def experiment_file_random(path_features, path_folder_save_results, options,
classifier, fold, random, name):
print("start weka")
cls = Classifier(classname=classifier,
options=weka.core.classes.split_options(options))
d_results = {
'percent_correct': [],
'percent_incorrect': [],
'confusion_matrix': []
}
data = converters.load_any_file(path_features)
data.class_is_last()
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.CSV")
evl = Evaluation(data)
evl.crossvalidate_model(cls, data, fold, Random(random), pout)
d_results['percent_correct'].append(evl.percent_correct)
d_results['percent_incorrect'].append(evl.percent_incorrect)
d_results['confusion_matrix'].append(
evl.matrix()) # Generates the confusion matrix.
d_results = pd.DataFrame(data=d_results)
d_results.to_csv(path_folder_save_results + '/' + str(name) + '.csv',
index=False)
save = pout.buffer_content()
with open(
path_folder_save_results + '/' + 'prediction/' + str(name) +
'.csv', 'w') as f:
f.write(save)
def Boost_J48(data, rnm):
data.class_is_last()
fc1 = FilteredClassifier()
fc1.classifier = Classifier(classname="weka.classifiers.trees.J48", options=["-C", "0.25", "-M", "2"])
fc1.filter = Filter(classname="weka.filters.unsupervised.attribute.Remove", options=["-R", "first"])
fc2 = SingleClassifierEnhancer(classname="weka.classifiers.meta.AdaBoostM1", options=["-P", "100", "-S", "1", "-I", "10"])
fc2.classifier = fc1
pred_output = PredictionOutput(classname="weka.classifiers.evaluation.output.prediction.CSV", options=["-p", "1"])
folds = 10
fc2.build_classifier(data)
evaluation = Evaluation(data)
evaluation.crossvalidate_model(fc2, data, folds, Random(1), pred_output)
f0 = open(rnm + '_Boost_J48_Tree.txt', 'w')
print >> f0, "Filename: ", rnm
print >> f0, '\n\n'
print >> f0, str(fc2)
f0.close()
f1 = open(rnm + '_Boost_J48_Prediction.txt', 'w')
print >> f1, 'Filename:', rnm
print >> f1, 'Prediction Summary:', (pred_output.buffer_content())
f1.close()
f2 = open(rnm + '_Boost_j48_Evaluation.txt', 'w')
print >> f2, 'Filename:', rnm
print >> f2, 'Evaluation Summary:', (evaluation.summary())
print >> f2, '\n\n\n'
print >> f2, (evaluation.class_details())
f2.close()
plot_roc(evaluation, class_index=[0,1], title=rnm, key_loc='best', outfile=rnm + '_Boost_J48_ROC.png', wait=False)
value_Boost_J48 = str(evaluation.percent_correct)
return value_Boost_J48
def RandomTree(data, rnm):
data.class_is_last()
fc = FilteredClassifier()
fc.classifier = Classifier(classname="weka.classifiers.trees.RandomTree", options=["-K", "0", "-M", "1.0", "-V", "0.001", "-S", "1"])
fc.filter = Filter(classname="weka.filters.unsupervised.attribute.Remove", options=["-R", "first"])
pred_output = PredictionOutput(classname="weka.classifiers.evaluation.output.prediction.CSV", options=["-p", "1"])
folds = 10
evl = Evaluation(data)
evl.crossvalidate_model(fc, data, folds, Random(1), pred_output)
fc.build_classifier(data)
f0 = open(rnm + '_RT_Tree.txt', 'w')
print >> f0, "Filename: ", rnm
print >> f0, '\n\n'
print >> f0, str(fc)
f0.close()
f1 = open(rnm + '_RT_Prediction.txt', 'w')
print >> f1, 'Filename:', rnm
print >> f1, 'Prediction Summary:', (pred_output.buffer_content())
f1.close()
f2 = open(rnm + '_RT_Evaluation.txt', 'w')
print >> f2, 'Filename:', rnm
print >> f2, 'Evaluation Summary:', (evl.summary())
print >> f2, '\n\n\n'
print >> f2, (evl.class_details())
f2.close()
plot_roc(evl, class_index=[0,1], title=rnm, key_loc='best', outfile=rnm+'_RT_ROC.png', wait=False)
value_RT = str(evl.percent_correct)
return value_RT
def experiment_more_file(path_files, path_folder_save_results, fold, options,
classifier, random, name):
cls = Classifier(classname=classifier,
options=weka.core.classes.split_options(options))
file_list = os.listdir(path_files)
for file in file_list:
if ".csv" not in file:
file_list.remove(file)
d_results = {
'name_file': [],
'percent_correct': [],
'percent_incorrect': [],
'confusion_matrix': []
}
print(file_list)
for file in file_list:
print(str(file))
data = converters.load_any_file(path_files + "/" + file)
data.class_is_last()
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.CSV")
evl = Evaluation(data)
evl.crossvalidate_model(cls, data, fold, Random(random), pout)
d_results['name_file'].append(str(file))
d_results['percent_correct'].append(evl.percent_correct)
d_results['percent_incorrect'].append(evl.percent_incorrect)
d_results['confusion_matrix'].append(
evl.matrix()) # Generates the confusion matrix.
save = pout.buffer_content()
with open(
path_folder_save_results + '/' + 'prediction/' + str(name) +
str(file)[:-4] + 'pred_data.csv', 'w') as f:
f.write(save)
d_results = pd.DataFrame(data=d_results)
d_results.to_csv(path_folder_save_results + '/' + str(name) + ".csv",
index=False)
def runSMO(file, bound):
loader = Loader(classname="weka.core.converters.CSVLoader")
data = loader.load_file(file)
data.class_is_first()
remove = Filter(classname="weka.filters.unsupervised.attribute.Remove",
options=["-R", bound])
cls = KernelClassifier(
classname="weka.classifiers.functions.SMO",
options=["-C", "1.0", "-L", "0.001", "-P", "1.0E-12", "-N", "0"])
kernel = Kernel(
classname="weka.classifiers.functions.supportVector.PolyKernel",
options=["-C", "250007", "-E", "1.0"])
cls.kernel = kernel
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
remove.inputformat(data)
filtered = remove.filter(data)
evl = Evaluation(filtered)
evl.crossvalidate_model(cls, filtered, 10, Random(1), pout)
#print(pout.buffer_content())
print(evl.percent_correct)
#print(evl.summary())
result = evl.class_details()
print(result)
return result
def proses(): #diluar def index = 0
import math
from weka.classifiers import Kernel, KernelClassifier
from weka.classifiers import PredictionOutput
import numpy as np
klasifi = KernelClassifier(classname="weka.classifiers.functions.SMOreg",
options=["-N", "0"])
vm = Kernel(classname="weka.classifiers.functions.supportVector.RBFKernel",
options=["-G", "0.1"])
klasifi.vm = vm
output_x = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
kelola = Evaluation(anomali)
kelola.crossvalidate_model(klasifi,
anomali,
10,
Random(0),
output=output_x)
process = 0
for x in anomali.values(anomali.class_index):
data_inst.append(x)
for x in kelola.predictions:
i = str(x)
index = i.split()
data_pred.append(float(index[2]))
data_std.insert(idx, math.ceil(np.std(data_inst)) * 0.1)
print('\n DONE PROCESSING DATASET ATTRIBUTE ',
anomali.attribute(anomali.class_index), '...')
