def initFromFile(self, labels_filename):
filename = dir_tools.getDatasetDirectory(self.project, self.dataset)
filename += 'labels/' + labels_filename
if not dir_tools.checkFileExists(filename):
raise ValueError('The labels file %s does not exist.' % filename)
## Check whether the file contains families
families = False
with open(filename, 'r') as f:
header = f.readline()
fields = header.split(',')
if len(fields) == 3:
families = True
query = 'LOAD DATA LOCAL INFILE \'' + filename + '\' '
query += 'INTO TABLE ' + 'Labels' + ' '
query += 'FIELDS TERMINATED BY \',\' '
query += 'IGNORE 1 LINES '
if families:
query += '(instance_id, label, family) '
else:
query += '(instance_id, label) '
query += 'SET experiment_label_id = ' + str(
self.experiment_label_id) + ', '
if not families:
query += 'family = "other",'
query += 'iteration = 0, '
query += 'method = "init", '
query += 'annotation = "0"'
query += ';'
self.cursor.execute(query)
self.db.commit()
self.checkLabelsValidity()
def getFeaturesFilesFullpaths(self):
features_filenames = self.getFeaturesFilenames()
features_directory = dir_tools.getDatasetDirectory(
self.project, self.dataset) + 'features/'
features_filenames = [
features_directory + f for f in features_filenames
]
return features_filenames
def saveLabeledInstances(self):
for i in ['annotations', 'labels']:
filename = dir_tools.getDatasetDirectory(
self.experiment.project,
self.experiment.dataset)
filename += 'labels/' + i + '_'
filename += self.experiment.labeling_method + '_'
filename += 'exp' + str(self.experiment.experiment_id) + '_'
filename += 'it' + str(self.iteration_number) + '.csv'
self.datasets.saveLabeledInstances(i, filename)
def loadIdents(self):
idents_file = dir_tools.getDatasetDirectory(
self.project, self.dataset) + 'idents.csv'
fields = ['instance_id', 'ident', 'row_number']
types = [
'INT', 'VARCHAR(200) CHARACTER SET utf8',
'INT NOT NULL AUTO_INCREMENT'
]
mysql_tools.createTableFromFields(self.cursor, 'Idents', fields, types,
['row_number', 'instance_id'])
mysql_tools.loadCsvFile(self.cursor, idents_file, 'Idents',
['row_number'])
def saveLabeledInstances(self, iteration_number):
for i in ['annotations', 'labels']:
filename = dir_tools.getDatasetDirectory(self.experiment.project,
self.experiment.dataset)
filename += 'labels/' + i + '_'
filename += self.experiment.labeling_method + '_'
filename += 'exp' + str(self.experiment.experiment_id) + '_'
filename += 'it' + str(iteration_number) + '.csv'
if i == 'annotations':
instances = self.instances.getAnnotatedInstances()
elif i == 'labels':
instances = self.instances.getLabeledInstances()
instances.saveInstancesLabels(filename)
def loadTrueLabels(self):
labels_file = dir_tools.getDatasetDirectory(self.project, self.dataset)
labels_file += 'labels/true_labels.csv'
# Loads the true labels in the table TrueLabels if the file exists
# Otherwise the table TrueLabels is not created
if not dir_tools.checkFileExists(labels_file):
print >> sys.stderr, 'No ground truth labels for this dataset'
return
exp = Experiment(self.project,
self.dataset,
self.db,
self.cursor,
experiment_name='true_labels')
exp.initLabels('true_labels.csv')
def loadIdents(self):
filename = dir_tools.getDatasetDirectory(self.project, self.dataset)
filename += 'idents.csv'
db, cursor = db_tools.getRawConnection()
if db_tools.isMysql():
query = 'LOAD DATA LOCAL INFILE \'' + filename + '\' '
query += 'INTO TABLE ' + 'instances' + ' '
query += 'CHARACTER SET UTF8 '
query += 'FIELDS TERMINATED BY \',\' '
query += 'OPTIONALLY ENCLOSED BY \'"\' '
query += 'IGNORE 1 LINES '
query += 'SET dataset_id = ' + str(self.dataset_id) + ','
