python-cogent 1.5.3-2 / usr / share / pyshared / cogent / recalculation / definition.py

#!/usr/bin/env python
"""A recalculation engine, something like a spreadsheet.

Goals:
 - Allow construction of a calculation in a flexible and declarative way.
 - Enable caching at any step in the calculation where it makes sense.

Terms:
 - Definition - defines one cachable step in a complex calculation.
 - ParameterController - Sets parameter scope rules on a DAG of Definitions.
 - Calculator - An instance of an internally caching function.
 - Category - An arbitrary label.
 - Dimension - A named set of categories.
 - Scope - A subset of the categories from each dimension.
 - Setting - A variable (Var) or constant (ConstVal).
 - Assignments - A mapping from Scopes to Settings.
 - Cell - Evaluates one Scope of one Definition.
 - OptPar - A cell with indegree 0.

Structure:
 - A Calculator holds a list of Cells: OptPars and EvaluatedCells.
 - EvaluatedCells take their arguments from other Cells.
 - Each type of cell (motifs, Qs, Psubs) made by a different CalculationDefn.
 - No two cells from the same CalculationDefn have the same inputs, so nothing
   is calculated twice.

Interface:
  1) Define a function for each step in the calculation.
  2) Instantiate a DAG of ParamDefns and CalcDefns, each CalcDefn like
     CalcDefn(f)(*args) where 'f' is one of your functions and the '*args'
     are Defns that correspond to the arguments of 'f'.
  3) With your final CalcDefn called say 'top', PC = ParameterController(top)
     to get a ParameterController.
  4) PC.assignAll(param, value=value, **scope) to define the parameter
     scopes.  'value' can be a constant float or an instance of Var.
  5) calculator = PC.makeCalculator() to get a live Calculator.
  6) calculator.optimise() etc.

Caching:
  In addition to the caching provided by the update strategy (not recalculating
  anything that hasn't changed), the calculator keeps a 1-deep cache of the
  previous value for each cell so that it has a 1-deep undo capability.  This
  is ideal for the behaviour of a one-change-at-a-time simanneal optimiser,
  which backtracks when a new value isn't accepted, ie it tries sequences like:
    [0,0,0] [0,0,3] [0,8,0] [7,0,0] [0,0,4] [0,6,0] ...
  when it isn't making progress, and
    [0,0,0] [0,0,3] [0,8,3] [7,8,3] [7,8,9] ...
  when it's having a lucky streak.
  
  Each cell knows when it's out of date, but doesn't know why (ie: what input
  changed) which limits the undo strategy to all-or-nothing.  An optimiser that
  tried values
    [0,0,0] [0,3,8] [0,3,0] ...
  (ie: the third step is a recombination of the previous two) would not get
  any help from caching.  This does keep things simple and fast though.

Recycling:
  If defn.recycling is True then defn.calc() will be passed the previous
  result as its first argument so it can be reused.  This is to avoid
  having to reallocate memory for say a large numpy array just at the
  very moment that an old one of the same shape is being disposed of.
  To prevent recycling from invalidating the caching system 3 values are
  stored for each cell - current, previous and spare.  The spare value is
  the one to be used next for recycling.
"""
from __future__ import division, with_statement
import warnings
import numpy

# In this module we bring together scopes, settings and calculations.
# Most of the classes are 'Defns' with their superclasses in scope.py.
# These supply a makeCells() method which instantiates 'Cell'
# classes from calculation.py

from .calculation import EvaluatedCell, OptPar, LogOptPar, ConstCell
from .scope import _NonLeafDefn, _LeafDefn, _Defn, ParameterController
from .setting import Var, ConstVal

from cogent.util.dict_array import DictArrayTemplate
from cogent.maths.stats.distribution import chdtri
from cogent.util import parallel

__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"


class CalculationDefn(_NonLeafDefn):
    """Defn for a derived value.  In most cases use CalcDefn instead
    
    The only reason for subclassing this directly would be to override
    .makeCalcFunction() or setup()."""
    
    recycling = False
    
    # positional arguments are inputs to this step of the calculation,
    # keyword arguments are passed on to self.setup(), likely to end up
    # as static attributes of this CalculationDefn, to be used (as self.X)
    # by its 'calc' method.
    
    def makeParamController(self):
        return ParameterController(self)
    
    def setup(self):
        pass
    
    def makeCalcFunction(self):
        return self.calc
    
    def makeCell(self, *args):
        calc = self.makeCalcFunction()
        # can't calc outside correct parallel context, so can't do
        # if [arg for arg in args if not arg.is_constant]:
        cell = EvaluatedCell(self.name, calc, args,
                recycling=self.recycling, default=self.default)
        return cell
        
    def makeCells(self, input_soup, variable=None):
        # input soups contains all necessary values for calc on self. 
        # Going from defns to cells.
        cells = []
        for input_nums in self.uniq:
            args = []
            for (arg, u) in zip(self.args, input_nums):
                arg = input_soup[id(arg)][u]
                args.append(arg)
            cell = self.makeCell(*args)
            cells.append(cell)
        return (cells, cells)
    

class _FuncDefn(CalculationDefn):
    def __init__(self, calc, *args, **kw):
        self.calc = calc
        CalculationDefn.__init__(self, *args, **kw)
    