def vote_classifier_train(dicrectory, nameOfDataSet, flag):
loader = Loader(classname="weka.core.converters.CSVLoader")
data = loader.load_file(dicrectory)
data.class_is_last()
meta = MultipleClassifiersCombiner(
classname="weka.classifiers.meta.Vote",
options=[
'-S', '1', '-B', 'weka.classifiers.trees.J48 -C 0.25 -M 2', '-B',
'weka.classifiers.trees.RandomTree -K 6 -M 1.0 -V 0.001 -S 1',
'-B',
'weka.classifiers.meta.Bagging -P 100 -S 1 -num-slots 1 -I 10 -W weka.classifiers.trees.REPTree -- '
'-M 2 -V 0.001 -N 3 -S 1 -L -1 -I 0.0', '-B',
'weka.classifiers.meta.AdaBoostM1 -P 100 -S 1 -I 10 -W weka.classifiers.trees.DecisionStump',
'-B',
'weka.classifiers.meta.Bagging -P 100 -S 1 -num-slots 1 -I 10 -W weka.classifiers.trees.REPTree -- '
'-M 2 -V 0.001 -N 3 -S 1 -L -1 -I 0.0', '-B',
'weka.classifiers.bayes.NaiveBayes ', '-R', 'AVG'
])
eval = Evaluation(data)
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
if flag:
eval.crossvalidate_model(meta, data, 10, Random(1), pout)
else:
eval.evaluate_train_test_split(meta, data, 80.0, Random(1), pout)
gc.collect()
print_and_save('Proposed model', flag, nameOfDataSet, eval)
def main(args):
"""
Loads a dataset, shuffles it, splits it into train/test set. Trains J48 with training set and
evaluates the built model on the test set.
The predictions get recorded in two different ways:
1. in-memory via the test_model method
2. directly to file (more memory efficient), but a separate run of making predictions
:param args: the commandline arguments (optional, can be dataset filename)
:type args: list
"""
# load a dataset
if len(args) <= 1:
data_file = helper.get_data_dir() + os.sep + "vote.arff"
else:
data_file = args[1]
helper.print_info("Loading dataset: " + data_file)
loader = Loader(classname="weka.core.converters.ArffLoader")
data = loader.load_file(data_file)
data.class_is_last()
# generate train/test split of randomized data
train, test = data.train_test_split(66.0, Random(1))
# build classifier
cls = Classifier(classname="weka.classifiers.trees.J48")
cls.build_classifier(train)
print(cls)
# evaluate and record predictions in memory
helper.print_title("recording predictions in-memory")
output = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.CSV",
options=["-distribution"])
evl = Evaluation(train)
evl.test_model(cls, test, output=output)
print(evl.summary())
helper.print_info("Predictions:")
print(output.buffer_content())
# record/output predictions separately
helper.print_title("recording/outputting predictions separately")
outputfile = helper.get_tmp_dir() + "/j48_vote.csv"
output = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.CSV",
options=["-distribution", "-suppress", "-file", outputfile])
output.header = test
output.print_all(cls, test)
helper.print_info("Predictions stored in:" + outputfile)
# by using "-suppress" we don't store the output in memory, the following statement won't output anything
print(output.buffer_content())
def SimpleLogistic():
# load a dataset
loader = Loader(classname="weka.core.converters.ArffLoader")
data = loader.load_file("First_trial_classification.arff")
data.class_is_last() # set class attribute
cls = Classifier(classname="weka.classifiers.functions.SimpleLogistic")
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
evl = Evaluation(data)
evl.crossvalidate_model(cls, data, 10, Random(486), pout)
print(evl.summary())
print(pout.buffer_content())
# save model
serialization.write_all("SimpleLogistic2.model", cls)
def index():
if request.method == "GET":
return render_template('bot.html')
if request.method == "POST":
# jvm.stop()
jvm.start()
f = open("instances.arff", "a")
args = request.form.to_dict()
weight_lb = float(args['weight']) * 2.20462
bmi = (weight_lb / pow(float(args['height']), 2)) * 703
hypertensive_status = args['hypertensive_status']
heart_disease_status = args['heart_disease_status']
if heart_disease_status == "Yes":
heart_disease_status = '1'
else:
heart_disease_status = '0'
if hypertensive_status == "Yes":
hypertensive_status = '1'
else:
hypertensive_status = '0'
st = "\n"+args['gender']+","+args['age']+","+hypertensive_status+","+heart_disease_status+","+args['marrital_status'] + \
","+args['work_type']+","+args['residence']+"," + \
args['hypertension']+","+str(bmi)+",'"+args['smoking_status'].lower()+"',?"
