def iter_import_from_settings(self, settings, scan_plates=None):
from cecog.io.importer import IniFileImporter, FlatFileImporter
settings.set_section(SECTION_NAME_GENERAL)
for info in self.iter_check_plates(settings):
plate_id, path_plate_in, path_plate_out, filename = info
# check whether this plate has to be rescanned
if not scan_plates is None:
scan_plate = scan_plates[plate_id]
else:
scan_plate = False
# if no structure file was found scan the plate
if filename is None:
scan_plate = True
# (re)scan the file structure
if scan_plate:
if settings.get2('image_import_namingschema'):
config_parser = CecogEnvironment.naming_schema
section_name = settings.get2('namingscheme')
importer = IniFileImporter(path_plate_in,
config_parser, section_name)
# read file structure according to dimension/structure file
elif settings.get2('image_import_structurefile'):
filename = settings.get2('structure_filename')
importer = FlatFileImporter(path_plate_in, filename)
# scan the file structure
importer.scan()
# serialize importer and register plate only upon successful scan
if importer.is_valid:
filename = self._get_structure_filename(settings, plate_id,
path_plate_in,
path_plate_out)
importer_pickle(importer, filename)
self.register_plate(plate_id, path_plate_in,
path_plate_out, filename)
else:
self.register_plate(plate_id, path_plate_in,
path_plate_out, filename)
yield info
def iter_import_from_settings(self, settings, scan_plates=None):
from cecog.io.importer import IniFileImporter, FlatFileImporter
settings.set_section(SECTION_NAME_GENERAL)
for info in self.iter_check_plates(settings):
plate_id, path_plate_in, path_plate_out, filename = info
# check whether this plate has to be rescanned
if not scan_plates is None:
scan_plate = scan_plates[plate_id]
else:
scan_plate = False
# if no structure file was found scan the plate
if filename is None:
scan_plate = True
# (re)scan the file structure
if scan_plate:
if settings.get2('image_import_namingschema'):
config_parser = CecogEnvironment.naming_schema
section_name = settings.get2('namingscheme')
importer = IniFileImporter(path_plate_in,
config_parser, section_name)
# read file structure according to dimension/structure file
elif settings.get2('image_import_structurefile'):
filename = settings.get2('structure_filename')
importer = FlatFileImporter(path_plate_in, filename)
# scan the file structure
importer.scan()
# serialize importer and register plate only upon successful scan
if importer.is_valid:
filename = self._get_structure_filename(settings, plate_id,
path_plate_in,
path_plate_out)
importer_pickle(importer, filename)
self.register_plate(plate_id, path_plate_in,
path_plate_out, filename)
else:
self.register_plate(plate_id, path_plate_in,
path_plate_out, filename)
yield info
def iter_import_from_settings(self, settings, plates_restriction=None, scan_plates=None):
settings.set_section(SECTION_NAME_GENERAL)
for info in self.iter_check_plates(settings, plates_restriction):
plate_id, path_plate_in, path_plate_out, filename = info
# check whether this plate has to be rescanned
if not scan_plates is None:
scan_plate = scan_plates[plate_id]
else:
scan_plate = False
# if no structure file was found scan the plate
if filename is None:
scan_plate = True
# (re)scan the file structure
if scan_plate:
config_parser = CecogEnvironment.naming_schema
section_name = settings.get2('namingscheme')
importer = IniFileImporter()
importer.setup(path_plate_in, config_parser, section_name)
importer.scan()
if importer.is_valid:
filename = self._get_structure_filename(settings, plate_id,
path_plate_in,
path_plate_out)
# make missing plate directories
if not os.path.isdir(path_plate_out):
os.mkdir(path_plate_out)
importer.save_xml(filename)
self.register_plate(plate_id, path_plate_in,
path_plate_out, filename)
else:
self.register_plate(plate_id, path_plate_in,
path_plate_out, filename)
yield info
def set_plate(self, plate):
if plate != self.current_plate:
self.current_plate = plate
filename = self._plates[plate]
self._importer = IniFileImporter.load_xml(filename)
self._importer.path = self._path_in[plate]
