def show_result(self, prediction, msg):
new_line(50)
print(msg)
new_line(50)
real = self.train_labels
print "Confusion Matrix: "
print str(confusion_matrix(real, prediction))
homo_score = homogeneity_score(real, prediction)
complete_score = completeness_score(real, prediction)
v_score = v_measure_score(real, prediction)
rand_score = adjusted_rand_score(real, prediction)
mutual_info = adjusted_mutual_info_score(real, prediction)
print("Homogeneity Score: %0.3f" % homo_score)
print("Completeness Score: %0.3f" % complete_score)
print("V-measure: %0.3f" % v_score)
print("Adjusted Rand Score: %0.3f" % rand_score)
print("Adjusted Mutual Info Score: %0.3f\n" % mutual_info)
return {
'Homogeneity': homo_score,
'Completeness': complete_score,
'V-measure': v_score,
'RAND': rand_score,
'Mutual': mutual_info
}
def __init__(self):
new_line(50)
print 'started to build all training and testing data...'
self.tfidf_transformer = TfidfTransformer()
self.vectorizer = CountVectorizer(analyzer='word', stop_words=stop_words, min_df=5, tokenizer=stemTokenizer)
self.svd = TruncatedSVD(n_components=50, random_state=42)
self.nmf = NMF(n_components=50, random_state=42)
self.mm = MinMaxScaler()
# build training data
self.train_data = fetch_data(categories, 'train')
self.train_labels = build_labels(self.train_data)
self.vectors = self.to_vec(self.train_data.data)
self.tfidf = self.to_tfidf(self.vectors)
self.tfidf_SVD = self.to_SVD(self.tfidf)
self.tfidf_NMF = self.to_NMF(self.tfidf)
self.tfidf_mm = self.mm.fit_transform(self.tfidf_SVD)
# build testing data
self.test_data = fetch_data(categories, 'test')
self.test_labels = build_labels(self.test_data)
self.test_vectors = self.vectorizer.transform(self.test_data.data)
self.test_tfidf = self.tfidf_transformer.transform(self.test_vectors)
self.test_tfidf_SVD = self.svd.transform(self.test_tfidf)
self.test_tfidf_NMF = self.nmf.transform(self.test_tfidf)
self.test_tfidf_mm = self.mm.fit_transform(self.test_tfidf_SVD)
print 'finished building all training and testing data...'
new_line(50)
print ' '
def parse_acquisitions(self):
src_paths = []
for f in self._files:
# Check if it is a DICOM
try:
ds = dicom.read_file(f)
except InvalidDicomError:
utils.warning('Not a DICOM file: {}'.format(f))
continue
# Filter by serie description
dsDesc = ds.SeriesDescription
if any(_ in dsDesc for _ in self.exclusionCriteria):
self._excluded.add(dsDesc)
else:
src_paths.append(f)
groups = dcmstack.parse_and_group(src_paths)
for key, group in groups.iteritems():
if self._isFromOneDirectory(group):
#utils.ok("Same directory: {}".format(key[2]))
stack = dcmstack.stack_group(group)
inDir = os.path.dirname(group[0][2])
self._acquisitions.append(
Acquisition(inDir, stack, self._session))
else:
#TODO: regroup dicoms in a tmp directory
utils.new_line()
utils.fail(
"DICOM of '{}' are not in the same directory.\nThis structure won't be compatible with dcm2niibatch"
.format(key[2]))
def generateNSISInstaller( self ):
""" runs makensis to generate the installer itself """
self.isInstalled()
if self.package.endswith( "-package" ):
shortPackage = self.package[ : -8 ]
else:
shortPackage = self.package
if not "setupname" in self.defines or not self.defines[ "setupname" ]:
self.defines[ "setupname" ] = "%s-%s-setup-%s.exe" % ( shortPackage, compiler.architecture(), self.buildTarget )
if not "srcdir" in self.defines or not self.defines[ "srcdir" ]:
self.defines[ "srcdir" ] = self.imageDir()