print(st)
f.write(st)
f.close()
objects = serialization.read_all("J48.model")
loader = Loader(classname="weka.core.converters.ArffLoader")
csr = Classifier(jobject=objects[0])
output_results = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.CSV")
data1 = loader.load_file("instances.arff")
data1.class_is_last()
ev2 = Evaluation(data1)
ev2.test_model(csr, data1, output_results)
TESTDATA = StringIO("Instance,Actual,Predicted," +
output_results.buffer_content())
df = pd.read_csv(TESTDATA)
prediction = list(df.Predicted).pop().split(":")[1]
print(prediction)
# jvm.stop()
response = {"status": "200", "prediction": prediction}
return Response(json.dumps(response, indent=2),
mimetype="application/json")
def run_bayesNet(file):
# Get filename from Pathlib object
filename = file.parts[-1]
dir = file.parents[0]
print("Running BayesNet on %s" % filename)
if not filename.endswith(".arff"):
print("%s not ARFF file." % filename)
return
# Removes '.arff' from filename
filename_base = filename[:-5]
# Load data with class as first attr
data = load_Arff_file(file)
data.class_is_first()
# Use BayesNet and set options
cls = Classifier(classname="weka.classifiers.bayes.BayesNet",
options=[
"-D", "-Q",
"weka.classifiers.bayes.net.search.local.TAN", "--",
"-P", "1", "-S", "BAYES", "-E",
"weka.classifiers.bayes.net.estimate.SimpleEstimator",
"--", "-A", "0.5"
])
# Predictions stored in pout
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
# Evaluate data
evaluation = Evaluation(data)
evaluation.crossvalidate_model(cls, data, 10, Random(1), output=pout)
print(evaluation.summary())
print(evaluation.class_details())
print(evaluation.confusion_matrix)
# Generate grid for ROC
# plcls.plot_roc(evaluation, class_index=[0,1], wait=True)
# mk dirs for output
dir = dir / "bayesNet_results"
dir.mkdir(parents=True, exist_ok=True)
# Save summary, class details and confusion matrix to file
result_output = filename_base + "_bayesNet_eval_results_TAN.txt"
output_eval(evaluation, dir / result_output)
# Save the predicited results to file
prediction_output = filename_base + "_bayesNet_pred_results_TAN.txt"
output_pred(pout, dir / prediction_output)
print("BayesNet complete")
def SMOreg():
loader = Loader(classname="weka.core.converters.ArffLoader")
data = loader.load_file("First_trial_regression.arff")
data.class_is_last()
cls = KernelClassifier(classname="weka.classifiers.functions.SMOreg",
options=["-N", "0"])
kernel = Kernel(
classname="weka.classifiers.functions.supportVector.RBFKernel",
options=["-G", "0.2"])
cls.kernel = kernel
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
evl = Evaluation(data)
evl.crossvalidate_model(cls, data, 10, Random(486), pout)
print(evl.summary())
print(pout.buffer_content())
# save model
serialization.write_all("SMOreg.model2", cls)
def naive_bayse(dicrectory, nameOfDataSet, flag):
loader = Loader(classname="weka.core.converters.CSVLoader")
data = loader.load_file(dicrectory)
data.class_is_last()
cls = Classifier(classname='weka.classifiers.bayes.NaiveBayes')
eval = Evaluation(data)
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
if flag:
eval.crossvalidate_model(cls, data, 10, Random(1), pout)
else:
eval.evaluate_train_test_split(cls, data, 80.0, Random(1), pout)
print_and_save('Naive Bayes model', flag, nameOfDataSet, eval)
gc.collect()
def trainAndMakePred(train, test):
#IBK test and prediction
classifierIBK = Classifier(classname="weka.classifiers.lazy.IBk", options=["-K", "5"])
classifierIBK.build_classifier(train)
evaluationIBK = Evaluation(train)
predicted_labelsIBK = evaluationIBK.test_model(classifierIBK, train)
print(" IBKTraining information ")
print(evaluationIBK.summary())
pred_outputIBK = PredictionOutput(classname="weka.classifiers.evaluation.output.prediction.CSV")
evaluationIBK = Evaluation(test)
predicted_indicesIBK = evaluationIBK.test_model(classifierIBK, test, pred_outputIBK)
print(" IBK Prediction information ")
print(pred_outputIBK)
#Naive bayes and prediction
classifierNB = Classifier(classname="weka.classifiers.bayes.NaiveBayes", options=["-D"])
classifierNB.build_classifier(train)
evaluationNB = Evaluation(train)
predicted_labelsNB = evaluationNB.test_model(classifierNB, train)
print(" Naive Bayes Training information ")
print(evaluationNB.summary())
pred_outputNB = PredictionOutput(classname="weka.classifiers.evaluation.output.prediction.CSV")
evaluationNB = Evaluation(test)
predicted_indicesNB = evaluationNB.test_model(classifierNB, test, pred_outputNB)
print(" Naive Bayes Prediction information ")
print(pred_outputNB)
#out put predictions to file
a = 1
ID = 901
f = open("predict.csv", "w")
f.write("ID,Predict 1,Predict 2\n")
for pred1, pred2 in zip(predicted_indicesIBK, predicted_indicesNB):
f.write("%s,%s,%s\n" % (ID,pred1,pred2))
ID += 1
f.close()
def run_ibk(file):
# Get filename from Pathlib object
filename = file.parts[-1]
dir = file.parents[0]
print("Running IBk on %s" % filename)
if not filename.endswith(".arff"):
print("%s not ARFF file." % filename)
return
# Removes '.arff' from filename
filename_base = filename[:-5]
# Load data with class as first attr
data = load_Arff_file(file)
data.class_is_first()
# Use IBk and set options
cls = Classifier(classname="weka.classifiers.lazy.IBk",
options=["-K", "3"])
# print(cls.options)
# Predictions stored in pout
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
# Evaluate data
evaluation = Evaluation(data)
evaluation.crossvalidate_model(cls, data, 10, Random(1), output=pout)
# Save summary, class details and confusion matrix to file
result_output = filename_base + "_eval_results.txt"
output_eval(evaluation, dir / result_output)
# Save the predicited results to file
prediction_output = filename_base + "_pred_results.txt"
output_pred(pout, dir / prediction_output)
print("IBk complete")
def run_weka_csv_train_test(train_file_path, test_file_path):
"""
1) From previous process, for each fold create input .csv's which will then be read here
1.1) Input csv will be on exact same data, which was fed to DT model
2) Extract the rules using JRip
3) Evaluate predictions with same metrics as was done for previous work
3.1) Accuracy, AUC, F-Score, Precision, Recall
need to make new .csv, which contains both, payload and usual stuff....
:return:
"""
train_df = read_df_csv(train_file_path)
test_df = read_df_csv(test_file_path)
cls = Classifier(classname="weka.classifiers.rules.JRip"
) #options=["-O", "2"]), default opt. is 2
loader = Loader(classname="weka.core.converters.CSVLoader")
# print(cls.to_help())
train_jrip_data = read_weka_csv(train_file_path, loader)
test_jrip_data = read_weka_csv(test_file_path, loader)
# If dataset included Case ID
#train_case_id = train_jrip_data.attribute_by_name("Case_ID")
#test_case_id = test_jrip_data.attribute_by_name("Case_ID")
#test_jrip_data.delete_attribute(test_case_id.index)
#train_jrip_data.delete_attribute(train_case_id.index)
train_label_attribute = train_jrip_data.attribute_by_name("Label")
test_label_attribute = test_jrip_data.attribute_by_name("Label")
# Convert numeric attribut to nominal. Required for label!
nominal = Filter(
classname="weka.filters.unsupervised.attribute.NumericToNominal",
options=["-R", "last"])
nominal.inputformat(train_jrip_data)
nominaldata1 = nominal.filter(train_jrip_data)
nominaldata1.class_index = train_label_attribute.index
nominaldata2 = nominal.filter(
test_jrip_data) # re-use the initialized filter!
