python-mdp 3.3-1 / usr / share / pyshared / mdp / linear_flows.py

from __future__ import with_statement
import mdp
import sys as _sys
import os as _os
import inspect as _inspect
import warnings as _warnings
import traceback as _traceback
import cPickle as _cPickle
import tempfile as _tempfile
import copy as _copy

from mdp import numx

class CrashRecoveryException(mdp.MDPException):
    """Class to handle crash recovery """
    def __init__(self, *args):
        """Allow crash recovery.
        Arguments: (error_string, crashing_obj, parent_exception)
        The crashing object is kept in self.crashing_obj
        The triggering parent exception is kept in self.parent_exception.
        """
        errstr = args[0]
        self.crashing_obj = args[1]
        self.parent_exception = args[2]
        # ?? python 2.5: super(CrashRecoveryException, self).__init__(errstr)
        mdp.MDPException.__init__(self, errstr)

    def dump(self, filename=None):
        """
        Save a pickle dump of the crashing object on filename.
        If filename is None, the crash dump is saved on a file created by
        the tempfile module.
        Return the filename.
        """
        if filename is None:
            # This 'temporary file' should actually stay 'forever', i.e. until
            # deleted by the user.
            (fd, filename)=_tempfile.mkstemp(suffix=".pic", prefix="MDPcrash_")
            fl = _os.fdopen(fd, 'w+b', -1)
        else:
            fl = open(filename, 'w+b', -1)
        _cPickle.dump(self.crashing_obj, fl)
        fl.close()
        return filename

class FlowException(mdp.MDPException):
    """Base class for exceptions in Flow subclasses."""
    pass

class FlowExceptionCR(CrashRecoveryException, FlowException):
    """Class to handle flow-crash recovery """

    def __init__(self, *args):
        """Allow crash recovery.

        Arguments: (error_string, flow_instance, parent_exception)
        The triggering parent exception is kept in self.parent_exception.
        If flow_instance._crash_recovery is set, save a crash dump of
        flow_instance on the file self.filename"""
        CrashRecoveryException.__init__(self, *args)
        rec = self.crashing_obj._crash_recovery
        errstr = args[0]
        if rec:
            if isinstance(rec, str):
                name = rec
            else:
                name = None
            name = CrashRecoveryException.dump(self, name)
            dumpinfo = '\nA crash dump is available on: "%s"' % name
            self.filename = name
            errstr = errstr+dumpinfo

        Exception.__init__(self, errstr)

class Flow(object):
    """A 'Flow' is a sequence of nodes that are trained and executed
    together to form a more complex algorithm.  Input data is sent to the
    first node and is successively processed by the subsequent nodes along
    the sequence.

    Using a flow as opposed to handling manually a set of nodes has a
    clear advantage: The general flow implementation automatizes the
    training (including supervised training and multiple training phases),
    execution, and inverse execution (if defined) of the whole sequence.

    Crash recovery is optionally available: in case of failure the current
    state of the flow is saved for later inspection. A subclass of the
    basic flow class ('CheckpointFlow') allows user-supplied checkpoint
    functions to be executed at the end of each phase, for example to save
    the internal structures of a node for later analysis.
    Flow objects are Python containers. Most of the builtin 'list'
    methods are available. A 'Flow' can be saved or copied using the
    corresponding 'save' and 'copy' methods.
    """

    def __init__(self, flow, crash_recovery=False, verbose=False):
        """
        Keyword arguments:

        flow -- a list of Nodes
        crash_recovery -- set (or not) Crash Recovery Mode (save node
                          in case a failure)
        verbose -- if True, print some basic progress information
        """
        self._check_nodes_consistency(flow)
        self.flow = flow
        self.verbose = verbose
        self.set_crash_recovery(crash_recovery)

    def _propagate_exception(self, except_, nodenr):
        # capture exception. the traceback of the error is printed and a
        # new exception, containing the identity of the node in the flow
        # is raised. Allow crash recovery.
        (etype, val, tb) = _sys.exc_info()
        prev = ''.join(_traceback.format_exception(except_.__class__,
                                                   except_,tb))
        act = "\n! Exception in node #%d (%s):\n" % (nodenr,
                                                     str(self.flow[nodenr]))
        errstr = ''.join(('\n', 40*'-', act, 'Node Traceback:\n', prev, 40*'-'))
        raise FlowExceptionCR(errstr, self, except_)

    def _train_node(self, data_iterable, nodenr):
        """Train a single node in the flow.