if not "company" in self.defines or not self.defines[ "company" ]:
self.defines[ "company" ] = "KDE"
if not "productname" in self.defines or not self.defines[ "productname" ]:
self.defines[ "productname" ] = shortPackage.capitalize()
if not "version" in self.defines or not self.defines[ "version" ]:
self.defines[ "version" ] = self.buildTarget
if not "executable" in self.defines or not self.defines[ "executable" ]:
self.defines[ "executable" ] = ""
if "license" in self.defines and self.defines[ "license" ]:
self.defines[ "license" ] = "!insertmacro MUI_PAGE_LICENSE \"%s\"" % self.defines[ "license" ]
else:
self.defines[ "license" ] = ""
if "icon" in self.defines and self.defines[ "icon" ]:
self.defines[ "icon" ] = "!define MUI_ICON \"%s\"" % self.defines[ "icon" ]
else:
self.defines[ "icon" ] = ""
if not self.scriptname:
self.scriptname = os.path.join( os.path.dirname( __file__ ), "NullsoftInstaller.nsi" )
self.defines[ "architecture" ] = compiler.architecture()
# make absolute path for output file
if not os.path.isabs( self.defines[ "setupname" ] ):
dstpath = self.packageDestinationDir()
self.defines[ "setupname" ] = os.path.join( dstpath, self.defines[ "setupname" ] )
definestring = ""
for key in self.defines:
definestring += " /D" + key + "=\"" + self.defines[ key ] + "\""
utils.new_line()
utils.debug( "generating installer %s" % self.defines[ "setupname" ] )
if self.isInstalled:
if not utils.systemWithoutShell( "\"%s\" %s %s" % ( os.path.join(
self.nsisInstallPath, 'makensis.exe' ), definestring,
self.scriptname ), cwd = os.path.abspath( self.packageDir() ) ):
utils.die("Error in makensis execution")
targetInstalled = installdb.isInstalled( mainCategory, mainPackage, mainVersion, os.getenv( "EMERGE_TARGET_PLATFORM" ) )
msg += portage.getHostAndTarget( hostEnabled and not hostInstalled, targetEnabled and not targetInstalled )
else:
msg = ""
utils.warning( "pretending %s/%s-%s%s" % ( mainCategory, mainPackage, mainVersion, msg ) )
else:
mainAction = mainBuildAction
if mainBuildAction == "install-deps":
mainAction = "all"
if not handlePackage( mainCategory, mainPackage, mainVersion, mainAction, mainOpts ):
utils.error( "fatal error: package %s/%s-%s %s failed" % \
( mainCategory, mainPackage, mainVersion, mainBuildAction ) )
exit( 1 )
utils.new_line()
if len( nextArguments ) > 0:
command = "\"" + sys.executable + "\" -u " + executableName + " " + " ".join( nextArguments )
#for element in environ.keys():
# if environ[ element ]:
# os.environ[ element ] = environ[ element ]
# elif element == "EMERGE_VERBOSE":
# os.environ[ element ] = "1"
# else:
# os.environ[ element ] = ""
if not utils.system(command):
utils.die( "cannot execute next commands cmd: %s" % command )
utils.stopTimer("Emerge")
def run(self):
utils.new_line()
utils.info('Parse and group DICOM directory')
self._parser.parse_acquisitions()
utils.new_line()
utils.info('Sort and set up acquisitions')
self._parser.sort_acquisitions()
#utils.new_line()
#utils.ok('Acquisitions of interest:')
#for _ in self._parser.caught: utils.info(_)
utils.new_line()
utils.warning('Acquisitions excluded:')
for _ in self._parser._excluded:
utils.info(_)
utils.new_line()
utils.info('Create YAML file for dcm2niibatch')
for acq in self._parser.acquisitions:
self._batch.add(acq)
self._batch.write()
utils.new_line()
utils.ok('Batch file:')
self._batch.show()
if self._yes:
launchBatch = True
else:
msg = "Do you want to launch dcm2niibatch ?"