nominaldata2.class_index = test_label_attribute.index
msg = nominaldata1.equal_headers(nominaldata2)
if msg is not None:
raise Exception("Train and test not compatible:\n" + msg)
# Build classifier
cls.build_classifier(nominaldata1)
# Get rules
print(cls.jwrapper)
pred_output = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText",
options=["-distribution"])
# Perform evaluation on train and test data
evl = Evaluation(nominaldata1)
evl.test_model(cls, nominaldata2, output=pred_output)
evl2 = Evaluation(nominaldata1)
evl2.test_model(cls, nominaldata1, output=pred_output)
# Return interesting metrics for both train and test.
return get_interesting(evl2), get_interesting(evl)
if isreal(classvarStr) == True:
classifier = Classifier(classname="weka.classifiers.trees.M5P",
options=["-U", "-M", "500.0"])
print("\n--> building:")
print(classifier.to_commandline())
classifier.build_classifier(dataA)
print("\n--> classifier:\n")
print(classifier)
print("\n--> graph:\n")
print(classifier.graph)
outputfile = helper.get_tmp_dir() + "/result.csv"
output = PredictionOutput(
classname='weka.classifiers.evaluation.output.prediction.CSV',
options=["-distribution", "-suppress", "-file", outputfile])
print("\n--> Output:\n")
output.header = dataA
output.print_all(classifier, dataA)
helper.print_info("Predictions stored in:" + outputfile)
print(output.buffer_content())
Eval = Evaluation(dataA)
Eval.test_model(classifier, dataA, output=output)
print(Eval.summary())
ListEval = []
Corr = []
Corrf = []
ListEval = Eval.summary().split('Mean absolute error')
print("ListEval :")
print(ListEval)
def experiment_sequential_file(path_indices, path_features,
path_folder_save_results, options, classifier,
name, indicator_col, images):
ind_f = load(path_indices)
lst = ind_f.files
for item in lst:
ind = ind_f[item] + 1
cls = Classifier(classname=classifier,
options=weka.core.classes.split_options(options))
data = converters.load_any_file(path_features)
ind = np.append(ind, len(data))
data.class_is_last()
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.CSV")
d_results = {
'index': [],
'percent_correct': [],
'percent_incorrect': [],
'precision': [],
'recall': [],
'f-score': [],
'confusion_matrix': []
}
for j in range(len(ind) - 1):
first = ind[j]
if j == len(ind) - 2:
last = ind[j + 1]
else:
last = ind[j + 1] - 1
d_test = data.subset(row_range=str(first) + '-' + str(last))
if j == 0: # first
d_train = data.subset(row_range=str(last + 1) + '-' +
str(ind[-1])) # last element
print(str(last + 1) + '-' + str(ind[-1]))
elif j == len(ind) - 2: # last
d_train = data.subset(row_range='1-' +
str(first - 1)) # last element
print('1-' + str(first - 1))
else: # central
s = '1-' + str(first - 1) + ',' + str(last + 1) + '-' + str(
ind[-1])
print(s)
d_train = data.subset(row_range=s)
cls.build_classifier(d_train)
evl = Evaluation(data)
evl.test_model(cls, d_test, pout)
# print(type(d_train))
# print(type(d_test))
d_results['index'].append(str(ind[j]))
d_results['percent_correct'].append(evl.percent_correct)
d_results['percent_incorrect'].append(evl.percent_incorrect)
d_results['precision'].append(evl.precision(1))
d_results['recall'].append(evl.recall(1))
d_results['f-score'].append(evl.f_measure(1))
d_results['confusion_matrix'].append(
evl.matrix()) # Generates the confusion matrix.
save = pout.buffer_content()
check_folder_or_create(path_folder_save_results + '/' + 'prediction')
with open(
path_folder_save_results + '/' + 'prediction/' + name +
'pred_data.csv', 'w') as f:
f.write(save)
buffer_save = pd.read_csv(path_folder_save_results + '/' + 'prediction/' +
name + 'pred_data.csv',
index_col=False,
header=None)
col_label = buffer_save[1]
col_prediction = buffer_save[2]
col_different = buffer_save[3]
create_prediction(col_label, col_prediction, col_different, indicator_col,
images, name, path_folder_save_results + '/prediction/')
d_results = pd.DataFrame(data=d_results)
d_results.to_csv(path_folder_save_results + '/' + name + 'results.csv',
index=False)
def experiment_more_file(path_files,
path_folder_save_results,
fold,
options,
classifier,
random,
name,
voting=False):
cls = Classifier(classname=classifier,
options=weka.core.classes.split_options(options))
file_list = os.listdir(path_files)
for file in file_list:
if ".csv" not in file:
file_list.remove(file)
d_results = {
'name_file': [],
'percent_correct': [],
'percent_incorrect': [],
'precision': [],
'recall': [],
'f-score': [],
'confusion_matrix': []
}
for file in file_list:
indicator_table = pd.read_csv(path_files + '/indicator/' + file[0] +
'_indicator.csv')
indicator = list(indicator_table['indicator'])
images = list(indicator_table['image'])
data = converters.load_any_file(path_files + "/" + file)
data.class_is_last()
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.CSV")
evl = Evaluation(data)
evl.crossvalidate_model(cls, data, fold, Random(random), pout)
d_results['name_file'].append(str(file))
d_results['percent_correct'].append(evl.percent_correct)
d_results['percent_incorrect'].append(evl.percent_incorrect)
d_results['precision'].append(evl.precision(1))
d_results['recall'].append(evl.recall(1))
d_results['f-score'].append(evl.f_measure(1))
d_results['confusion_matrix'].append(
evl.matrix()) # Generates the confusion matrix.
