From b1240a8e9cf3500fe74338394e12652ef306b258 Mon Sep 17 00:00:00 2001
From: bbauvin <baptiste.bauvin@centrale-marseille.fr>
Date: Mon, 23 Oct 2017 14:48:49 -0400
Subject: [PATCH] python3 usable
---
Code/MonoMultiViewClassifiers/ExecClassif.py | 6 +++---
.../Metrics/__init__.py | 4 +++-
.../Monoview/ExecClassifMonoView.py | 6 +++---
.../Monoview/MonoviewUtils.py | 2 +-
.../Monoview/__init__.py | 2 +-
.../MonoviewClassifiers/__init__.py | 2 +-
.../Multiview/Fusion/FusionModule.py | 2 +-
.../Methods/EarlyFusionPackage/__init__.py | 2 +-
.../LateFusionPackage/MajorityVoting.py | 2 +-
.../Methods/LateFusionPackage/__init__.py | 2 +-
.../Multiview/Fusion/analyzeResults.py | 4 ++--
.../Multiview/GetMultiviewDb.py | 10 +++++-----
.../Mumbo/Classifiers/DecisionTree.py | 2 +-
.../Multiview/Mumbo/Classifiers/__init__.py | 2 +-
.../Multiview/Mumbo/MumboModule.py | 2 +-
.../Multiview/Mumbo/analyzeResults.py | 2 +-
.../MonoMultiViewClassifiers/utils/Dataset.py | 4 ++--
.../utils/Interpret.py | 4 ++--
.../utils/__init__.py | 2 +-
.../utils/execution.py | 6 +++---
Code/Versions.py | 20 ++++++++++++-------
21 files changed, 48 insertions(+), 40 deletions(-)
diff --git a/Code/MonoMultiViewClassifiers/ExecClassif.py b/Code/MonoMultiViewClassifiers/ExecClassif.py
index 4dd5ee27..d1be6b7a 100644
--- a/Code/MonoMultiViewClassifiers/ExecClassif.py
+++ b/Code/MonoMultiViewClassifiers/ExecClassif.py
@@ -22,7 +22,7 @@ from . import MonoviewClassifiers
from .Multiview.ExecMultiview import ExecMultiview, ExecMultiview_multicore
from .Monoview.ExecClassifMonoView import ExecMonoview, ExecMonoview_multicore
from .Multiview import GetMultiviewDb as DB
-from ResultAnalysis import resultAnalysis, analyzeLabels, analyzeIterResults, analyzeIterLabels, genNamesFromRes
+from .ResultAnalysis import resultAnalysis, analyzeLabels, analyzeIterResults, analyzeIterLabels, genNamesFromRes
from .utils import execution, Dataset
# Author-Info
@@ -87,7 +87,7 @@ def initMonoviewKWARGS(args, classifiersNames):
for classifiersName in classifiersNames:
classifierModule = getattr(MonoviewClassifiers, classifiersName)
monoviewKWARGS[classifiersName + "KWARGSInit"] = classifierModule.getKWARGS(
- [(key, value) for key, value in vars(args).iteritems() if key.startswith("CL_" + classifiersName)])
+ [(key, value) for key, value in vars(args).items() if key.startswith("CL_" + classifiersName)])
return monoviewKWARGS
@@ -295,7 +295,7 @@ def execClassif(arguments):
views, viewsIndices, allViews = execution.initViews(DATASET, args)
if not views:
- raise ValueError, "Empty views list, modify selected views to match dataset " + args.views
+ raise ValueError("Empty views list, modify selected views to match dataset " + args.views)
NB_VIEW = len(views)
NB_CLASS = DATASET.get("Metadata").attrs["nbClass"]
diff --git a/Code/MonoMultiViewClassifiers/Metrics/__init__.py b/Code/MonoMultiViewClassifiers/Metrics/__init__.py
index 2e9bab08..c5f17c0f 100644
--- a/Code/MonoMultiViewClassifiers/Metrics/__init__.py
+++ b/Code/MonoMultiViewClassifiers/Metrics/__init__.py
@@ -1,8 +1,10 @@
import os
+modules = []
for module in os.listdir(os.path.dirname(os.path.realpath(__file__))):
if module == '__init__.py' or module[-3:] != '.py':
continue
- __import__(module[:-3], locals(), globals())
+ __import__(module[:-3], locals(), globals(), [], 1)
+ pass
del module
del os
diff --git a/Code/MonoMultiViewClassifiers/Monoview/ExecClassifMonoView.py b/Code/MonoMultiViewClassifiers/Monoview/ExecClassifMonoView.py
index e8d0b308..661b44cd 100644