        nodenr -- index of the node in the flow
        """
        node = self.flow[nodenr]
        if (data_iterable is not None) and (not node.is_trainable()):
            # attempted to train a node although it is not trainable.
            # raise a warning and continue with the next node.
            # wrnstr = "\n! Node %d is not trainable" % nodenr + \
            #        "\nYou probably need a 'None' iterable for"+\
            #         " this node. Continuing anyway."
            #_warnings.warn(wrnstr, mdp.MDPWarning)
            return
        elif (data_iterable is None) and node.is_training():
            # None instead of iterable is passed to a training node
            err_str = ("\n! Node %d is training"
                       " but instead of iterable received 'None'." % nodenr)
            raise FlowException(err_str)
        elif (data_iterable is None) and (not node.is_trainable()):
            # skip training if node is not trainable
            return

        try:
            train_arg_keys = self._get_required_train_args(node)
            train_args_needed = bool(len(train_arg_keys))
            ## We leave the last training phase open for the
            ## CheckpointFlow class.
            ## Checkpoint functions must close it explicitly if needed!
            ## Note that the last training_phase is closed
            ## automatically when the node is executed.
            while True:
                empty_iterator = True
                for x in data_iterable:
                    empty_iterator = False
                    # the arguments following the first are passed only to the
                    # currently trained node, allowing the implementation of
                    # supervised nodes
                    if (type(x) is tuple) or (type(x) is list):
                        arg = x[1:]
                        x = x[0]
                    else:
                        arg = ()
                    # check if the required number of arguments was given
                    if train_args_needed:
                        if len(train_arg_keys) != len(arg):
                            err = ("Wrong number of arguments provided by " +
                                   "the iterable for node #%d " % nodenr +
                                   "(%d needed, %d given).\n" %
                                   (len(train_arg_keys), len(arg)) +
                                   "List of required argument keys: " +
                                   str(train_arg_keys))
                            raise FlowException(err)
                    # filter x through the previous nodes
                    if nodenr > 0:
                        x = self._execute_seq(x, nodenr-1)
                    # train current node
                    node.train(x, *arg)
                if empty_iterator:
                    if node.get_current_train_phase() == 1:
                        err_str = ("The training data iteration for node "
                                   "no. %d could not be repeated for the "
                                   "second training phase, you probably "
                                   "provided an iterator instead of an "
                                   "iterable." % (nodenr+1))
                        raise FlowException(err_str)
                    else:
                        err_str = ("The training data iterator for node "
                                   "no. %d is empty." % (nodenr+1))
                        raise FlowException(err_str)
                self._stop_training_hook()
                if node.get_remaining_train_phase() > 1:
                    # close the previous training phase
                    node.stop_training()
                else:
                    break
        except mdp.TrainingFinishedException, e:
            # attempted to train a node although its training phase is already
            # finished. raise a warning and continue with the next node.
            wrnstr = ("\n! Node %d training phase already finished"
                      " Continuing anyway." % nodenr)
            _warnings.warn(wrnstr, mdp.MDPWarning)
        except FlowExceptionCR, e:
            # this exception was already propagated,
            # probably during the execution  of a node upstream in the flow
            (exc_type, val) = _sys.exc_info()[:2]
            prev = ''.join(_traceback.format_exception_only(e.__class__, e))
            prev = prev[prev.find('\n')+1:]
            act = "\nWhile training node #%d (%s):\n" % (nodenr,
                                                         str(self.flow[nodenr]))
            err_str = ''.join(('\n', 40*'=', act, prev, 40*'='))
            raise FlowException(err_str)
        except Exception, e:
            # capture any other exception occured during training.
            self._propagate_exception(e, nodenr)

    def _stop_training_hook(self):
        """Hook method that is called before stop_training is called."""
        pass

    @staticmethod
    def _get_required_train_args(node):
        """Return arguments in addition to self and x for node.train.

        Argumentes that have a default value are ignored.
        """
        train_arg_spec = _inspect.getargspec(node._train)
        train_arg_keys = train_arg_spec[0][2:]  # ignore self, x
        if train_arg_spec[3]:
            # subtract arguments with a default value
            train_arg_keys = train_arg_keys[:-len(train_arg_spec[3])]
        return train_arg_keys

    def _train_check_iterables(self, data_iterables):
        """Return the data iterables after some checks and sanitizing.