save = pout.buffer_content()
check_folder_or_create(path_folder_save_results + '/' + name + '/' +
'prediction')
with open(
path_folder_save_results + '/' + name + '/' +
'prediction/pred_data.csv', 'w') as f:
f.write(save)
buffer_save = pd.read_csv(path_folder_save_results + '/' + name + '/' +
'prediction/pred_data.csv',
index_col=False)
col_label = buffer_save['actual']
col_prediction = buffer_save['predicted']
col_different = buffer_save['error']
create_prediction(
col_label, col_prediction, col_different, indicator, images,
file[:-4], path_folder_save_results + '/' + name + '/prediction/')
d_results = pd.DataFrame(data=d_results)
d_results.to_csv(path_folder_save_results + '/' + str(name) + ".csv")
def experiment_sequential_file(path_indices, path_features,
path_folder_save_results, options, classifier,
name):
ind_f = load(path_indices)
lst = ind_f.files
for item in lst:
ind = ind_f[item] + 1
cls = Classifier(classname=classifier,
options=weka.core.classes.split_options(options))
data = converters.load_any_file(path_features)
ind = np.append(ind, len(data))
data.class_is_last()
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.CSV")
d_results = {
'index': [],
'percent_correct': [],
'percent_incorrect': [],
'confusion_matrix': []
}
for j in range(len(ind) - 1):
print(j)
print(str(ind[j]) + '-' + str(ind[j + 1]))
d_test = data.subset(row_range=str(ind[j]) + '-' + str(ind[j + 1]))
if j == 0: # first
d_train = data.subset(row_range=str(ind[j + 1] + 1) + '-' +
str(ind[-1])) # last element
elif j == len(ind) - 2: # last
d_train = data.subset(row_range='1-' +
str(ind[j] - 1)) # last element
else: # central
s = '1-' + str(ind[j] - 1) + ',' + str(ind[j + 1] + 1) + '-' + str(
ind[-1])
d_train = data.subset(row_range=s)
cls.build_classifier(d_train)
evl = Evaluation(data)
evl.test_model(cls, d_test, pout)
save = pout.buffer_content()
with open(
path_folder_save_results + '/' + '/prediction/' + name +
str(j) + 'pred_data.csv', 'w') as f:
f.write(save)
d_results['index'].append(str(ind[j]))
d_results['percent_correct'].append(evl.percent_correct)
d_results['percent_incorrect'].append(evl.percent_incorrect)
d_results['confusion_matrix'].append(
evl.matrix()) # Generates the confusion matrix.
d_results = pd.DataFrame(data=d_results)
d_results.to_csv(path_folder_save_results + '/' + name + 'results.csv',
index=False)
def run_multilayerPercepton(file, file2=None):
# Get filename from Pathlib object
filename = file.parts[-1]
dir = file.parents[0]
print("Running Multilayer Percepton on %s" % filename)
if not filename.endswith(".arff"):
print("%s not ARFF file." % filename)
return
# Removes '.arff' from filename
filename_base = filename[:-5]
print("loading data...")
# Load data with class as first attr
data = load_Arff_file(file)
data.class_is_first()
# If 2nd file load that data too
if file2:
print("Loading test...")
test = load_Arff_file(file2)
test.class_is_first()
file_names = [
"MP_N-500_default_H-1",
"MP_N-500_H-3",
"MP_N-500_H-5",
"MP_N-500_H-7",
"MP_N-500_H-3-5",
"MP_N-500_H-5-3",
"MP_N-500_H-3-5-7",
"MP_N-500_H-7-3-5",
"MP_N-500_H-5-7-3",
"MP_N-500_L-01",
"MP_N-500_L-02",
"MP_N-500_L-04",
"MP_N-500_L-05",
"MP_N-500_M-01",
"MP_N-500_M-03",
"MP_N-500_M-04",
"MP_N-500_M-05",
"MP_N-500_E-5",
"MP_N-500_E-10",
"MP_N-500_E-15",
"MP_N-500_E-25",
]
options_list = [
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
], # DEFAULT
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "3"
], # -H START
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "5"
],
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "7"
],
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "3, 5"
],
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "5, 3"
],
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "3, 5, 7"
],
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "7, 3, 5"
],
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "5, 7, 3"
], # -H END
[
"-L", "0.1", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
], # -L START
[
"-L", "0.2", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
],
[
"-L", "0.4", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
],
[
"-L", "0.5", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
], # -L END
[
"-L", "0.3", "-M", "0.1", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
], # -M START
[
"-L", "0.3", "-M", "0.3", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
],
[
"-L", "0.3", "-M", "0.4", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
],
[
"-L", "0.3", "-M", "0.5", "-N", "500", "-V", "0", "-S", "0", "-E",
"20", "-H", "1"
], # -M END
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"5", "-H", "1"
], # -E START
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"10", "-H", "1"
],
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"15", "-H", "1"
],
[
"-L", "0.3", "-M", "0.2", "-N", "500", "-V", "0", "-S", "0", "-E",
"25", "-H", "1"
], # -E END
]
for i in range(len(options_list)):
start = time.time()
print("Beginning iteration " + str(i) + ": " + file_names[i])
# Use MultilayerPercepton and set options
cls = Classifier(
classname="weka.classifiers.functions.MultilayerPerceptron",
options=options_list[i])
# Build classifier with train data
cls.build_classifier(data)
# Predictions stored in pout
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText"
)
# Evaluate data on test data
evaluation = Evaluation(data)
evaluation.test_model(cls, test, output=pout)
print(evaluation.summary())
print(evaluation.class_details())
print(evaluation.confusion_matrix)
# Generate grid for ROC
# plcls.plot_roc(evaluation, class_index=[0,1], wait=True)
# mk dirs for output
tempdir = dir / "Results/" / "MP-ALL_N-500_results/" / (file_names[i] +
"_results/")
tempdir.mkdir(parents=True, exist_ok=True)
# Save summary, class details and confusion matrix to file
result_output = file_names[i] + "_results.txt"
print(tempdir)
print(result_output)
print((tempdir / result_output).absolute())
output_eval(evaluation, tempdir / result_output)
# Save the predicited results to file
prediction_output = file_names[i] + "_prediction.txt"
output_pred(pout, tempdir / prediction_output)
end = time.time()
timetaken = round(end - start, 2)
print("Time taken to run iteration " + str(i) + ": %s seconds" %
(timetaken))
print("Multilayer Percepton complete")
def main():
"""
Just runs some example code.
