python-pymc 2.2+ds-1.1 / usr / lib / python2.7 / dist-packages / pymc / database / sqlite.py

"""
SQLite database backend

Store traces from tallyable objects in individual SQL tables.

Implementation Notes
--------------------
For each object, a table is created with the following format:

key (INT), trace (INT),  v1 (FLOAT), v2 (FLOAT), v3 (FLOAT) ...

For multidimensional objects, ndim>1, eg (2,2) the table has the following format:

key (INT), trace (INT),  v1_1 (FLOAT), v1_2 (FLOAT), v2_1 (FLOAT), v2_2 (FLOAT)

The key is autoincremented each time a new row is added to the table.
trace denotes the chain index, and starts at 0.

Additional Dependencies
-----------------------
sqlite3 <http://www.sqlite.org>

Changeset
---------
Created by Chris Fonnesbeck on 2007-02-01.
Updated by DH on 2007-04-04.
DB API changes, October 2008, DH.
Added support for multidimensional arrays, DH Oct. 2009
"""

# TODO: Add support for integer valued objects.

import numpy as np
from numpy import zeros, shape, squeeze, transpose
import sqlite3
from sqlite3 import OperationalError
import pymc
from pymc.database import base, pickle, ram
import pdb, os, warnings

__all__ = ['Trace', 'Database', 'load']

class Trace(base.Trace):
    """SQLite Trace class."""
    
    def _initialize(self, chain, length):
        """Create an SQL table.
        """
        
        if self._getfunc is None:
            self._getfunc = self.db.model._funs_to_tally[self.name]
        
        # Determine size
        try:
            self._shape = np.shape(self._getfunc())
        except TypeError:
            self._shape = None
        
        self._vstr = ', '.join(var_str(self._shape))
        
        # If the table already exists, exit now.
        if chain != 0:
            return
        
        # Create the variable name strings.
        vstr = ', '.join(v + ' FLOAT' for v in var_str(self._shape))
        
        try:
            query = "create table [%s] (recid INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT, trace  int(5), %s )" % (self.name, vstr)
        
            self.db.cur.execute(query)
        except OperationalError:
            "Table already exists"
            return


    
    def tally(self, chain):
        """Adds current value to trace."""
        
        try:
            # I changed str(x) to '%f'%x to solve a bug appearing due to
            # locale settings. In french for instance, str prints a comma
            # instead of a colon to indicate the decimal, which confuses
            # the database into thinking that there are more values than there
            # is.  A better solution would be to use another delimiter than the
            # comma. -DH
            valstring = ', '.join(['%f'%x for x in np.ravel(self._getfunc())])
        except:
            valstring = str(self._getfunc())

        
        # Add value to database
        query = "INSERT INTO [%s] (recid, trace, %s) values (NULL, %s, %s)" % \
            (self.name, self._vstr, chain, valstring)
        self.db.cur.execute(query)


    
    def gettrace(self, burn=0, thin=1, chain=-1, slicing=None):
        """Return the trace (last by default).
        
        Input:
          - burn (int): The number of transient steps to skip.
          - thin (int): Keep one in thin.
          - chain (int): The index of the chain to fetch. If None, return all
            chains. By default, the last chain is returned.
          - slicing: A slice, overriding burn and thin assignement.
        """
        # warnings.warn('Use Sampler.trace method instead.', DeprecationWarning)
        if not slicing:
            slicing = slice(burn, None, thin)
        
        # If chain is None, get the data from all chains.
        if chain is None:
            self.db.cur.execute('SELECT * FROM [%s]' % self.name)
            trace = self.db.cur.fetchall()
        else:
            # Deal with negative chains (starting from the end)
            if chain < 0:
                chain = range(self.db.chains)[chain]
            self.db.cur.execute('SELECT * FROM [%s] WHERE trace=%s' % (self.name, chain))
            trace = self.db.cur.fetchall()
        trace = np.array(trace)[:,2:]
        if len(self._shape) > 1:
            trace = trace.reshape(-1, *self._shape)
        return squeeze(trace[slicing])
    
    def __getitem__(self, index):
        chain = self._chain
        
        if chain is None:
            self.db.cur.execute('SELECT * FROM [%s]' % self.name)
            trace = self.db.cur.fetchall()
        else:
            # Deal with negative chains (starting from the end)
            if chain < 0:
                chain = range(self.db.chains)[chain]
            self.db.cur.execute('SELECT * FROM [%s] WHERE trace=%s' % (self.name, chain))
            trace = self.db.cur.fetchall()
        
        trace = np.array(trace)[:,2:]
        if len(self._shape) > 1:
            trace = trace.reshape(-1, *self._shape)
        else:
            trace = np.squeeze(trace)
        
        return trace[index]
    
    __call__ = gettrace
    
    def length(self, chain=-1):
        """Return the sample length of given chain. If chain is None,
        return the total length of all chains."""
        return len(self.gettrace(chain=chain))

class Database(base.Database):
    """SQLite database.
    """
    
    def __init__(self, dbname, dbmode='a'):
        """Open or create an SQL database.
        
