def _createSubSetFromClasses(self, inputClasses):
outputClassName = self.outputClassName.get()
if (outputClassName.startswith('SetOfAverages') or
outputClassName.startswith('SetOfVolumes') or
outputClassName.startswith('SetOfParticles')):
# We need to distinguish two cases:
# a) when we want to create images by grouping class images
# b) create a subset from a particular class images
from pyworkflow.mapper.sqlite import SqliteFlatDb
db = SqliteFlatDb(dbName=self._dbName, tablePrefix=self._dbPrefix)
itemClassName = db.getSelfClassName()
if itemClassName.startswith('Class'):
if outputClassName.startswith('SetOfParticles'):
return self._createImagesFromClasses(inputClasses)
else:
return self._createRepresentativesFromClasses(inputClasses,
outputClassName.split(',')[0])
else:
def callback(output):
self._copyInfoAndSetAlignment(inputClasses, output)
return self._createSubSetFromImages(inputClasses.getImages(),
copyInfoCallback=callback)
elif outputClassName.startswith('SetOfClasses'):
return self._createClassesFromClasses(inputClasses)
else:
raise Exception("Unrecognized output type: '%s'" % outputClassName)
def _createSubSetFromClasses(self, inputClasses):
outputClassName = self.outputClassName.get()
if (outputClassName.startswith('SetOfAverages')
or outputClassName.startswith('SetOfVolumes')
or outputClassName.startswith('SetOfParticles')):
# We need to distinguish two cases:
# a) when we want to create images by grouping class images
# b) create a subset from a particular class images
from pyworkflow.mapper.sqlite import SqliteFlatDb
db = SqliteFlatDb(dbName=self._dbName, tablePrefix=self._dbPrefix)
itemClassName = db.getSelfClassName()
if itemClassName.startswith('Class'):
if outputClassName.startswith('SetOfParticles'):
return self._createImagesFromClasses(inputClasses)
else:
return self._createRepresentativesFromClasses(
inputClasses,
outputClassName.split(',')[0])
else:
def callback(output):
self._copyInfoAndSetAlignment(inputClasses, output)
return self._createSubSetFromImages(inputClasses.getImages(),
copyInfoCallback=callback)
elif outputClassName.startswith('SetOfClasses'):
return self._createClassesFromClasses(inputClasses)
else:
raise Exception("Unrecognized output type: '%s'" % outputClassName)
def loadSetFromDb(dbName, dbPrefix=''):
from pyworkflow.mapper.sqlite import SqliteFlatDb
db = SqliteFlatDb(dbName=dbName, tablePrefix=dbPrefix)
setClassName = db.getProperty('self') # get the set class name
setObj = getObjects()[setClassName](filename=dbName, prefix=dbPrefix)
return setObj
def loadSetFromDb(dbName, dbPrefix=''):
from pyworkflow.mapper.sqlite import SqliteFlatDb
db = SqliteFlatDb(dbName=dbName, tablePrefix=dbPrefix)
setClassName = db.getProperty('self') # get the set class name
setObj = Domain.getObjects()[setClassName](filename=dbName,
prefix=dbPrefix)
return setObj
def _loadSet(self, dbName, dbPreffix):
from pyworkflow.mapper.sqlite import SqliteFlatDb
db = SqliteFlatDb(dbName=dbName, tablePrefix=dbPreffix)
if dbPreffix:
setClassName = "SetOf%ss" % db.getSelfClassName()
else:
setClassName = db.getProperty('self') # get the set class name
from pyworkflow.em import getObjects
setObj = getObjects()[setClassName](filename=dbName, prefix=dbPreffix)
return setObj
def _loadSet(self, dbName, dbPreffix):
from pyworkflow.mapper.sqlite import SqliteFlatDb
db = SqliteFlatDb(dbName=dbName, tablePrefix=dbPreffix)
if dbPreffix:
setClassName = "SetOf%ss" % db.getSelfClassName()
else:
setClassName = db.getProperty('self') # get the set class name
from pyworkflow.em import getObjects
setObj = getObjects()[setClassName](filename=dbName, prefix=dbPreffix)
return setObj
def test_SqliteFlatDb(self):
""" Create a SqliteDataset """
from pyworkflow.mapper.sqlite import SqliteFlatDb
print ">>> test_SqliteFlatDb: dbName = '%s'" % self.modelGoldSqlite
db = SqliteFlatDb(self.modelGoldSqlite)
# Test the 'self' class name is correctly retrieved
self.assertEqual("Micrograph", db.getSelfClassName())
# Check the count is equal to 3
self.assertEqual(3, db.count())
db.close()
def __init__(self, filename):
self._dbName = filename
db = SqliteDb()
db._createConnection(filename, 1000)
# Tables should be at pairs:
# PREFIX_Classes
# PREFIX_Objects
# where PREFIX can be empty
self.tablePrefixes = OrderedDict()
tables = db.getTables()
for t in tables:
if t.endswith('Classes'):
prefix = t.replace('Classes', '')
to = prefix + 'Objects'
if to not in tables:
raise Exception('SqliteDataSet: table "%s" found, but not "%s"' % (t, to))
flatDb = SqliteFlatDb(filename, tablePrefix=prefix)
tableName = prefix + self._getPlural(flatDb.getSelfClassName())
self.tablePrefixes[tableName] = prefix
#tablePrefixes.append(prefix)
DataSet.__init__(self, self.tablePrefixes.keys())
db.close()
def __init__(self, filename):
self._dbName = filename
db = SqliteDb()
db._createConnection(filename, 1000)
# Tables should be at pairs:
# PREFIX_Classes
# PREFIX_Objects
# where PREFIX can be empty
self.tablePrefixes = OrderedDict()
tables = db.getTables()
for t in tables:
if t.endswith('Classes'):
prefix = t.replace('Classes', '')
to = prefix + 'Objects'
if to not in tables:
raise Exception('SqliteDataSet: table "%s" found, but not "%s"' % (t, to))
flatDb = SqliteFlatDb(filename, tablePrefix=prefix)
tableName = prefix + self._getPlural(flatDb.getSelfClassName())
self.tablePrefixes[tableName] = prefix
#tablePrefixes.append(prefix)
DataSet.__init__(self, self.tablePrefixes.keys())
db.close()
def test_SqliteFlatDb(self):
""" Create a SqliteDataset """
from pyworkflow.mapper.sqlite import SqliteFlatDb
print ">>> test_SqliteFlatDb: dbName = '%s'" % self.modelGoldSqlite
db = SqliteFlatDb(self.modelGoldSqlite)
# Old db version 0
self.assertEqual(0, db.getVersion())
# Test the 'self' class name is correctly retrieved
self.assertEqual('Micrograph', db.getSelfClassName())
# Check the count is equal to 3
self.assertEqual(3, db.count())
db.close()