"""
# load a dataset
iris_file = helper.get_data_dir() + os.sep + "iris.arff"
helper.print_info("Loading dataset: " + iris_file)
loader = Loader("weka.core.converters.ArffLoader")
iris_data = loader.load_file(iris_file)
iris_data.class_is_last()
# classifier help
helper.print_title("Creating help string")
classifier = Classifier(classname="weka.classifiers.trees.J48")
print(classifier.to_help())
# partial classname
helper.print_title("Creating classifier from partial classname")
clsname = ".J48"
classifier = Classifier(classname=clsname)
print(clsname + " --> " + classifier.classname)
# classifier from commandline
helper.print_title("Creating SMO from command-line string")
cmdline = 'weka.classifiers.functions.SMO -K "weka.classifiers.functions.supportVector.NormalizedPolyKernel -E 3.0"'
classifier = from_commandline(cmdline,
classname="weka.classifiers.Classifier")
classifier.build_classifier(iris_data)
print("input: " + cmdline)
print("output: " + classifier.to_commandline())
print("model:\n" + str(classifier))
# kernel classifier
helper.print_title("Creating SMO as KernelClassifier")
kernel = Kernel(
classname="weka.classifiers.functions.supportVector.RBFKernel",
options=["-G", "0.001"])
classifier = KernelClassifier(classname="weka.classifiers.functions.SMO",
options=["-M"])
classifier.kernel = kernel
classifier.build_classifier(iris_data)
print("classifier: " + classifier.to_commandline())
print("model:\n" + str(classifier))
# build a classifier and output model
helper.print_title("Training J48 classifier on iris")
classifier = Classifier(classname="weka.classifiers.trees.J48")
# Instead of using 'options=["-C", "0.3"]' in the constructor, we can also set the "confidenceFactor"
# property of the J48 classifier itself. However, being of type float rather than double, we need
# to convert it to the correct type first using the double_to_float function:
classifier.set_property("confidenceFactor", types.double_to_float(0.3))
classifier.build_classifier(iris_data)
print(classifier)
print(classifier.graph)
print(classifier.to_source("MyJ48"))
plot_graph.plot_dot_graph(classifier.graph)
# evaluate model on test set
helper.print_title("Evaluating J48 classifier on iris")
evaluation = Evaluation(iris_data)
evl = evaluation.test_model(classifier, iris_data)
print(evl)
print(evaluation.summary())
# evaluate model on train/test split
helper.print_title("Evaluating J48 classifier on iris (random split 66%)")
classifier = Classifier(classname="weka.classifiers.trees.J48",
options=["-C", "0.3"])
evaluation = Evaluation(iris_data)
evaluation.evaluate_train_test_split(classifier, iris_data, 66.0,
Random(1))
print(evaluation.summary())
# load a dataset incrementally and build classifier incrementally
helper.print_title("Build classifier incrementally on iris")
helper.print_info("Loading dataset: " + iris_file)
loader = Loader("weka.core.converters.ArffLoader")
iris_inc = loader.load_file(iris_file, incremental=True)
iris_inc.class_is_last()
classifier = Classifier(
classname="weka.classifiers.bayes.NaiveBayesUpdateable")
classifier.build_classifier(iris_inc)
for inst in loader:
classifier.update_classifier(inst)
print(classifier)
# construct meta-classifiers
helper.print_title("Meta classifiers")
# generic FilteredClassifier instantiation
print("generic FilteredClassifier instantiation")
meta = SingleClassifierEnhancer(
classname="weka.classifiers.meta.FilteredClassifier")
meta.classifier = Classifier(
classname="weka.classifiers.functions.LinearRegression")
flter = Filter("weka.filters.unsupervised.attribute.Remove")
flter.options = ["-R", "first"]
meta.set_property("filter", flter.jobject)
print(meta.to_commandline())
# direct FilteredClassifier instantiation
print("direct FilteredClassifier instantiation")
meta = FilteredClassifier()
meta.classifier = Classifier(
classname="weka.classifiers.functions.LinearRegression")
flter = Filter("weka.filters.unsupervised.attribute.Remove")
flter.options = ["-R", "first"]
meta.filter = flter
print(meta.to_commandline())
# generic Vote
print("generic Vote instantiation")
meta = MultipleClassifiersCombiner(classname="weka.classifiers.meta.Vote")
classifiers = [
Classifier(classname="weka.classifiers.functions.SMO"),
Classifier(classname="weka.classifiers.trees.J48")
]
meta.classifiers = classifiers
print(meta.to_commandline())
# cross-validate nominal classifier
helper.print_title("Cross-validating NaiveBayes on diabetes")
diabetes_file = helper.get_data_dir() + os.sep + "diabetes.arff"
helper.print_info("Loading dataset: " + diabetes_file)
loader = Loader("weka.core.converters.ArffLoader")
diabetes_data = loader.load_file(diabetes_file)
diabetes_data.class_is_last()
classifier = Classifier(classname="weka.classifiers.bayes.NaiveBayes")
pred_output = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText",
options=["-distribution"])
evaluation = Evaluation(diabetes_data)
evaluation.crossvalidate_model(classifier,
diabetes_data,
10,
Random(42),
output=pred_output)
print(evaluation.summary())
print(evaluation.class_details())
print(evaluation.matrix())
print("areaUnderPRC/0: " + str(evaluation.area_under_prc(0)))
print("weightedAreaUnderPRC: " + str(evaluation.weighted_area_under_prc))
print("areaUnderROC/1: " + str(evaluation.area_under_roc(1)))
print("weightedAreaUnderROC: " + str(evaluation.weighted_area_under_roc))
print("avgCost: " + str(evaluation.avg_cost))
print("totalCost: " + str(evaluation.total_cost))
print("confusionMatrix: " + str(evaluation.confusion_matrix))
print("correct: " + str(evaluation.correct))
print("pctCorrect: " + str(evaluation.percent_correct))
print("incorrect: " + str(evaluation.incorrect))
print("pctIncorrect: " + str(evaluation.percent_incorrect))
print("unclassified: " + str(evaluation.unclassified))
print("pctUnclassified: " + str(evaluation.percent_unclassified))
print("coverageOfTestCasesByPredictedRegions: " +
str(evaluation.coverage_of_test_cases_by_predicted_regions))
print("sizeOfPredictedRegions: " +
str(evaluation.size_of_predicted_regions))
print("falseNegativeRate: " + str(evaluation.false_negative_rate(1)))
print("weightedFalseNegativeRate: " +
str(evaluation.weighted_false_negative_rate))
print("numFalseNegatives: " + str(evaluation.num_false_negatives(1)))
print("trueNegativeRate: " + str(evaluation.true_negative_rate(1)))