--- a/Code/MonoMultiViewClassifiers/Monoview/ExecClassifMonoView.py
+++ b/Code/MonoMultiViewClassifiers/Monoview/ExecClassifMonoView.py
@@ -16,13 +16,13 @@ import h5py
# Import own modules
from .. import MonoviewClassifiers
-from analyzeResult import execute
+from .analyzeResult import execute
from ..utils.Dataset import getValue, extractSubset
# Author-Info
__author__ = "Nikolas Huelsmann, Baptiste BAUVIN"
__status__ = "Prototype" # Production, Development, Prototype
-__date__ = 2016 - 03 - 25
+# __date__ = 2016 - 03 - 25
def ExecMonoview_multicore(directory, name, labelsNames, classificationIndices, KFolds, datasetFileIndex, databaseType,
@@ -114,7 +114,7 @@ def ExecMonoview(directory, X, Y, name, labelsNames, classificationIndices, KFol
clKWARGS, labelsNames, X.shape,
y_train, y_train_pred, y_test, y_test_pred, t_end,
randomState, cl_res, outputFileName)
- cl_desc = [value for key, value in sorted(clKWARGS.iteritems())]
+ cl_desc = [value for key, value in sorted(clKWARGS.items())]
logging.debug("Done:\t Getting Results")
logging.info(stringAnalysis)
# labelsString = "-".join(labelsNames)
diff --git a/Code/MonoMultiViewClassifiers/Monoview/MonoviewUtils.py b/Code/MonoMultiViewClassifiers/Monoview/MonoviewUtils.py
index 7eed810f..53e33323 100644
--- a/Code/MonoMultiViewClassifiers/Monoview/MonoviewUtils.py
+++ b/Code/MonoMultiViewClassifiers/Monoview/MonoviewUtils.py
@@ -17,7 +17,7 @@ import numpy as np
# Author-Info
__author__ = "Nikolas Huelsmann, Baptiste Bauvin"
__status__ = "Prototype" # Production, Development, Prototype
-__date__ = 2016 - 03 - 25
+# __date__ = 2016 - 03 - 25
def isUseful(labelSupports, index, CLASS_LABELS, labelDict):
diff --git a/Code/MonoMultiViewClassifiers/Monoview/__init__.py b/Code/MonoMultiViewClassifiers/Monoview/__init__.py
index f0fc97ad..8bbd0830 100644
--- a/Code/MonoMultiViewClassifiers/Monoview/__init__.py
+++ b/Code/MonoMultiViewClassifiers/Monoview/__init__.py
@@ -1 +1 @@
-from . import ExecClassifMonoView, MonoviewUtils
+from . import ExecClassifMonoView, MonoviewUtils, analyzeResult
diff --git a/Code/MonoMultiViewClassifiers/MonoviewClassifiers/__init__.py b/Code/MonoMultiViewClassifiers/MonoviewClassifiers/__init__.py
index bc6cdc28..03d92693 100644
--- a/Code/MonoMultiViewClassifiers/MonoviewClassifiers/__init__.py
+++ b/Code/MonoMultiViewClassifiers/MonoviewClassifiers/__init__.py
@@ -2,7 +2,7 @@ import os
for module in os.listdir(os.path.dirname(os.path.realpath(__file__))):
if module == '__init__.py' or module[-3:] != '.py':
continue
- __import__(module[:-3], locals(), globals())
+ __import__(module[:-3], locals(), globals(), [],1)
del module
del os
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Fusion/FusionModule.py b/Code/MonoMultiViewClassifiers/Multiview/Fusion/FusionModule.py
index 30da0f52..f6445eac 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Fusion/FusionModule.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Fusion/FusionModule.py
@@ -158,7 +158,7 @@ class FusionClass:
fusionMethodClass = getattr(fusionMethodModule, fusionMethod)
nbCores = NB_CORES
classifierKWARGS = dict(
- (key, value) for key, value in kwargs.iteritems() if key not in ['fusionType', 'fusionMethod'])
+ (key, value) for key, value in kwargs.items() if key not in ['fusionType', 'fusionMethod'])
self.classifier = fusionMethodClass(randomState, NB_CORES=nbCores, **classifierKWARGS)
def setParams(self, paramsSet):
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/EarlyFusionPackage/__init__.py b/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/EarlyFusionPackage/__init__.py
