def k_means_transform(book_at, k=100, load_model=True):
'''
input: attribute feature matrix of all books
output: transformed matrix including cluster assignment
This function is used to cluster all books for faster calculation for knn later
'''
if load_model == False:
###k-means clustering###
#Since the data is too big to do knn, first cluster them
from pyspark.ml.clustering import KMeans
kmeans = KMeans(
k=k, seed=42
) #divide all books to 1000 clusters (1/1000, less computation for knn)
model = kmeans.fit(book_at.select('features'))
#model.save('k-means_model_001_10')
else:
from pyspark.ml.clustering import KMeansModel
model = KMeansModel.load('hdfs:/user/yw2115/k-means_model_001')
#add the cluster col to original attribute matrix
transformed = model.transform(book_at)
transformed = transformed.withColumnRenamed("prediction", "cluster")
#transormed.show(3)
return transformed
def useModel(path):
model_path = '/home/hadoop/PycharmProjects/SparkMlib/model/kmeans'
df = createDataframeKMeans(path)
df = df.where(df.TotalFee != '0').where(df.DiseaseCode == '24495')
df = df.withColumn("Age", df.Age.cast(IntegerType())) \
.withColumn("TotalFee", df.TotalFee.cast(FloatType()))
data = df.drop("DiseaseCode")
data.show()
# 转换数据
featureCreator = VectorAssembler(inputCols=data.columns[1:], outputCol='feature')
data = featureCreator.transform(data)
model = KMeansModel.load(model_path)
# 聚合
test = model.transform(data)
test.show()
points = []
for i in test.select("Age", "TotalFee", "prediction", "HosRegisterCode").collect():
temp = [float(i['Age']), float(i['TotalFee']), int(i['prediction']), i['HosRegisterCode']]
points.append(temp)
centers = model.clusterCenters()
centerPoints = []
for i in centers:
temp = [float(i[0]), float(i[1])]
centerPoints.append(temp)
getDistance(points, centerPoints)
def predict(bucket_name, feature_path, feature_name, output_path, plot_path):
sc = SparkContext.getOrCreate()
sqlCtx = SQLContext(sc)
# load existing model
model_path = output_path + "k-means.model"
model = KMeansModel.load(model_path)
# read from s3 csv and store to local
path = feature_path + feature_name # used both locally and remotely: features/pca.csv
s3 = boto3.resource('s3')
s3.Object(bucket_name, path).download_file(path)
df_spark = sqlCtx.read.csv(path, header=True, inferSchema=True)
# Dataframe to rdd
vecAssembler = VectorAssembler(inputCols=df_spark.columns,
outputCol="features")
df_spark = vecAssembler.transform(df_spark)
rdd = df_spark.rdd.map(lambda x: array(x["features"]))
print rdd.take(10)
# From here: K-means model use for prediction
data = model.transform(df_spark).toPandas()
print output_path + "pred-" + feature_name
data.to_csv(path_or_buf=(output_path + "pred-" + feature_name))
def loadModel(path):
'''
Loading model from path.
Input: path
Output: loaded model
'''
model = KMeansModel.load(path)
return model
def add_high_low_flag(_data, original_features=True):
# Add features
_data = create_KMeans_features(_data, original=original_features)
# add high-low predictions
high_low_classifier = KMeansModel.load('KMeans_model')
_data = high_low_classifier.transform(_data)
return _data
def cluster(player_profile):
df = player_profile
#columns used for clustering -> features
FEATURES_COL = [
'fouls', 'goals', 'own_goals', 'pass1', 'pass2', 'pass3', 'st1', 'st2',
'st3'
]
for col in df.columns:
if col in FEATURES_COL: #converts all feature_cols to float datatype
df = df.withColumn(col, df[col].cast('float'))
df = df.na.drop()
#combines features columns to make a single feature vector
vecAssembler = VectorAssembler(inputCols=FEATURES_COL,
outputCol="features")
df_kmeans = vecAssembler.transform(df).select('Id', 'features')
k = 5 #number of clusters
kmeans = KMeans().setK(k).setMaxIter(20).setSeed(1).setFeaturesCol(
"features")
#seeing if a model exists, then we use that.Otherwise make a new model in except and save it
model_path = "/home/revanth/Desktop/SEM5/BD/Big_Data_SEM5/PROJECT_FPL_ANALYTICS/" + "kmeans_model"
try:
model = KMeansModel.load(model_path)
#print("loading saved model")
except:
model = kmeans.fit(df_kmeans) #this is the time consuming part
model.save(model_path)
centers = model.clusterCenters() #centroid of each cluster
transformed = model.transform(df_kmeans).select(
'Id', 'prediction'
) #applies our model to the given data, giving the cluster number for all id's
rows = transformed.collect()
df_pred = sqlContext.createDataFrame(rows)
df_pred = df_pred.join(df, 'Id')
#gives a mean rating for each cluster of players
ratings = df_pred.groupby('prediction').agg({
'player_rating': 'mean'
}).withColumnRenamed('avg(player_rating)',
'avg_player_rating').select("prediction",
"avg_player_rating")
for i in ratings.collect(): #convert dataframe to dictionary
ratings_di[i.__getitem__('prediction')] = i.__getitem__(
'avg_player_rating')
df_pred = df_pred.withColumn(
"player_rating",
when(df_pred.no_of_matches < 5,
udf_func(df_pred.prediction)).otherwise(df_pred.player_rating))
#returns the ratings
#print(df_pred.show())
return df_pred
def load_kmeans_model(_model_dir):
"""Load the specified model.
