)]
+
+    # 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)
+    limit = min(K_MAX, max_distinct)
+
+    i: int = 0
+    for n in range(2, limit):
+        X_h, Y_h = cluster_hierarchical(path, n, save_to_disk=False)
+        add_stat('hierarchical', n, Y_h, i)
+        i += 1
+        df.loc[n, 'hierarchical'] = silhouette_score(X_h, Y_h)
+        
+        X_k, Y_k = cluster_kmeans(path, n, save_to_disk=False)
+        add_stat('k_means', n, Y_k, i)
+        i += 1
+        df.loc[n, 'k_means'] = silhouette_score(X_k, Y_k)
+
+    k_kmeans = df[['k_means']].idxmax()[0]
+    k_hierarchical = df[['hierarchical']].idxmax()[0]
+
+    df_table.loc[clazz_name] = [k_kmeans, 0, k_hierarchical, 0]
+
+    df.to_csv(OUT_DIR + '/' + clazz_name + '_silhouette.csv')
+    df_stats.to_csv(OUT_DIR + '/' + clazz_name + '_stats.csv')
+
+    if autorun:
+        cluster_hierarchical(path, k_hierarchical)
+        cluster_kmeans(path, k_kmeans)
+
+    # Plot stats
+    sns.set_theme(palette="hls")
+
+    # Initialize the matplotlib figure
+    f = plt.figure(figsize=(14, 12))
+    gs = f.add_gridspec(2, 2)
+    ax1 = f.add_subplot(gs[0, 0])
+    ax2 = f.add_subplot(gs[0, 1])
+    ax3 = f.add_subplot(gs[1, :])
+
+    df_k = df_stats.loc[df_stats.algorithm == 'k_means', ['k', 'min', 'mean', 'max']].set_index('k', drop=True)
+    df_h = df_stats.loc[df_stats.algorithm == 'hierarchical', ['k', 'min', 'mean', 'max']].set_index('k', drop=True)
+        
+    sns.lineplot(data=df_k, palette="tab10", ax=ax1)
+    sns.lineplot(data=df_h, palette="tab10", ax=ax2)
+    sns.lineplot(data=df, palette="tab10", ax=ax3)
+
+    # Add a legend and informative axis label
+    ax1.set(ylabel="# of elements", ylim=[0, 130], xlabel="# of clusters", xlim=[2, limit])
+    ax1.set_title("K-Means cluster sizes")
+    ax2.set(ylabel="# of elements", ylim=[0, 130], xlabel="# of clusters", xlim=[2, limit])
+    ax2.set_title("Hierarchical cluster sizes")
+    ax3.set(ylabel="Silhouette", ylim=[0, 1], xlabel="# of clusters", xlim=[2, limit])
+    ax3.set_title("Silhouette metrics per # of clusters")
+    
+    sns.despine(left=True, bottom=True)
+    f.savefig(OUT_DIR + '/' + clazz_name + '_stats.png')
+    plt.clf()
+
+
+def compute_silhouette(path: str, clazz_name: str, suffix: str) -> float:
+    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()
+
+    s = round(silhouette_score(X, Y), 4)
+
+    print("Silhouette for " + suffix + ": " + str(s))
+    return s
+
+
+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()
+
+    df_table = pd.DataFrame(columns=['KMeans K', 'KMeans silhouette', 'Hierarchical K', 'Hierarchical silhouette'])
+
+    filelist = glob.glob(IN_DIR + '/*.csv')
+    for f in filelist:
+        clazz_name = os.path.basename(f)
+        clazz_name = clazz_name[:clazz_name.rfind('.')]
+
+        if args.validate:
+            validate(f, clazz_name, args.autorun, df_table)
+        
+        sk = compute_silhouette(f, clazz_name, 'kmeans')
+        sh = compute_silhouette(f, clazz_name, 'hierarchical')
+
+        if args.validate:
+            df_table.loc[clazz_name, 'KMeans silhouette'] = sk
+            df_table.loc[clazz_name, 'Hierarchical silhouette'] = sh
+        
+    df_table.index.name = 'Class Name'
+    print(df_table.to_markdown())
+
+
+if __name__ == '__main__':
+    main()