query += 'row_number = NULL'
query += ';'
cursor.execute(query)
query = 'SET @pos = 0;'
cursor.execute(query)
query = 'UPDATE instances SET row_number = '
query += '( SELECT @pos := @pos + 1 ) WHERE dataset_id = ' + str(
self.dataset_id)
query += ';'
cursor.execute(query)
elif db_tools.isPostgresql():
query = 'CREATE TEMPORARY TABLE instances_import('
query += 'user_instance_id integer, '
query += 'ident varchar(200), '
query += 'dataset_id integer DEFAULT ' + str(self.dataset_id) + ','
query += 'row_number serial PRIMARY KEY'
query += ');'
cursor.execute(query)
with open(filename, 'r') as f:
query = 'COPY instances_import(user_instance_id,ident) '
query += 'FROM STDIN '
query += 'WITH CSV HEADER DELIMITER AS \',\' ;'
cursor.copy_expert(sql=query, file=f)
query = 'INSERT INTO instances(user_instance_id,ident,dataset_id,row_number) '
query += 'SELECT user_instance_id, ident, dataset_id, row_number '
query += 'FROM instances_import;'
cursor.execute(query)
db_tools.closeRawConnection(db, cursor)
def loadTrueLabels(self):
labels_file = dir_tools.getDatasetDirectory(self.project, self.dataset)
labels_file += 'labels/true_labels.csv'
# Loads the true labels in the table TrueLabels if the file exists
# Otherwise the table TrueLabels is not created
if not dir_tools.checkFileExists(labels_file):
print >> sys.stderr, 'No ground truth labels for this dataset'
return
## Check whether the file contains families
families = False
with open(labels_file, 'r') as f:
header = f.readline()
fields = header.split(',')
if len(fields) == 3:
families = True
db, cursor = db_tools.getRawConnection()
if db_tools.isMysql():
query = 'CREATE TEMPORARY TABLE true_labels_import('
query += 'user_instance_id integer PRIMARY KEY, '
query += 'label varchar(200), '
query += 'family varchar(200) DEFAULT \'other\', '
query += 'dataset_id integer DEFAULT ' + str(
self.dataset_id) + ', '
query += 'id integer DEFAULT NULL'
query += ');'
cursor.execute(query)
query = 'LOAD DATA LOCAL INFILE \'' + labels_file + '\' '
query += 'INTO TABLE ' + 'true_labels_import' + ' '
query += 'FIELDS TERMINATED BY \',\' '
query += 'IGNORE 1 LINES '
if families:
query += '(user_instance_id, label, family) '
else:
query += '(user_instance_id, label) '
query += ';'
cursor.execute(query)
query = 'UPDATE true_labels_import t '
query += 'JOIN instances i '
query += 'ON i.user_instance_id = t.user_instance_id '
query += 'AND i.dataset_id = t.dataset_id '
query += 'SET t.id = i.id;'
cursor.execute(query)
query = 'INSERT INTO true_labels(instance_id, dataset_id, label, family) '
query += 'SELECT t.id, t.dataset_id, t.label, t.family '
query += 'FROM true_labels_import AS t;'
cursor.execute(query)
elif db_tools.isPostgresql():
query = 'CREATE TEMPORARY TABLE true_labels_import('
query += 'user_instance_id integer PRIMARY KEY, '
query += 'label true_labels_enum, '
query += 'family varchar(200) DEFAULT \'other\', '
query += 'dataset_id integer DEFAULT ' + str(
self.dataset_id) + ', '
query += 'id integer DEFAULT NULL'
query += ');'
cursor.execute(query)
with open(labels_file, 'r') as f:
if families:
query = 'COPY true_labels_import(user_instance_id,label,family) '
else:
query = 'COPY true_labels_import(user_instance_id,label) '
query += 'FROM STDIN '
query += 'WITH CSV HEADER DELIMITER AS \',\' ;'
cursor.copy_expert(sql=query, file=f)
query = 'UPDATE true_labels_import AS t '
query += 'SET id = i.id '
query += 'FROM instances AS i '
query += 'WHERE i.user_instance_id = t.user_instance_id '
query += 'AND i.dataset_id = t.dataset_id;'
cursor.execute(query)
query = 'INSERT INTO true_labels(instance_id, dataset_id, label, family) '