print("weightedTrueNegativeRate: " +
str(evaluation.weighted_true_negative_rate))
print("numTrueNegatives: " + str(evaluation.num_true_negatives(1)))
print("falsePositiveRate: " + str(evaluation.false_positive_rate(1)))
print("weightedFalsePositiveRate: " +
str(evaluation.weighted_false_positive_rate))
print("numFalsePositives: " + str(evaluation.num_false_positives(1)))
print("truePositiveRate: " + str(evaluation.true_positive_rate(1)))
print("weightedTruePositiveRate: " +
str(evaluation.weighted_true_positive_rate))
print("numTruePositives: " + str(evaluation.num_true_positives(1)))
print("fMeasure: " + str(evaluation.f_measure(1)))
print("weightedFMeasure: " + str(evaluation.weighted_f_measure))
print("unweightedMacroFmeasure: " +
str(evaluation.unweighted_macro_f_measure))
print("unweightedMicroFmeasure: " +
str(evaluation.unweighted_micro_f_measure))
print("precision: " + str(evaluation.precision(1)))
print("weightedPrecision: " + str(evaluation.weighted_precision))
print("recall: " + str(evaluation.recall(1)))
print("weightedRecall: " + str(evaluation.weighted_recall))
print("kappa: " + str(evaluation.kappa))
print("KBInformation: " + str(evaluation.kb_information))
print("KBMeanInformation: " + str(evaluation.kb_mean_information))
print("KBRelativeInformation: " + str(evaluation.kb_relative_information))
print("SFEntropyGain: " + str(evaluation.sf_entropy_gain))
print("SFMeanEntropyGain: " + str(evaluation.sf_mean_entropy_gain))
print("SFMeanPriorEntropy: " + str(evaluation.sf_mean_prior_entropy))
print("SFMeanSchemeEntropy: " + str(evaluation.sf_mean_scheme_entropy))
print("matthewsCorrelationCoefficient: " +
str(evaluation.matthews_correlation_coefficient(1)))
print("weightedMatthewsCorrelation: " +
str(evaluation.weighted_matthews_correlation))
print("class priors: " + str(evaluation.class_priors))
print("numInstances: " + str(evaluation.num_instances))
print("meanAbsoluteError: " + str(evaluation.mean_absolute_error))
print("meanPriorAbsoluteError: " +
str(evaluation.mean_prior_absolute_error))
print("relativeAbsoluteError: " + str(evaluation.relative_absolute_error))
print("rootMeanSquaredError: " + str(evaluation.root_mean_squared_error))
print("rootMeanPriorSquaredError: " +
str(evaluation.root_mean_prior_squared_error))
print("rootRelativeSquaredError: " +
str(evaluation.root_relative_squared_error))
print("prediction output:\n" + str(pred_output))
plot_cls.plot_roc(evaluation,
title="ROC diabetes",
class_index=range(
0, diabetes_data.class_attribute.num_values),
wait=False)
plot_cls.plot_prc(evaluation,
title="PRC diabetes",
class_index=range(
0, diabetes_data.class_attribute.num_values),
wait=False)
# train 2nd classifier on diabetes dataset
classifier2 = Classifier(classname="weka.classifiers.trees.RandomForest")
evaluation2 = Evaluation(diabetes_data)
evaluation2.crossvalidate_model(classifier2, diabetes_data, 10, Random(42))
plot_cls.plot_rocs({
"NB": evaluation,
"RF": evaluation2
},
title="ROC diabetes",
class_index=0,
wait=False)
plot_cls.plot_prcs({
"NB": evaluation,
"RF": evaluation2
},
title="PRC diabetes",
class_index=0,
wait=False)
# load a numeric dataset
bolts_file = helper.get_data_dir() + os.sep + "bolts.arff"
helper.print_info("Loading dataset: " + bolts_file)
loader = Loader("weka.core.converters.ArffLoader")
bolts_data = loader.load_file(bolts_file)
bolts_data.class_is_last()
# build a classifier and output model
helper.print_title("Training LinearRegression on bolts")
classifier = Classifier(
classname="weka.classifiers.functions.LinearRegression",
options=["-S", "1", "-C"])
classifier.build_classifier(bolts_data)
print(classifier)
# cross-validate numeric classifier
helper.print_title("Cross-validating LinearRegression on bolts")
classifier = Classifier(
classname="weka.classifiers.functions.LinearRegression",
options=["-S", "1", "-C"])
evaluation = Evaluation(bolts_data)
evaluation.crossvalidate_model(classifier, bolts_data, 10, Random(42))
print(evaluation.summary())
print("correlationCoefficient: " + str(evaluation.correlation_coefficient))
print("errorRate: " + str(evaluation.error_rate))
helper.print_title("Header - bolts")
print(str(evaluation.header))
helper.print_title("Predictions on bolts")
for index, pred in enumerate(evaluation.predictions):
print(
str(index + 1) + ": " + str(pred) + " -> error=" + str(pred.error))
plot_cls.plot_classifier_errors(evaluation.predictions, wait=False)
# train 2nd classifier and show errors in same plot
classifier2 = Classifier(classname="weka.classifiers.functions.SMOreg")
evaluation2 = Evaluation(bolts_data)
evaluation2.crossvalidate_model(classifier2, bolts_data, 10, Random(42))
plot_cls.plot_classifier_errors(
{
"LR": evaluation.predictions,
"SMOreg": evaluation2.predictions
},
wait=False)
# learning curve
cls = [
Classifier(classname="weka.classifiers.trees.J48"),
Classifier(classname="weka.classifiers.bayes.NaiveBayesUpdateable")
]
plot_cls.plot_learning_curve(cls,
diabetes_data,
increments=0.05,
label_template="[#] !",
metric="percent_correct",
wait=True)
# access classifier's Java API
labor_file = helper.get_data_dir() + os.sep + "labor.arff"
helper.print_info("Loading dataset: " + labor_file)
loader = Loader("weka.core.converters.ArffLoader")
labor_data = loader.load_file(labor_file)
labor_data.class_is_last()
helper.print_title("Using JRip's Java API to access rules")
jrip = Classifier(classname="weka.classifiers.rules.JRip")
jrip.build_classifier(labor_data)
rset = jrip.jwrapper.getRuleset()
for i in xrange(rset.size()):
r = rset.get(i)
print(str(r.toString(labor_data.class_attribute.jobject)))
def handle_message(message):
global accel_x
global accel_y
global accel_z
global gyro_x
global gyro_y
global gyro_z
if message['sensorName'] == 'accelerometer':
accel_x.append(float(message['x']))
accel_y.append(float(message['y']))
accel_z.append(float(message['z']))
elif message['sensorName'] == 'gyroscope':
gyro_x.append(float(message['x']))
gyro_y.append(float(message['y']))
gyro_z.append(float(message['z']))
elif message['sensorName'] == "stop":
# stop signal
stop()
if len(gyro_x) >= 25 and len(accel_x) >= 25:
# only classify when both gyroscope and accelerometer data has more than 25 samples
processDataToArff(accel_x, accel_y, accel_z, gyro_x, gyro_y, gyro_z)