        Note that this method does not distinguish between iterables and
        iterators, so this must be taken care of later.
        """
        # verifies that the number of iterables matches that of
        # the signal nodes and multiplies them if needed.
        flow = self.flow

        # if a single array is given wrap it in a list of lists,
        # note that a list of 2d arrays is not valid
        if isinstance(data_iterables, numx.ndarray):
            data_iterables = [[data_iterables]] * len(flow)

        if not isinstance(data_iterables, list):
            err_str = ("'data_iterables' must be either a list of "
                       "iterables or an array, and not %s" %
                       type(data_iterables))
            raise FlowException(err_str)

        # check that all elements are iterable
        for i, iterable in enumerate(data_iterables):
            if (iterable is not None) and (not hasattr(iterable, '__iter__')):
                err = ("Element number %d in the data_iterables"
                       " list is not an iterable." % i)
                raise FlowException(err)

        # check that the number of data_iterables is correct
        if len(data_iterables) != len(flow):
            err_str = ("%d data iterables specified,"
                       " %d needed" % (len(data_iterables), len(flow)))
            raise FlowException(err_str)

        return data_iterables

    def _close_last_node(self):
        if self.verbose:
            print "Close the training phase of the last node"
        try:
            self.flow[-1].stop_training()
        except mdp.TrainingFinishedException:
            pass
        except Exception, e:
            self._propagate_exception(e, len(self.flow)-1)

    def set_crash_recovery(self, state = True):
        """Set crash recovery capabilities.

        When a node raises an Exception during training, execution, or
        inverse execution that the flow is unable to handle, a FlowExceptionCR
        is raised. If crash recovery is set, a crash dump of the flow
        instance is saved for later inspection. The original exception
        can be found as the 'parent_exception' attribute of the
        FlowExceptionCR instance.

        - If 'state' = False, disable crash recovery.
        - If 'state' is a string, the crash dump is saved on a file
          with that name.
        - If 'state' = True, the crash dump is saved on a file created by
          the tempfile module.
        """
        self._crash_recovery = state

    def train(self, data_iterables):
        """Train all trainable nodes in the flow.

        'data_iterables' is a list of iterables, one for each node in the flow.
        The iterators returned by the iterables must return data arrays that
        are then used for the node training (so the data arrays are the 'x' for
        the nodes). Note that the data arrays are processed by the nodes
        which are in front of the node that gets trained, so the data dimension
        must match the input dimension of the first node.

        If a node has only a single training phase then instead of an iterable
        you can alternatively provide an iterator (including generator-type
        iterators). For nodes with multiple training phases this is not
        possible, since the iterator cannot be restarted after the first
        iteration. For more information on iterators and iterables see
        http://docs.python.org/library/stdtypes.html#iterator-types .

        In the special case that 'data_iterables' is one single array,
        it is used as the data array 'x' for all nodes and training phases.

        Instead of a data array 'x' the iterators can also return a list or
        tuple, where the first entry is 'x' and the following are args for the
        training of the node (e.g. for supervised training).
        """

        data_iterables = self._train_check_iterables(data_iterables)

        # train each Node successively
        for i in range(len(self.flow)):
            if self.verbose:
                print "Training node #%d (%s)" % (i, str(self.flow[i]))
            self._train_node(data_iterables[i], i)
            if self.verbose:
                print "Training finished"

        self._close_last_node()

    def _execute_seq(self, x, nodenr = None):
        # Filters input data 'x' through the nodes 0..'node_nr' included
        flow = self.flow
        if nodenr is None:
            nodenr = len(flow)-1
        for i in range(nodenr+1):
            try:
                x = flow[i].execute(x)
            except Exception, e:
                self._propagate_exception(e, i)
        return x

    def execute(self, iterable, nodenr = None):
        """Process the data through all nodes in the flow.

        'iterable' is an iterable or iterator (note that a list is also an
        iterable), which returns data arrays that are used as input to the flow.
        Alternatively, one can specify one data array as input.

        If 'nodenr' is specified, the flow is executed only up to
        node nr. 'nodenr'. This is equivalent to 'flow[:nodenr+1](iterable)'.
        """
        if isinstance(iterable, numx.ndarray):
            return self._execute_seq(iterable, nodenr)
        res = []
        empty_iterator = True
        for x in iterable:
            empty_iterator = False
            res.append(self._execute_seq(x, nodenr))
        if empty_iterator:
            errstr = ("The execute data iterator is empty.")
            raise FlowException(errstr)
        return numx.concatenate(res)

    def _inverse_seq(self, x):
        #Successively invert input data 'x' through all nodes backwards
        flow = self.flow
        for i in range(len(flow)-1, -1, -1):
            try:
                x = flow[i].inverse(x)
            except Exception, e:
                self._propagate_exception(e, i)
        return x

    def inverse(self, iterable):
        """Process the data through all nodes in the flow backwards
        (starting from the last node up to the first node) by calling the
        inverse function of each node. Of course, all nodes in the
        flow must be invertible.