index 406f941a..3636ca90 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/EarlyFusionPackage/__init__.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/EarlyFusionPackage/__init__.py
@@ -3,6 +3,6 @@ import os
for module in os.listdir(os.path.dirname(os.path.realpath(__file__))):
if module == '__init__.py' or module[-3:] != '.py':
continue
- __import__(module[:-3], locals(), globals())
+ __import__(module[:-3], locals(), globals(), [], 1)
del module
del os
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/LateFusionPackage/MajorityVoting.py b/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/LateFusionPackage/MajorityVoting.py
index 966b0ca3..6b0b0692 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/LateFusionPackage/MajorityVoting.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/LateFusionPackage/MajorityVoting.py
@@ -86,7 +86,7 @@ class MajorityVoting(LateFusionClassifier):
try:
assert nbMaximum != nbView
except:
- print "Majority voting can't decide, each classifier has voted for a different class"
+ print("Majority voting can't decide, each classifier has voted for a different class")
raise
predictedLabels = np.argmax(votes, axis=1)
# Can be upgraded by restarting a new classification process if
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/LateFusionPackage/__init__.py b/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/LateFusionPackage/__init__.py
index 406f941a..3636ca90 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/LateFusionPackage/__init__.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Fusion/Methods/LateFusionPackage/__init__.py
@@ -3,6 +3,6 @@ import os
for module in os.listdir(os.path.dirname(os.path.realpath(__file__))):
if module == '__init__.py' or module[-3:] != '.py':
continue
- __import__(module[:-3], locals(), globals())
+ __import__(module[:-3], locals(), globals(), [], 1)
del module
del os
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Fusion/analyzeResults.py b/Code/MonoMultiViewClassifiers/Multiview/Fusion/analyzeResults.py
index 05526fdb..87d7d3a0 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Fusion/analyzeResults.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Fusion/analyzeResults.py
@@ -4,7 +4,7 @@ import matplotlib
# matplotlib.use('Agg')
import operator
-import Methods.LateFusion
+from .Methods import LateFusion
from ... import Metrics
# Author-Info
@@ -88,7 +88,7 @@ def execute(classifier, trainLabels,
" folds\n\nClassification configuration : \n\t-Algorithm used : " + fusionType + " " + fusionConfiguration
if fusionType == "LateFusion":
- stringAnalysis += Methods.LateFusion.getScores(classifier)
+ stringAnalysis += LateFusion.getScores(classifier)
metricsScores = getMetricsScores(metrics, trainLabels, testLabels,
DATASET, validationIndices, learningIndices)
stringAnalysis += printMetricScore(metricsScores, metrics)
diff --git a/Code/MonoMultiViewClassifiers/Multiview/GetMultiviewDb.py b/Code/MonoMultiViewClassifiers/Multiview/GetMultiviewDb.py
index 18fa2efd..28139df7 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/GetMultiviewDb.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/GetMultiviewDb.py
@@ -36,13 +36,13 @@ def getPlausibleDBhdf5(features, pathF, name, NB_CLASS, LABELS_NAME, nbView=3,
if exc.errno != errno.EEXIST:
raise
datasetFile = h5py.File(pathF + "/Plausible.hdf5", "w")
- CLASS_LABELS = np.array([0 for i in range(datasetLength / 2)] + [1 for i in range(datasetLength / 2)])