"""
if os.path.exists(_model_dir):
print("Loading model from {} direcory...".format(_model_dir))
model = KMeansModel.load(_model_dir)
else:
print('Model {} not found.'.format(_model_dir))
sys.exit(1)
return model
def find_anomalies(points):
global cur_model
if cur_model is None:
model_path = os.getcwd() + "/kmean_model"
cur_model = KMeansModel.load(model_path)
labels = cur_model.transform(points).select('prediction')
points_array = np.asarray(points.collect())
labels_array = np.asarray(labels.collect())
results = list()
for item, label in zip(points_array, labels_array):
temp = list()
temp.append(item[0][0])
temp.append(item[0][1])
temp.append(item[0][2])
temp.append(label[0])
results.append(temp)
return results
def k_means():
spark = SparkSession \
.builder \
.appName("Python Spark SQL basic example") \
.config("spark.some.config.option", "some-value") \
.getOrCreate()
from pyspark.ml.linalg import Vectors
data = [(Vectors.dense([0.0, 0.0]), ), (Vectors.dense([1.0, 1.0]), ),
(Vectors.dense([9.0, 8.0]), ), (Vectors.dense([8.0, 9.0]), )]
df = spark.createDataFrame(data, ["features"])
kmeans = KMeans(k=2, seed=1)
model = kmeans.fit(df)
centers = model.clusterCenters()
len(centers)
# 2
model.computeCost(df)
# 2.000...
transformed = model.transform(df).select("features", "prediction")
rows = transformed.collect()
rows[0].prediction == rows[1].prediction
# True
rows[2].prediction == rows[3].prediction
# True
model.hasSummary
# True
summary = model.summary
summary.k
# 2
summary.clusterSizes
# [2, 2]
temp_path = "./"
kmeans_path = temp_path + "/kmeans"
kmeans.save(kmeans_path)
kmeans2 = KMeans.load(kmeans_path)
kmeans2.getK()
# 2
model_path = temp_path + "/kmeans_model"
model.save(model_path)
model2 = KMeansModel.load(model_path)
model2.hasSummary
# False
model.clusterCenters()[0] == model2.clusterCenters()[0]
# array([ True, True], dtype=bool)
model.clusterCenters()[1] == model2.clusterCenters()[1]
#load test data
test_data = sc.textFile(golden_file)
parsed_test_data = test_data.map(
kup.parse_as_binaryTuple).filter(lambda x: x[0] != -1.0)
parsed_test_data_df = spark.createDataFrame(parsed_test_data,
["label", "features"])
# load the scaler model, perform feature scaling on test data
scalerModel = StandardScalerModel.load(scaler_model_path)
test_df_tmp = scalerModel.transform(parsed_test_data_df)
test_df = test_df_tmp.drop("features").withColumnRenamed(
"scaledFeatures", "features")
#load the kmeans model
best_model = KMeansModel.load(model_path)
start = time()
# assign clusters to test data
predict_df = best_model.transform(test_df).select(
col("label").alias("actualLabel"), "prediction")
# assign the label to test data according to the assigned clusters
labelPredictedLabel = predict_df.join(
cluster_label,
cluster_label.prediction == predict_df.prediction).select(
predict_df.actualLabel, cluster_label.label)
labelPredictedLabel.show(3)
testTime = time() - start
print("Test time: {} ".format(round(testTime, 3)))
pathVD = args["visualDictionaryPath"]
descriptorName = args["descriptor"]
output = args["output"]
#estimating VLAD descriptors for the whole dataset
print("estimating VLAD descriptors using " + descriptorName +
" for dataset: /" + path + " and visual dictionary: /" + pathVD)
# with open(pathVD, 'rb') as f:
# visualDictionary=pickle.load(f)
# xianjie parallel
spark = SparkSession\
.builder\
.appName("PythonKMeans")\
.getOrCreate()
visualDictionary = KMeansModel.load(pathVD)
##
#computing the VLAD descriptors
dict = {"SURF": describeSURF, "SIFT": describeSIFT, "ORB": describeORB}
V, idImages = getVLADDescriptors(path, dict[descriptorName], visualDictionary)
#output
file = output + ".pickle"
with open(file, 'wb') as f:
pickle.dump([idImages, V, path], f)
print("The VLAD descriptors are saved in " + file)
# plt.plot(centroid1[0], centroid1[1], 'ro')
# plt.annotate("Centroid 1", (centroid1[0], centroid1[1]))
# plt.plot(centroid2[0], centroid2[1], 'ro')
# plt.annotate("Centroid 2", (centroid2[0], centroid2[1]))
#
# plt.savefig("{}VS{}".format(xVar, yVar))
sc = SparkContext()
