Omero-pychrm
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General
OmeroPychrm scripts
__init__.py
- empty
TableConnection.py
class PychrmStorageError(Exception): pass class Connection(object): def __init__(self, user = None, passwd = None, host = None, client = None): """A wrapper for omero.client.""" self.log = logging.getLogger(__name__) self.conn = BlitzGateway(client_obj = client) self.res = omero.client.getSession().sharedResources() def __enter__(self): return self.log.debug('Entering Connection') def __exit__(self): self.log.debug('Exiting Connection') self.conn._closeSession() class TableConnection(Connection): """A basic client-side wrapper for OMERO.tables which handles opening and closing tables.""" def __init__(self, user = None, passwd = None, host = None, client = None, tableName = None): """Create a new table handler, either by specifying user and passwd or by providing a client object (for scripts).""" # call base class constructor self.rid = self.res.repositories().descriptions[0].id.val self.tableName = tableName self.tableId = None self.table = None def close(self, parent=True): """standard cleanup stuff""" pass def openTable(self, tableId): """Opens an existing table by ID"""
PychrmStorage.py
class PychrmStorageError(Exception): pass def parseFeatureName( name ): """Separate bin number and feature group name""" pass def createFeatureName(ft, idx): """Concatenate feature group name and feature bin number""" pass def featureSizes(names): """Return a dictionary of feature groups and corresponding numbers of features in them""" pass