        :Parameters:
        dbname : string
          The name of the database file.
        dbmode : {'a', 'w'}
          File mode.  Use `a` to append values, and `w` to overwrite
          an existing file.
        """
        self.__name__ = 'sqlite'
        self.dbname = dbname
        self.__Trace__ = Trace
        
        self.trace_names = []   # A list of sequences of names of the objects to tally.
        self._traces = {} # A dictionary of the Trace objects.

        if os.path.exists(dbname) and dbmode=='w':
            os.remove(dbname)
        
        self.DB = sqlite3.connect(dbname, check_same_thread=False)
        self.cur = self.DB.cursor()
        
        existing_tables = get_table_list(self.cur)
        if existing_tables:
            # Get number of existing chains
            self.cur.execute('SELECT MAX(trace) FROM [%s]'%existing_tables[0])
            self.chains = self.cur.fetchall()[0][0]+1
            self.trace_names = self.chains * [existing_tables,]
        else:
            self.chains = 0
    
    def commit(self):
        """Commit updates to database"""
        self.DB.commit()
    
    def close(self, *args, **kwds):
        """Close database."""
        self.cur.close()
        self.commit()
        self.DB.close()




# TODO: Code savestate and getstate to enable storing of the model's state.
# state is a dictionary with two keys: sampler and step_methods.
# state['sampler'] is another dictionary containing information about
# the sampler's state (_current_iter, _iter, _burn, etc.)
# state['step_methods'] is a dictionary with keys refering to ids for
# each samplingmethod defined in sampler.
# Each id refers to another dictionary containing the state of the
# step method.
# To do this efficiently, we would need functions that stores and retrieves
# a dictionary to and from a sqlite database. Unfortunately, I'm not familiar with
# SQL enough to do that without having to read too much SQL documentation
# for my taste.
    
    def savestate(self, state):
        """Store a dictionnary containing the state of the Sampler and its
        StepMethods."""
        pass
    
    def getstate(self):
        """Return a dictionary containing the state of the Sampler and its
        StepMethods."""
        return {}

def load(dbname):
    """Load an existing SQLite database.
    
    Return a Database instance.
    """
    db = Database(dbname)
    
    # Get the name of the objects
    tables = get_table_list(db.cur)
    
    # Create a Trace instance for each object
    chains = 0
    for name in tables:
        db._traces[name] = Trace(name=name, db=db)
        db._traces[name]._shape = get_shape(db.cur, name)
        setattr(db, name, db._traces[name])
        db.cur.execute('SELECT MAX(trace) FROM [%s]'%name)
        chains = max(chains, db.cur.fetchall()[0][0]+1)
    
    db.chains=chains
    db.trace_names = chains * [tables,]
    db._state_ = {}
    return db


# Copied form Django.
def get_table_list(cursor):
    """Returns a list of table names in the current database."""
    # Skip the sqlite_sequence system table used for autoincrement key
    # generation.
    cursor.execute("""
        SELECT name FROM sqlite_master
        WHERE type='table' AND NOT name='sqlite_sequence'
        ORDER BY name""")
    return [row[0] for row in cursor.fetchall()]

def get_shape(cursor, name):
    """Return the shape of the table ``name``."""
    cursor.execute('select * from [%s]'% name)
    inds = cursor.description[-1][0][1:].split('_')
    return tuple([int(i) for i in inds])


def var_str(shape):
    """Return a sequence of strings naming the element of the tallyable object.
    
    :Examples:
    >>> var_str((5,))
    ['v1', 'v2', 'v3', 'v4', 'v5']
    
    >>> var_str((2,2))
    ['v1_1', 'v1_2', 'v2_1', 'v2_2']
    """
    
    if shape in [None, ()]:
        return ['v1',]
    
    size = np.prod(shape)
    indices = (np.indices(shape) + 1).reshape(-1, size)
    return ['v'+'_'.join(map(str, i)) for i in zip(*indices)]
    if shape in [None, ()]:
        return ['v1',]
    
    size = np.prod(shape)
    indices = (np.indices(shape) + 1).reshape(-1, size)
    return ['v'+'_'.join(map(str, i)) for i in zip(*indices)]