sqlContext = SQLContext(sc)
spark = SparkSession \
.builder \
.appName("ChessKMeans") \
.config("spark.mongodb.input.uri", "mongodb://127.0.0.1/chess_data_testing.games?readPreference=primaryPreferred") \
.getOrCreate()
model = KMeansModel.load("KMeansModel_final_both_norm")
df = spark.read.parquet("sample.parquet")
# Combine all normalized columns into one "features" column
assembler = VectorAssembler(inputCols=[
"w_attack_norm", "w_defend_norm", "b_attack_norm", "b_defend_norm",
"evals_norm"
],
outputCol="features")
testing = assembler.transform(df)
transformed = model.transform(testing).select('w_attack_norm', 'w_defend_norm',
'b_attack_norm', 'b_defend_norm',
'evals_norm', 'prediction')
dataDF = assembler.transform(dataDF)
#dataDF.show()
if mode == "training":
# splitting datasets for training and testing
(training, testdata) = dataDF.randomSplit([0.7, 0.3], seed=5043)
kmeans = KMeans().setK(k)
model = kmeans.fit(training)
# Predicting the cluster that each id will belong
transformed = model.transform(testdata).withColumnRenamed(
"prediction", "cluster_id")
#archives old model
model_old = KMeansModel.load(modelpath)
model_old.write().overwrite().save(modelpath_archives)
logger.info(
'Old Daily Clustering Bikes by location Model has been archived on the {}'
.format(datetime.now()))
##### Save model
model.write().overwrite().save(modelpath)
logger.info(
'New Daily Clustering Bikes by location Model has been trained on the {}'
.format(datetime.now()))
if mode == "predicting":
model = KMeansModel.load(modelpath)
logger.info(
'Daily Clustering Bikes by location Started on the {} '.format(
datetime.now()))
from pyspark.ml.linalg import DenseVector
spark.read.load("test_fet.csv", format="csv", inferSchema="true", header="true").rdd \
.map(lambda x: (x[2], x[1], DenseVector(lis(x[0])))) \
.toDF(["index", "file", "features"])
.write.parquet("test_fet.parquet")
# Now I get the Bag of Visual Words representation using K-means model built on training data
from pyspark import StorageLevel
schema = spark.read.parquet("test_fet.parquet").persist(StorageLevel(True, True, False, False, 1))
import numpy as np
from pyspark.ml.clustering import KMeansModel
model = KMeansModel.load('KmeansModel')
P = np.load('P.npy')
from pyspark.ml.linalg import DenseVector
predictions = model.transform(schema)
df = predictions.rdd \
.map(lambda x: (x[2], x[0], DenseVector(np.matmul(np.array(x[0]), P.T)), x[1], x[3])) \
.toDF(["Index", "Features", "Projections", "File", "VisualWords"])
# Then, I generate binary signatures for all test images
tau = np.load('tau.npy')
from pyspark.ml.linalg import DenseVector
def binsig(z, c, tau):
return DenseVector((z > tau[c,:]))
def calc_error(rdd):
now = datetime.now()
data = rdd.toDF()
output = transform_model.transform(data)
predictions = model.transform(output)
get_logger().info("Processing logfiles")
wssse = predictions.select(['endpoint','method','response_code','features','prediction'])\
.rdd\
.map(lambda line: (error(line.features,clusterCenters[line.prediction]), line.response_code, line.endpoint, line.method))\
.filter(lambda x: x[0] > 100.0)
if wssse.count() > 0:
for line in wssse.collect():
get_logger().warning(line)
return wssse
model = KMeansModel.load(MODEL_LOCATION)
transform_model = PipelineModel.load(TRANSFORM_MODEL_LOCATION)
clusterCenters = model.clusterCenters()
access_logs = ssc.socketTextStream(SOCKET_HOST, SOCKET_PORT)
struc_logs = access_logs.flatMap(lambda line: parse_apache_log_line(line))
struc_logs.pprint()
rc_dstream = struc_logs.map(lambda parsed_line: (parsed_line.response_code, 1))
rc_count = rc_dstream.reduceByKey(lambda x,y: x+y)
rc_count.pprint(num = 30)
struc_logs.foreachRDD(calc_error)
ssc.start()
ssc.awaitTermination()
from pyspark.ml.clustering import KMeansModel