query += 'SELECT t.id, t.dataset_id, t.label, t.family '
query += 'FROM true_labels_import AS t;'
cursor.execute(query)
db_tools.closeRawConnection(db, cursor)
def initFromFile(self, labels_filename):
if labels_filename is None:
labels_type = 'none'
elif labels_filename == 'true_labels.csv':
labels_type = 'true_labels'
else:
labels_type = 'partial_labels'
exp_labels = db_tables.ExperimentsLabelsAlchemy(
experiment_id=self.experiment_id, labels_type=labels_type)
self.session.add(exp_labels)
self.session.commit()
self.labels_id = exp_labels.labels_id
self.labels_type = labels_type
if labels_type == 'partial_labels':
filename = dir_tools.getDatasetDirectory(self.project,
self.dataset)
filename += 'labels/' + labels_filename
if not dir_tools.checkFileExists(filename):
raise ValueError('The labels file %s does not exist.' %
filename)
## Check whether the file contains families
families = False
with open(filename, 'r') as f:
header = f.readline()
fields = header.split(',')
if len(fields) == 3:
families = True
db, cursor = db_tools.getRawConnection()
if db_tools.isMysql():
query = 'CREATE TEMPORARY TABLE labels_import('
query += 'instance_id integer, '
query += 'labels_id integer DEFAULT ' + str(
self.labels_id) + ', '
query += 'user_instance_id integer, '
query += 'label varchar(200), '
query += 'family varchar(200) DEFAULT \'other\', '
query += 'iteration integer DEFAULT 0, '
query += 'method varchar(200) DEFAULT \'init\', '
query += 'annotation boolean DEFAULT True'
query += ');'
cursor.execute(query)
query = 'LOAD DATA LOCAL INFILE \'' + filename + '\' '
query += 'INTO TABLE ' + 'labels_import' + ' '
query += 'FIELDS TERMINATED BY \',\' '
query += 'IGNORE 1 LINES '
if families:
query += '(user_instance_id, label, family) '
else:
query += '(user_instance_id, label) '
query += ';'
cursor.execute(query)
query = 'UPDATE labels_import l '
query += 'JOIN instances i '
query += 'ON i.user_instance_id = l.user_instance_id '
query += 'AND i.dataset_id = ' + str(self.dataset_id) + ' '
query += 'SET l.instance_id = i.id;'
cursor.execute(query)
query = 'INSERT INTO labels(instance_id,labels_id,label,family,iteration,method,annotation) '
query += 'SELECT instance_id,labels_id,label,family,iteration,method,annotation '
query += 'FROM labels_import;'
cursor.execute(query)
elif db_tools.isPostgresql():
query = 'CREATE TEMPORARY TABLE labels_import('
query += 'instance_id integer, '
query += 'labels_id integer DEFAULT ' + str(
self.labels_id) + ', '
query += 'user_instance_id integer, '
query += 'label labels_enum, '
query += 'family varchar(200) DEFAULT \'other\', '
query += 'iteration integer DEFAULT 0, '
query += 'method varchar(200) DEFAULT \'init\', '
query += 'annotation boolean DEFAULT True'
query += ');'
cursor.execute(query)
with open(filename, 'r') as f:
if families:
query = 'COPY labels_import(user_instance_id,label,family) '
else:
query = 'COPY labels_import(user_instance_id,label) '
query += 'FROM STDIN '
query += 'WITH CSV HEADER DELIMITER AS \',\' ;'
cursor.copy_expert(sql=query, file=f)
query = 'UPDATE labels_import AS l '
query += 'SET instance_id = i.id '
query += 'FROM instances AS i '
query += 'WHERE i.user_instance_id = l.user_instance_id '
query += 'AND i.dataset_id = ' + str(self.dataset_id) + ';'
cursor.execute(query)
query = 'INSERT INTO labels(instance_id,labels_id,label,family,iteration,method,annotation) '
query += 'SELECT instance_id,labels_id,label,family,iteration,method,annotation '
query += 'FROM labels_import;'
cursor.execute(query)
db_tools.closeRawConnection(db, cursor)
self.session.commit()