        'iterable' is an iterable or iterator  (note that a list is also an
        iterable), which returns data arrays that are used as input to the flow.
        Alternatively, one can specify one data array as input.

        Note that this is _not_ equivalent to 'flow[::-1](iterable)',
        which also executes the flow backwards but calls the 'execute'
        function of each node."""

        if isinstance(iterable, numx.ndarray):
            return self._inverse_seq(iterable)
        res = []
        empty_iterator = True
        for x in iterable:
            empty_iterator = False
            res.append(self._inverse_seq(x))
        if empty_iterator:
            errstr = ("The inverse data iterator is empty.")
            raise FlowException(errstr)
        return numx.concatenate(res)

    def copy(self, protocol=None):
        """Return a deep copy of the flow.

        The protocol parameter should not be used.
        """
        if protocol is not None:
            _warnings.warn("protocol parameter to copy() is ignored",
                           mdp.MDPDeprecationWarning, stacklevel=2)
        return _copy.deepcopy(self)

    def save(self, filename, protocol=-1):
        """Save a pickled serialization of the flow to 'filename'.
        If 'filename' is None, return a string.

        Note: the pickled Flow is not guaranteed to be upward or
        backward compatible."""
        if filename is None:
            return _cPickle.dumps(self, protocol)
        else:
            # if protocol != 0 open the file in binary mode
            mode = 'w' if protocol == 0 else 'wb'
            with open(filename, mode) as flh:
                _cPickle.dump(self, flh, protocol)

    def __call__(self, iterable, nodenr = None):
        """Calling an instance is equivalent to call its 'execute' method."""
        return self.execute(iterable, nodenr=nodenr)

    ###### string representation

    def __str__(self):
        nodes = ', '.join([str(x) for x in self.flow])
        return '['+nodes+']'

    def __repr__(self):
        # this should look like a valid Python expression that
        # could be used to recreate an object with the same value
        # eval(repr(object)) == object
        name = type(self).__name__
        pad = len(name)+2
        sep = ',\n'+' '*pad
        nodes = sep.join([repr(x) for x in self.flow])
        return '%s([%s])' % (name, nodes)

    ###### private container methods

    def __len__(self):
        return len(self.flow)

    def _check_dimension_consistency(self, out, inp):
        """Raise ValueError when both dimensions are set and different."""
        if ((out and inp) is not None) and out != inp:
            errstr = "dimensions mismatch: %d != %d" % (out, inp)
            raise ValueError(errstr)

    def _check_nodes_consistency(self, flow = None):
        """Check the dimension consistency of a list of nodes."""
        if flow is None:
            flow = self.flow
        len_flow = len(flow)
        for i in range(1, len_flow):
            out = flow[i-1].output_dim
            inp = flow[i].input_dim
            self._check_dimension_consistency(out, inp)

    def _check_value_type_isnode(self, value):
        if not isinstance(value, mdp.Node):
            raise TypeError("flow item must be Node instance")

    def __getitem__(self, key):
        if isinstance(key, slice):
            flow_slice = self.flow[key]
            self._check_nodes_consistency(flow_slice)
            return self.__class__(flow_slice)
        else:
            return self.flow[key]

    def __setitem__(self, key, value):
        if isinstance(key, slice):
            [self._check_value_type_isnode(item) for item in value]
        else:
            self._check_value_type_isnode(value)

        # make a copy of list
        flow_copy = list(self.flow)
        flow_copy[key] = value
        # check dimension consistency
        self._check_nodes_consistency(flow_copy)
        # if no exception was raised, accept the new sequence
        self.flow = flow_copy

    def __delitem__(self, key):
        # make a copy of list
        flow_copy = list(self.flow)
        del flow_copy[key]
        # check dimension consistency
        self._check_nodes_consistency(flow_copy)
        # if no exception was raised, accept the new sequence
        self.flow = flow_copy

    def __contains__(self, item):
        return self.flow.__contains__(item)

    def __iter__(self):
        return self.flow.__iter__()

    def __add__(self, other):
        # append other to self
        if isinstance(other, Flow):
            flow_copy = list(self.flow).__add__(other.flow)
            # check dimension consistency
            self._check_nodes_consistency(flow_copy)
            # if no exception was raised, accept the new sequence
            return self.__class__(flow_copy)
        elif isinstance(other, mdp.Node):
            flow_copy = list(self.flow)
            flow_copy.append(other)
            # check dimension consistency
            self._check_nodes_consistency(flow_copy)
            # if no exception was raised, accept the new sequence
            return self.__class__(flow_copy)
        else:
            err_str = ('can only concatenate flow or node'
                       ' (not \'%s\') to flow' % (type(other).__name__))
            raise TypeError(err_str)

    def __iadd__(self, other):
        # append other to self
        if isinstance(other, Flow):
            self.flow += other.flow
        elif isinstance(other, mdp.Node):
            self.flow.append(other)
        else:
            err_str = ('can only concatenate flow or node'
                       ' (not \'%s\') to flow' % (type(other).__name__))
            raise TypeError(err_str)
        self._check_nodes_consistency(self.flow)
        return self