+ CLASS_LABELS = np.array([0 for i in range(int(datasetLength / 2))] + [1 for i in range(int(datasetLength / 2))])
for viewIndex in range(nbView):
- viewData = np.array([np.zeros(nbFeatures) for i in range(datasetLength / 2)] + [np.ones(nbFeatures)
+ viewData = np.array([np.zeros(nbFeatures) for i in range(int(datasetLength / 2))] + [np.ones(nbFeatures)
for i in
- range(datasetLength / 2)])
- fakeTrueIndices = randomState.randint(0, datasetLength / 2 - 1, datasetLength / 5)
- fakeFalseIndices = randomState.randint(datasetLength / 2, datasetLength - 1, datasetLength / 5)
+ range(int(datasetLength / 2))])
+ fakeTrueIndices = randomState.randint(0, int(datasetLength / 2) - 1, int(datasetLength / 5))
+ fakeFalseIndices = randomState.randint(int(datasetLength / 2), datasetLength - 1, int(datasetLength / 5))
viewData[fakeTrueIndices] = np.ones((len(fakeTrueIndices), nbFeatures))
viewData[fakeFalseIndices] = np.zeros((len(fakeFalseIndices), nbFeatures))
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Mumbo/Classifiers/DecisionTree.py b/Code/MonoMultiViewClassifiers/Multiview/Mumbo/Classifiers/DecisionTree.py
index 13f8ef38..874f3ce5 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Mumbo/Classifiers/DecisionTree.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Mumbo/Classifiers/DecisionTree.py
@@ -2,7 +2,7 @@ import sklearn
from sklearn.base import BaseEstimator, ClassifierMixin
import numpy as np
# from ModifiedMulticlass import OneVsRestClassifier
-from SubSampling import subSample
+from .SubSampling import subSample
import logging
# Add weights
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Mumbo/Classifiers/__init__.py b/Code/MonoMultiViewClassifiers/Multiview/Mumbo/Classifiers/__init__.py
index 67fe9de3..8db5fdba 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Mumbo/Classifiers/__init__.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Mumbo/Classifiers/__init__.py
@@ -8,6 +8,6 @@ import os
for module in os.listdir(os.path.dirname(os.path.realpath(__file__))):
if module == '__init__.py' or module[-3:] != '.py':
continue
- __import__(module[:-3], locals(), globals())
+ __import__(module[:-3], locals(), globals(), [], 1)
del module
del os
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Mumbo/MumboModule.py b/Code/MonoMultiViewClassifiers/Multiview/Mumbo/MumboModule.py
index 35836ea8..d4cf238d 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Mumbo/MumboModule.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Mumbo/MumboModule.py
@@ -7,7 +7,7 @@ import pkgutil
import logging
from sklearn.metrics import accuracy_score
-import Classifiers
+from . import Classifiers
from ...utils.Dataset import getV
# Author-Info
diff --git a/Code/MonoMultiViewClassifiers/Multiview/Mumbo/analyzeResults.py b/Code/MonoMultiViewClassifiers/Multiview/Mumbo/analyzeResults.py
index dc5c7016..b38eead5 100644
--- a/Code/MonoMultiViewClassifiers/Multiview/Mumbo/analyzeResults.py
+++ b/Code/MonoMultiViewClassifiers/Multiview/Mumbo/analyzeResults.py
@@ -6,7 +6,7 @@ from datetime import timedelta as hms
# import logging
# import Mumbo
-import Classifiers
+from . import Classifiers
from ... import Metrics
from ...utils.Dataset import getV, getShape
diff --git a/Code/MonoMultiViewClassifiers/utils/Dataset.py b/Code/MonoMultiViewClassifiers/utils/Dataset.py
index 1ce96122..a2a1bd16 100644
--- a/Code/MonoMultiViewClassifiers/utils/Dataset.py
+++ b/Code/MonoMultiViewClassifiers/utils/Dataset.py
@@ -92,7 +92,7 @@ def confirm(resp=True, timeout=15):
if not ans:
return resp
if ans not in ['y', 'Y', 'n', 'N']:
- print 'please enter y or n.'