launchBatch = utils.query_yes_no(msg)
if launchBatch:
self._batch.launch()
for acq in self._parser.acquisitions:
acq.update_json()
else:
utils.new_line()
utils.ok("To launch dcm2niibatch later:")
utils.info("cd {}".format(self._codeDir))
utils.info(self._batch.command)
return 0
def main():
""" Testing the class"""
# add two databases
tempdbpath1 = os.path.join( os.getenv("KDEROOT"), "tmp", "temp1.db" )
tempdbpath2 = os.path.join( os.getenv("KDEROOT"), "tmp", "temp2.db" )
if not os.path.exists( os.path.join( os.getenv( "KDEROOT" ), "tmp" ) ):
os.makedirs( os.path.join( os.getenv( "KDEROOT" ), "tmp" ) )
if os.path.exists( tempdbpath1 ):
os.remove( tempdbpath1 )
if os.path.exists( tempdbpath2 ):
os.remove( tempdbpath2 )
db_temp = InstallDB( tempdbpath1 )
db = InstallDB( tempdbpath2 )
utils.debug( 'testing installation database' )
utils.debug( 'testing if package win32libs/dbus-src with version 1.4.0 is installed: %s' %
db.isPkgInstalled( 'win32libs', 'dbus-src', '1.4.0' ) )
# in case the package is still installed, remove it first silently
if db.isInstalled( 'win32libs', 'dbus-src', '1.4.0' ):
packageList = db.remInstalled( 'win32libs', 'dbus-src', '1.4.0' )
# really commit uninstall
for package in packageList:
package.uninstall()
utils.debug_line()
utils.new_line()
# add a package
utils.debug( 'installing package win32libs/dbus-src-1.4.0 (release)' )
package = db.addInstalled( 'win32libs', 'dbus-src', '1.4.0', 'release' )
package.addFiles( dict().fromkeys( [ 'test', 'test1', 'test2' ], 'empty hash' ) )
# now really commit the package
package.install()
# add another package in a different prefix
utils.debug( 'installing package win32libs/dbus-src-1.4.0 (debug)' )
package = db.addInstalled( 'win32libs', 'dbus-src', '1.4.0', 'debug' )
package.addFiles( dict().fromkeys( [ 'test', 'test1', 'test2' ], 'empty hash' ) )
# now really commit the package
package.install()
utils.debug_line()
utils.new_line()
utils.debug( 'checking installed packages' )
utils.debug( 'get installed package (release): %s' % db.getInstalled( 'win32libs', 'dbus-src', 'release' ) )
utils.debug( 'get installed package (debug): %s' % db.getInstalled( 'win32libs', 'dbus-src', 'debug' ) )
utils.new_line()
utils.debug( 'now trying to remove package & revert it again later' )
# remove the package again
packageList = db.remInstalled( 'win32libs', 'dbus-src', '1.4.0' )
for pac in packageList:
for line in pac.getFiles(): # pylint: disable=W0612
# we could remove the file here
# print line
pass
utils.debug_line()
utils.new_line()
utils.debug( 'checking installed packages' )
utils.debug( 'get installed package (release): %s' % db.getInstalled( 'win32libs', 'dbus-src', 'release' ) )
utils.debug( 'get installed package (debug): %s' % db.getInstalled( 'win32libs', 'dbus-src', 'debug' ) )
utils.debug_line()
utils.new_line()
utils.debug( 'reverting removal' )
# now instead of completing the removal, revert it
for pac in packageList:
pac.revert()
utils.debug( 'checking installed packages' )
utils.debug( 'get installed package (release): %s' % db.getInstalled( 'win32libs', 'dbus-src', 'release' ) )
utils.debug( 'get installed package (debug): %s' % db.getInstalled( 'win32libs', 'dbus-src', 'debug' ) )
utils.debug_line()
db.getInstalled()
db.getInstalled( category='win32libs', prefix='debug' )
db.getInstalled( package='dbus-src' )
utils.new_line()
utils.debug( 'now really remove the package' )
packageList = db.remInstalled( 'win32libs', 'dbus-src', '1.4.0')
for pac in packageList:
utils.debug( 'removing %s files' % len( pac.getFiles() ) )
pac.uninstall()
utils.debug( 'get installed package (release): %s' % db.getInstalled( 'win32libs', 'dbus-src', 'release' ) )
utils.debug( 'get installed package (debug): %s' % db.getInstalled( 'win32libs', 'dbus-src', 'debug' ) )
utils.debug_line()
# test the import from the old style (manifest based) databases
utils.new_line()
db_temp.importExistingDatabase()
print("getInstalled:", db_temp.getInstalled())
print("findInstalled:", portage.findInstalled( 'win32libs', 'dbus-src' ))
print("getFileListFromManifest:", len( utils.getFileListFromManifest( os.getenv( "KDEROOT" ), 'dbus-src' ) ))