from pyspark.ml.evaluation import ClusteringEvaluator
from pyspark.ml.linalg import Vectors
from pyspark.sql import SparkSession
if __name__ == "__main__":
sparkSession = SparkSession\
.builder\
.appName("Spark ML KMeans")\
.getOrCreate()
model = KMeansModel.load("KMEANSMODELDF")
print("Model loaded")
# Prepare test data
test = sparkSession.createDataFrame([
(1, Vectors.dense([1.1, 3.2])),
(2, Vectors.dense([5.1, 1.4])),
(3, Vectors.dense([5.2, 2.0])),
(4, Vectors.dense([1.0, 4.0]))],
["id", "features"])\
.cache()
for row in test.collect():
print(row)
prediction = model.transform(test)
prediction.printSchema()
prediction.show()
def load_model(self, path_to_model):
"""Load K-Means model from path_to_model."""
from pyspark.ml.clustering import KMeansModel
model = KMeansModel.load(path_to_model)
return (model)
# заготовка для API
from pyspark.ml.clustering import KMeans, KMeansModel
from pyspark.ml.evaluation import ClusteringEvaluator
from pyspark.ml.feature import VectorAssembler
from pyspark.ml import PipelineModel
from pyspark import SparkConf, SparkContext
spark = SparkContext()
df1 = spark.createDataFrame([
(1353, 1347),
], ['user', 'summa'])
va = VectorAssembler(inputCols=['user', 'summa'], outputCol="features")
modelka = KMeansModel.load('./models/clusters.model')
result = modelka.transform(
va.transform(df1)).select('prediction').take(1)[0][0]
# Проверка на новенького.
# Если страый юзер - тянем монгу
# Иначе поднимаем мини-инстанс.
from pyspark.ml.clustering import KMeansModel
from pyspark.ml.linalg import Vectors
from pyspark.sql import SparkSession
if __name__ == "__main__":
sparkSession = SparkSession\
.builder\
.appName("Spark ML KMeans")\
.getOrCreate()
model = KMeansModel.load("KMEANSMODELML")
print("Model loaded")
# Prepare test data
test = sparkSession.createDataFrame([
(1, Vectors.dense([1.1, 3.2])),
(2, Vectors.dense([5.1, 1.4])),
(3, Vectors.dense([5.2, 2.0])),
(4, Vectors.dense([1.0, 4.0]))],
["id", "features"])\
.cache()
for row in test.collect():
print(row)
prediction = model.transform(test)
prediction.printSchema()
prediction.show()
selected = prediction.select("id", "prediction")
tfIdf = PipelineModel.load(tfIdf_model_path)
dataset = tfIdf.transform(dataset)
# VectorAssembler
vector_assembler_output_path = "{}/data/vectorAssemblerModel.bin".format(base_path)
vector_assembler = VectorAssembler.load(vector_assembler_output_path)
dataset = vector_assembler.transform(dataset)
print('# Modelos de preprocesamiento cargados')
print('> Cargando KMeans')
# Clasificación
model_path = "{}/data/distanceKmeansRfModel.bin".format(base_path)
model = KMeansModel.load(model_path)
predictions = model.transform(dataset)
centers = model.clusterCenters()
vectorCent = F.udf(lambda k: centroid(k,centers), ArrayType(DoubleType()))
euclDistance = F.udf(lambda data,centroid: distToCentroid(data,centroid),FloatType())
detectAnom = F.udf(lambda prediction, distance: anomalia(prediction, distance, threshold, limit), BooleanType())
predictions = predictions.withColumn('centroid', vectorCent(F.col('prediction')))
predictions = predictions.withColumn('distance', euclDistance(F.col('features'),F.col('centroid')))
predictions = predictions.withColumn('anomalia', detectAnom(F.col('prediction'),F.col('distance')))
print('# KMeans cargado ')
only_predictions = predictions.select('version','timestamp','id','type','event','signal','freq','mod','payload','time','anomalia','distance','prediction')
def kmeans_inference(
original_data,
msg_col,
id_col,
w2v_model_path,
tks_vec,
ft_col,
kmeans_mode,
kmeans_model_path,
pred_mode="static",
new_cluster_thresh=None,
k_list=[12, 16, 20], # update_model_path=None,
distance="cosine",
opt_initSteps=10,
opt_tol=0.0001,
opt_maxIter=30,
log_path=None,
n_cores=5,
# K_optim
tr_initSteps=200,
tr_tol=0.000001,
tr_maxIter=100, # train_kmeans
):
"""Perform inference on new error messages (Note: only K-Means can be re-trained/updated).
-- params:
original_data (pyspark.sql.dataframe.DataFrame): data frame with at least error string and id columns
msg_col (string): name of the error string column
id_col (string): name of the message id column
model_path (string): path where to load pre-trained word2vec model
tks_vec (string): name of the word2vec representations column
ft_col (string): name of the features column
kmeans_mode (\"load\" or \"train\"): kmeans mode: \"load\" uses pre-trained model, while \"train\" performs online training
kmeans_model_path (string): path to pre-trained model (Specify None for re-training)
pred_mode (\"static\" or \"update\"): prediction mode: \"static\" does not allow for creating new clusters
new_cluster_thresh (float): distance threshold: if closest centroid is more distant than new_cluster_thresh
then a new cluster is created for the new observation
k_list (list): grid of K values to try
distance (\"euclidean\" or \"cosine\"): distance measure for the kmeans algorithm
opt_initStep (int): number of different random intializations for the kmeans algorithm in the optimization phase
opt_tol (int): tolerance for kmeans algorithm convergence in the optimization phase
opt_maxIter (int): maximum number of iterations for the kmeans algorithm in the optimization phase
n_cores (int): number of cores to use
log_path (string): where to save optimization stats. Default None (no saving)
tr_initStep (int): number of different random intializations for the kmeans algorithm in the training phase
tr_tol (int): tolerance for kmeans algorithm convergence in the training phase
tr_maxIter (int): maximum number of iterations for the kmeans algorithm in the training phase
Returns:
original_data (pyspark.sql.dataframe.DataFrame): the input data frame with an extra \"prediction\" column
"""
from language_models import w2v_preproc
from pyspark.ml.clustering import KMeansModel
import time
import datetime
from pyspark.ml.evaluation import ClusteringEvaluator
from pathlib import Path
if kmeans_mode not in ["load", "train"]:
print(
"""WARNING: invalid param \"kmeans_mode\". Specify either \"load\" to train load a pre-trained model
or \"train\" to train it online.""")
return (None)
original_data = w2v_preproc(original_data, msg_col, id_col, w2v_model_path)
if kmeans_mode == "load":
original_data = kmeans_preproc(original_data, tks_vec)
kmeans_model = KMeansModel.load(kmeans_model_path)
else:
# K_optim()
# initialize a grid of K (number of clusters) values
# k_list = [12, 16, 20]
# train for different Ks
res = K_optim(k_list,
dataset=original_data,
tks_vec=tks_vec,
ft_col=ft_col,
distance=distance,
initSteps=opt_initSteps,
tol=opt_tol,
maxIter=opt_maxIter,
n_cores=n_cores,
log_path=log_path)
k_sil = get_k_best(res, "silhouette")
if pred_mode == "update":
save_mode = "overwrite"
kmeans_model_path = "temp_ciccio"
# elif kmeans_mode=="load":
# kmeans_model_path = None
# save_mode = "new"
# else:
# save_mode = "new"
else:
kmeans_model_path = None
save_mode = "new"
best_k_log_path = Path(log_path).parent / "best_K={}.txt".format(k_sil)
original_data = kmeans_preproc(original_data, tks_vec)
kmeans_model = train_kmeans(original_data,
ft_col=ft_col,
k=k_sil,
distance=distance,
initSteps=tr_initSteps,
tol=tr_tol,
maxIter=tr_maxIter,
save_path=kmeans_model_path,
mode=save_mode,
log_path=best_k_log_path)
original_data = kmeans_predict(original_data,
kmeans_model["model"],
pred_mode=pred_mode,
new_cluster_thresh=None,
update_model_path=kmeans_model_path)
return (original_data)
def _init_model(self):
model_path = self._model_path
if os.path.exists(model_path):
self._kmeans_model = KMeansModel.load(model_path)
def __load_from_hdfs(self):
sameModel = KMeansModel.load(self.hdfs_uri)
print("k-means() - model loaded from uri {}".format(self.hdfs_uri))
return sameModel