    ###### public container methods

    def append(self, x):
        """flow.append(node) -- append node to flow end"""
        self[len(self):len(self)] = [x]

    def extend(self, x):
        """flow.extend(iterable) -- extend flow by appending
        elements from the iterable"""
        if not isinstance(x, Flow):
            err_str = ('can only concatenate flow'
                       ' (not \'%s\') to flow' % (type(x).__name__))
            raise TypeError(err_str)
        self[len(self):len(self)] = x

    def insert(self, i, x):
        """flow.insert(index, node) -- insert node before index"""
        self[i:i] = [x]

    def pop(self, i = -1):
        """flow.pop([index]) -> node -- remove and return node at index
        (default last)"""
        x = self[i]
        del self[i]
        return x

class CheckpointFlow(Flow):
    """Subclass of Flow class that allows user-supplied checkpoint functions
    to be executed at the end of each phase, for example to
    save the internal structures of a node for later analysis."""

    def _train_check_checkpoints(self, checkpoints):
        if not isinstance(checkpoints, list):
            checkpoints = [checkpoints]*len(self.flow)

        if len(checkpoints) != len(self.flow):
            error_str = ("%d checkpoints specified,"
                         " %d needed" % (len(checkpoints), len(self.flow)))
            raise FlowException(error_str)

        return checkpoints


    def train(self, data_iterables, checkpoints):
        """Train all trainable nodes in the flow.

        In addition to the basic behavior (see 'Node.train'), calls the
        checkpoint function 'checkpoint[i]' when the training phase of node #i
        is over.

        A checkpoint function takes as its only argument the trained node.
        If the checkpoint function returns a dictionary, its content is
        added to the instance dictionary.

        The class CheckpointFunction can be used to define user-supplied
        checkpoint functions.
        """

        data_iterables = self._train_check_iterables(data_iterables)
        checkpoints = self._train_check_checkpoints(checkpoints)

        # train each Node successively
        for i in range(len(self.flow)):
            node = self.flow[i]
            if self.verbose:
                print "Training node #%d (%s)" % (i, type(node).__name__)
            self._train_node(data_iterables[i], i)
            if (i <= len(checkpoints)) and (checkpoints[i] is not None):
                dic = checkpoints[i](node)
                if dic:
                    self.__dict__.update(dic)
            if self.verbose:
                print "Training finished"

        self._close_last_node()

class CheckpointFunction(object):
    """Base class for checkpoint functions.

    This class can be subclassed to build objects to be used as a checkpoint
    function in a CheckpointFlow. Such objects would allow to define parameters
    for the function and save informations for later use."""

    def __call__(self, node):
        """Execute the checkpoint function.

        This is the method that is going to be called at the checkpoint.
        Overwrite it to match your needs."""
        pass

class CheckpointSaveFunction(CheckpointFunction):
    """This checkpoint function saves the node in pickle format.
    The pickle dump can be done either before the training phase is finished or
    right after that.
    In this way, it is for example possible to reload it in successive sessions
    and continue the training.
    """

    def __init__(self, filename, stop_training=0, binary=1, protocol=2):
        """CheckpointSaveFunction constructor.

        'filename'      -- the name of the pickle dump file.
        'stop_training' -- if set to 0 the pickle dump is done before
                           closing the training phase
                           if set to 1 the training phase is closed and then
                           the node is dumped
        'binary'        -- sets binary mode for opening the file.
                           When using a protocol higher than 0, make sure
                           the file is opened in binary mode.
        'protocol'      -- is the 'protocol' argument for the pickle dump
                           (see Pickle documentation for details)
        """
        self.filename = filename
        self.proto = protocol
        self.stop_training = stop_training
        if binary or protocol > 0:
            self.mode = 'wb'
        else:
            self.mode = 'w'

    def __call__(self, node):
        with open(self.filename, self.mode) as fid:
            if self.stop_training:
                node.stop_training()
            _cPickle.dump(node, fid, self.proto)