jvm.start()
loader = Loader(classname="weka.core.converters.ArffLoader")
# load the training data
train = loader.load_file("train.arff")
train.class_is_last()
cls = Classifier(classname="weka.classifiers.trees.LMT")
# train the classifier
cls.build_classifier(train)
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
evl = Evaluation(train)
# load the classify data
test = loader.load_file("classify.arff")
test.class_is_last()
evl.test_model(cls, test, pout)
result = pout.buffer_content()
resultLines = result.splitlines()
for i in range(len(resultLines)):
if (resultLines[i].find("upDown") != -1):
result = 1
elif (resultLines[i].find("leftRight") != -1):
result = 2
elif (resultLines[i].find("inOut") != -1):
result = 3
elif (resultLines[i].find("rotation") != -1):
result = 4
else:
result = "error"
if result == 1:
stop()
playD()
elif result == 2:
stop()
playBm()
elif result == 3:
stop()
playA()
elif result == 4:
stop()
playG()
# clear the arrays for new data
gyro_x = []
gyro_y = []
gyro_z = []
accel_x = []
accel_y = []
accel_z = []
processDataToArff("train.arff", False)
processDataToArff("test.arff", True)
# setup training model
loader = Loader(classname="weka.core.converters.ArffLoader")
train = loader.load_file("train.arff")
train.class_is_last()
test = loader.load_file("test.arff")
test.class_is_last()
# print(train)
cls = Classifier(
classname="weka.classifiers.trees.LMT") #use LMT as our algorithm
cls.build_classifier(train) #train the model using train.arff
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
evl = Evaluation(train)
evl.test_model(cls, test, pout)
# print the result
result = pout.buffer_content()
#print(result)
# split the result and only print the gesture
resultLines = result.splitlines()
for i in range(len(resultLines)):
if (resultLines[i].find("upDown") != -1):
print("%d upDown" % (i + 1))
elif (resultLines[i].find("leftRight") != -1):
print("%d leftRight" % (i + 1))
elif (resultLines[i].find("inOut") != -1):
sampled = pd.merge_asof(X_resampled,y_resampled,right_index=True,left_index=True)
print(sampled)
#corpus_name = 'data/bugs/resampled.csv'
#corpus = os.path.join("/content/gdrive/My Drive", corpus_name)
#sampled.to_csv(corpus,index = False)
loader = Loader(classname="weka.core.converters.CSVLoader")
data = loader.load_file(corpus)
data.class_is_last()
"""Naive Bayes Classifier for Bug Prediction"""
classifier = Classifier(classname="weka.classifiers.bayes.NaiveBayes")
pred_output = PredictionOutput(classname="weka.classifiers.evaluation.output.prediction.PlainText", options=["-distribution"])
evaluation = Evaluation(data)
evaluation.crossvalidate_model(classifier, data, 10, Random(42), output=pred_output)
plot_cls.plot_roc(evaluation, title="ROC bugs",class_index=range(0, data.class_attribute.num_values), wait=False)
plot_cls.plot_prc(evaluation, title="PRC bugs - NaiveBayes",class_index=range(0, data.class_attribute.num_values), wait=False)
"""Performance Metrics - Naive Bayes Classifier"""
print(evaluation.summary())
print(evaluation.class_details())
print(evaluation.matrix())
print("confusionMatrix: " + str(evaluation.confusion_matrix))
print("fMeasure: " + str(evaluation.f_measure(1)))
print("precision: " + str(evaluation.precision(1)))
print("recall: " + str(evaluation.recall(1)))
# load diabetes
loader = Loader(classname="weka.core.converters.ArffLoader")
fname = data_dir + os.sep + "diabetes.arff"
print("\nLoading dataset: " + fname + "\n")
data = loader.load_file(fname)
# we'll set the class attribute after filtering
# apply NominalToBinary filter and set class attribute
fltr = Filter("weka.filters.unsupervised.attribute.NominalToBinary")
fltr.inputformat(data)
filtered = fltr.filter(data)
filtered.class_is_last()
# cross-validate LinearRegression on filtered data, display model
cls = Classifier(classname="weka.classifiers.functions.LinearRegression")
pout = PredictionOutput(
classname="weka.classifiers.evaluation.output.prediction.PlainText")
evl = Evaluation(filtered)
evl.crossvalidate_model(cls, filtered, 10, Random(1), pout)
print("10-fold cross-validation:\n" + evl.summary())
print("Predictions:\n\n" + str(pout))
cls.build_classifier(filtered)
print("Model:\n\n" + str(cls))
# use AddClassification filter with LinearRegression on filtered data
print("Applying AddClassification to filtered data:\n")
fltr = Filter(classname="weka.filters.supervised.attribute.AddClassification",
options=[
"-W", "weka.classifiers.functions.LinearRegression",
"-classification"
])
fltr.inputformat(filtered)
print(evl.to_summary())
print(str(cls))
plg.plot_dot_graph(cls.graph())
# 2. filtered classifier
fname = data_dir + os.sep + "simpletext-test.arff"
print("\nLoading dataset: " + fname + "\n")
loader = Loader(classname="weka.core.converters.ArffLoader")
test = loader.load_file(fname)
test.set_class_index(test.num_attributes() - 1)
print("Building/evaluating filtered classifier...")
cls = FilteredClassifier()
cls.set_classifier(Classifier(classname="weka.classifiers.trees.J48"))
cls.set_filter(Filter(classname="weka.filters.unsupervised.attribute.StringToWordVector"))
cls.build_classifier(data)
pout = PredictionOutput(classname="weka.classifiers.evaluation.output.prediction.PlainText")
pout.set_header(test)
evl = Evaluation(data)
evl.test_model(cls, test, pout)
print(str(pout))
print(str(cls))
# load ReutersCorn-train
fname = data_dir + os.sep + "ReutersCorn-train.arff"
print("\nLoading dataset: " + fname + "\n")
loader = Loader(classname="weka.core.converters.ArffLoader")
data = loader.load_file(fname)
data.set_class_index(data.num_attributes() - 1)
# load ReutersCorn-test
fname = data_dir + os.sep + "ReutersCorn-test.arff"
f.close()
# In[4]:
f= open("instances.arff","r")
print(f.read())
f.close()
# In[10]:
from io import StringIO
output_results = PredictionOutput(classname="weka.classifiers.evaluation.output.prediction.CSV")
data1 = loader.load_file("instances.arff")
data1.class_is_last()
ev2 = Evaluation(data1)
ev2.test_model(csr,data1,output_results)
print("Class prediction: ",output_results.buffer_content()[-13:-10])
print("\n\n Instance"," Actual"," Predicted")
print(output_results.buffer_content())
TESTDATA = StringIO("Instance,Actual,Predicted,"+output_results.buffer_content())
# jvm.stop()
x = pd.read_csv(TESTDATA)
# In[14]:
