def install_package(pkg):
# install weka package if necessary
if not packages.is_installed(pkg):
print("Installing %s..." % pkg)
packages.install_package(pkg)
print("Installed %s, please re-run script!" % pkg)
jvm.stop()
sys.exit(0)
print('Package already installed.')
def main():
if not is_installed("CLOPE"):
print("CLOPE is not installed, installing now")
install_package("CLOPE")
print("please restart")
return
cls = Clusterer(classname="weka.clusterers.CLOPE")
print("CLOPE is installed:", cls.to_commandline())
def install_packages(path):
"""Install weka packages
Arguments:
path {str} -- path to install weka packages json
"""
with open(path, "r") as f:
weka_packages = json.load(f)
for package_name, package_path in weka_packages.items():
if not packages.is_installed(package_name):
v.app.logger.info("Installing: %s %s", package_name,
package_path)
packages.install_package(package_path)
from weka.classifiers import Classifier
from weka.classifiers import Evaluation
from weka.core.classes import Random
from weka.classifiers import PredictionOutput, KernelClassifier, Kernel
import weka.core.packages as packages
# start JVM with packages
jvm.start(packages=True)
# package install
chisq_name = "EvolutionarySearch"
chisq_installed = False
for p in pkg.installed_packages():
if p.name == chisq_name:
chisq_installed = True
if not chisq_installed:
pkg.install_package(chisq_name)
print("pkg %s installed, please restart" % chisq_name)
jvm.stop()
sys.exit(1)
data_dir = "\\\\egr-1l11qd2\\CLS_lab\\Junya Zhao\\GWAS SNPs_2018\\random50_combo_Nonoverlap_\\"
globbed_files = glob.glob(data_dir + "*.csv")
for csv in globbed_files:
data = converters.load_any_file(csv)
data.class_is_last()
search = ASSearch(classname="weka.attributeSelection.BestFirst",
options=["-D", "1", "-N", "10"])
evaluator = ASEvaluation(classname="weka.attributeSelection.CfsSubsetEval",
options=["-P", "1", "E", "1"])
attsel = AttributeSelection()
attsel.folds(10)
import weka.core.jvm as jvm
import weka.core.packages as packages
from weka.core.classes import complete_classname
jvm.start(packages=True)
pkg = "SMOTE"
# install package if necessary
if not packages.is_installed(pkg):
print("Installing %s..." % pkg)
packages.install_package(pkg)
print("Installed %s, please re-run script!" % pkg)
jvm.stop()
# testing classname completion
print(complete_classname(".SMOTE"))
jvm.stop()
data_dir = os.environ.get("WEKAMOOC_DATA")
if data_dir is None:
data_dir = "." + os.sep + "data"
import weka.core.jvm as jvm
from weka.core.converters import Loader
from weka.core.classes import Random
import weka.core.packages as packages
from weka.classifiers import Classifier, Evaluation
jvm.start(packages=True)
# install stackingC if necessary
if not packages.is_installed("stackingC"):
print("Installing stackingC...")
packages.install_package("stackingC")
jvm.stop()
print("Installed package, please restart")
exit()
# load glass
loader = Loader(classname="weka.core.converters.ArffLoader")
fname = data_dir + os.sep + "glass.arff"
print("\nLoading dataset: " + fname + "\n")
data = loader.load_file(fname)
data.class_is_last()
# compare several meta-classifiers with J48
for classifier in [("weka.classifiers.trees.J48", []),
("weka.classifiers.meta.Bagging", []),
("weka.classifiers.trees.RandomForest", []),
if data_dir is None:
data_dir = "." + os.sep + "data"
import os
import weka.core.jvm as jvm
from weka.core.converters import Loader
from weka.core.classes import Random
import weka.core.packages as packages
from weka.classifiers import Classifier, Evaluation
jvm.start(packages=True)
# install stackingC if necessary
if not packages.is_installed("stackingC"):
print("Installing stackingC...")
packages.install_package("stackingC")
jvm.stop()
print("Please restart")
exit()
# load glass
loader = Loader(classname="weka.core.converters.ArffLoader")
fname = data_dir + os.sep + "glass.arff"
print("\nLoading dataset: " + fname + "\n")
data = loader.load_file(fname)
data.set_class_index(data.num_attributes() - 1)
# compare several meta-classifiers with J48
for classifier in [("weka.classifiers.trees.J48", []), ("weka.classifiers.meta.Bagging", []),
("weka.classifiers.trees.RandomForest", []), ("weka.classifiers.meta.AdaBoostM1", []),
("weka.classifiers.meta.Stacking", []),
data_dir = os.environ.get("WEKAMOOC_DATA")
if data_dir is None:
data_dir = "." + os.sep + "data"
import os
import weka.core.jvm as jvm
import weka.core.packages as packages
from weka.core.converters import Loader
from weka.core.classes import Random
from weka.classifiers import Classifier, Evaluation
jvm.start(packages=True)
pkg = "simpleEducationalLearningSchemes"
if not packages.is_installed(pkg):
packages.install_package(pkg):
jvm.stop()
print("Please restart")
exit()
# load weather.nominal
fname = data_dir + os.sep + "weather.nominal.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)
# cross-validate classifiers
classifiers = [
"weka.classifiers.trees.J48",
"weka.classifiers.rules.Prism"
]
import weka.core.jvm as jvm
import weka.core.packages as packages
jvm.start()
# packages.refresh_cache()
packages.install_package("CLOPE")
print(packages.installed_packages())
jvm.stop()
from tqdm import tqdm
import time
import pandas as pd
start_time = time.time()
#jvm.start(packages=True, max_heap_size="12g") #max_heap_size 512m, 4g. packages=true searches for weka packages in installation program
jvm.start(packages='C:/Users/rolan/wekafiles', max_heap_size='12g')
pkg = "PBC4cip"
pkg_source = 'D:/GoogleDrive/ITESM/3rd Semester/Tecnicas de ML/Assignment 3/PBC4cip-1.0-weka.zip'
print(complete_classname("." + pkg))
# install package if necessary
if not packages.is_installed(pkg):
print("Installing %s..." % pkg)
#packages.install_package("http://prdownloads.sourceforge.net/weka/discriminantAnalysis1.0.3.zip?download")
packages.install_package(pkg_source)
print("Installed %s, please re-run script!" % pkg)
jvm.stop()
sys.exit(0)
# testing classname completion
print("\n\n\n\n\n")
print(">>> Start...")
data_dir = "D:/GoogleDrive/ITESM/3rd Semester/Tecnicas de ML/Assignment 3/"
arff_file = "universities.arff"
loader = Loader(classname="weka.core.converters.ArffLoader")
data = loader.load_file(data_dir + arff_file)
data.class_is_last()
# -*- coding: utf-8 -*-
import weka.core.jvm as jvm
import weka.core.packages as packages
jvm.start()
# checking for installed packages
#installed_packages = packages.installed_packages()
#for item in installed_packages:
# print item.name, item.url, "is installed\n"
# # Search for GridSearch and LibSVM, just to check package's names
# all_packages = packages.all_packages()
# for item in all_packages:
# if (item.name == "gridSearch") or (item.name == "LibSVM"):
# print(item.name + " " + item.url)
# To install gridSearch and LibSVM
# packages.install_package("gridSearch", "1.0.8")
#packages.install_package("LibSVM")
packages.install_package("/home/sebastian/Descargas/LibSVM1.0.8.zip")
# To install MultiSearch
#packages.install_package("https://github.com/fracpete/multisearch-weka-package/releases/download/" +
# "v2016.6.7/multisearch-2016.6.7.zip")
#packages.install_package("/home/sebastian/Descargas/multisearch-2016.6.7.zip")
#packages.uninstall_package("multisearch")
jvm.stop()
import os
data_dir = os.environ.get("WEKAMOOC_DATA")
if data_dir is None:
data_dir = "." + os.sep + "data"
import weka.core.jvm as jvm
import weka.core.packages as packages
from weka.core.converters import Loader
from weka.core.classes import Random
from weka.classifiers import Classifier, Evaluation
jvm.start(packages=True)
pkg = "simpleEducationalLearningSchemes"
if not packages.is_installed(pkg):
packages.install_package(pkg)
jvm.stop()
print("Installed package, please restart")
exit()
# load weather.nominal
fname = data_dir + os.sep + "weather.nominal.arff"
print("\nLoading dataset: " + fname + "\n")
loader = Loader(classname="weka.core.converters.ArffLoader")
data = loader.load_file(fname)
data.class_is_last()
# cross-validate classifiers
classifiers = [
"weka.classifiers.trees.J48",
"weka.classifiers.rules.Prism"
Description: Training and Testing a Logistic Model Tree that compensates for
class imbalancing using SMOTE by using the WEKA python wrapper.
"""
import weka.core.jvm as jvm
import weka.core.converters as converters
from weka.classifiers import Classifier, FilteredClassifier, Evaluation
from weka.core.classes import Random
from weka.filters import Filter
import weka.plot.classifiers as plcls
import weka.core.packages as packages
# Starts the Java Handler with packages set to True
jvm.start(packages=True)
packages.install_package("SMOTE")
# Loads the Data
train = converters.load_any_file("imbalanced_train.arff")
test = converters.load_any_file("imbalanced_test.arff")
train.class_is_last()
test.class_is_last()
# Minority Class is getting Sampled 5x
smote = Filter(classname="weka.filters.supervised.instance.SMOTE",
options=["-P", "500.0"])
# Base Classifier
cls = Classifier(classname="weka.classifiers.trees.LMT",
options=["-B", "-I", "10"])
import os
from weka.core.converters import Loader
from weka.attribute_selection import ASSearch, ASEvaluation, AttributeSelection
from weka.filters import Filter
########SetUp########################
os.environ["WEKA_HOME"] = os.path.abspath(
"./weka-3-8-4") #point it to your weka instalation folder
jvm.start(packages=True, max_heap_size='6g')
#####################################
########Install######################
packages.refresh_cache()
if not packages.is_installed('discriminantAnalysis'):
print("Installing discriminantAnalysis")
packages.install_package('discriminantAnalysis')
if not packages.is_installed('PBC4cip'):
print("Installing PBC4cip")
packages.install_package(os.path.abspath('./weka_packages/PBC4cip.zip'))
######################################
#############Data#####################
loader = Loader(classname="weka.core.converters.ArffLoader")
data = loader.load_file(os.path.abspath('./universities.arff'))
data.class_is_last()
######################################
#######rub1########################
print("rub1")
options = [
"-S", "1", "-miner",