+ print('please enter y or n.')
if ans == 'y' or ans == 'Y':
return True
if ans == 'n' or ans == 'N':
@@ -100,7 +100,7 @@ def confirm(resp=True, timeout=15):
def input_(timeout=15):
- print "You have " + str(timeout) + " seconds to stop the script by typing n"
+ print("You have " + str(timeout) + " seconds to stop the script by typing n")
i, o, e = select.select([sys.stdin], [], [], timeout)
if i:
return sys.stdin.readline().strip()
diff --git a/Code/MonoMultiViewClassifiers/utils/Interpret.py b/Code/MonoMultiViewClassifiers/utils/Interpret.py
index 6f1882a5..00562135 100644
--- a/Code/MonoMultiViewClassifiers/utils/Interpret.py
+++ b/Code/MonoMultiViewClassifiers/utils/Interpret.py
@@ -1,7 +1,7 @@
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import FuncFormatter
-import cPickle
+import pickle
def percent(x, pos):
@@ -26,7 +26,7 @@ def getFeatureImportance(classifier, directory, interpretString=""):
for featureIndex, featureImportance in enumerate(featureImportances)
if featureImportance != 0)
with open(directory+'-feature_importances.pickle', 'wb') as handle:
- cPickle.dump(featuresImportancesDict, handle)
+ pickle.dump(featuresImportancesDict, handle)
interpretString += "Feature importances : \n"
for featureIndex, featureImportance in zip(featureIndicesSorted, featureImportancesSorted):
if featureImportance>0:
diff --git a/Code/MonoMultiViewClassifiers/utils/__init__.py b/Code/MonoMultiViewClassifiers/utils/__init__.py
index 842d824c..5baa4d9c 100644
--- a/Code/MonoMultiViewClassifiers/utils/__init__.py
+++ b/Code/MonoMultiViewClassifiers/utils/__init__.py
@@ -1 +1 @@
-from . import Dataset, execution, HyperParameterSearch, Transformations
+from . import Dataset, execution, HyperParameterSearch, Transformations, Interpret
diff --git a/Code/MonoMultiViewClassifiers/utils/execution.py b/Code/MonoMultiViewClassifiers/utils/execution.py
index d4ebb75d..7552f068 100644
--- a/Code/MonoMultiViewClassifiers/utils/execution.py
+++ b/Code/MonoMultiViewClassifiers/utils/execution.py
@@ -1,6 +1,6 @@
import argparse
import numpy as np
-import cPickle
+import pickle
import time
import os
import errno
@@ -192,9 +192,9 @@ def initRandomState(randomStateArg, directory):
except ValueError:
fileName = randomStateArg
with open(fileName, 'rb') as handle:
- randomState = cPickle.load(handle)
+ randomState = pickle.load(handle)
with open(directory + "randomState.pickle", "wb") as handle:
- cPickle.dump(randomState, handle)
+ pickle.dump(randomState, handle)
return randomState
diff --git a/Code/Versions.py b/Code/Versions.py
index bd0becc0..0da83a60 100644
--- a/Code/Versions.py
+++ b/Code/Versions.py
@@ -12,7 +12,7 @@
# Author-Info
__author__ = "Baptiste Bauvin"
__status__ = "Prototype" # Production, Development, Prototype
-__date__ = 2016 - 03 - 25
+# __date__ = 2016 - 03 - 25
def testVersions():
@@ -96,14 +96,20 @@ def testVersions():
isUpToDate = False
toInstall.append("h5py")
- # try:
- # import graphviz #
- # except:
- # isUpToDate = False
- # toInstall.append("graphviz")
+ try:
+ import graphviz #
+ except:
+ isUpToDate = False
+ toInstall.append("graphviz")
+
+ try:
+ import pickle #
+ except:
+ isUpToDate = False
+ toInstall.append("pickle")
if not isUpToDate:
- print "You can't run at the moment, please install the following modules : \n"+ "\n".join(toInstall)
+ print("You can't run at the moment, please install the following modules : \n"+ "\n".join(toInstall))
quit()
if __name__== "__main__":
--
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