# Use this rather than having to subclass CalculationDefinition
# just to supply the 'calc' method.
class CalcDefn(object):
    """CalcDefn(function)(arg1, arg2)"""
    def __init__(self, calc, name=None, **kw):
        self.calc = calc
        
        if name is None:
            name = self.calc.__name__
        else:
            assert isinstance(name, basestring), name
        kw['name'] = name        
        self.kw = kw
    
    def __call__(self, *args):
        return _FuncDefn(self.calc, *args, **self.kw)

class WeightedPartitionDefn(CalculationDefn):
    """Uses a PartitionDefn (ie: N-1 optimiser parameters) to make
    an array of floats with weighted average of 1.0"""
    
    def __init__(self, weights, name):
        N = len(weights.bin_names)
        partition = PartitionDefn(size=N, name=name+'_partition')
        partition.user_param = False
        CalculationDefn.__init__(self, weights, partition,
                name=name+'_distrib')
    
    def calc(self, weights, values):
        scale = numpy.sum(weights * values)
        return values / scale
    

class MonotonicDefn(WeightedPartitionDefn):
    """Uses a PartitionDefn (ie: N-1 optimiser parameters) to make
    an ordered array of floats with weighted average of 1.0"""
    
    def calc(self, weights, increments):
        values = numpy.add.accumulate(increments)
        scale = numpy.sum(weights * values)
        return values / scale
    

class GammaDefn(MonotonicDefn):
    """Uses 1 optimiser parameter to define a gamma distribution, divides
    the distribution into N equal probability bins and makes an array of
    their medians.  If N > 2 medians are approx means so their average
    is approx 1.0, but not quite so we scale them to make it exactly 1.0"""
    
    name = 'gamma'
    
    def __init__(self, weights, name=None, default_shape=1.0,
            extra_label=None, dimensions=()):
        name = self.makeName(name, extra_label)
        shape = PositiveParamDefn(name+'_shape',
            default=default_shape, dimensions=dimensions, lower=1e-2)
        CalculationDefn.__init__(self, weights, shape, name=name+'_distrib')
    
    def calc(self, weights, a):
        from cogent.maths.stats.distribution import gdtri
        weights = weights / numpy.sum(weights)
        percentiles = (numpy.add.accumulate(weights) - weights*0.5)
        medians = numpy.array([gdtri(a,a,p) for p in percentiles])
        scale = numpy.sum(medians*weights)
        #assert 0.5 < scale < 2.0, scale # medians as approx. to means.
        return medians / scale


class _InputDefn(_LeafDefn):
    user_param = True
    
    def __init__(self, name=None, default=None, dimensions=None,
            lower=None, upper=None, **kw):
        _LeafDefn.__init__(self, name=name, dimensions=dimensions, **kw)
        if default is not None:
            if hasattr(default, '__len__'):
                default = numpy.array(default)
            self.default = default
        # these two have no effect on constants
        if lower is not None:
            self.lower = lower
        if upper is not None:
            self.upper = upper
    
    def makeParamController(self):
        return ParameterController(self)
    
    def updateFromCalculator(self, calc):
        outputs = calc.getCurrentCellValuesForDefn(self)
        for (output, setting) in zip(outputs, self.uniq):
            setting.value = output
    
    def getNumFreeParams(self):
        (cells, outputs) = self.makeCells({}, None)
        return len([c for c in cells if isinstance(c, OptPar)])    

class ParamDefn(_InputDefn):
    """Defn for an optimisable, scalar input to the calculation"""
    
    numeric = True
    const_by_default = False
    independent_by_default = False
    opt_par_class = OptPar
    
    # These can be overridden in a subclass or the constructor
    default = 1.0
    lower = -1e10
    upper = +1e10
    
    def makeDefaultSetting(self):
        return Var(bounds = (self.lower, self.default, self.upper))
    
    def checkSettingIsValid(self, setting):
        pass
    
    def makeCells(self, input_soup={}, variable=None):
        uniq_cells = []
        for (i, v) in enumerate(self.uniq):
            scope = [key for key in self.assignments
                    if self.assignments[key] is v]
            if v.is_constant or (variable is not None and variable is not v):
                cell = ConstCell(self.name, v.value)
            else:
                cell = self.opt_par_class(self.name, scope, v.getBounds())
            uniq_cells.append(cell)
        
        return (uniq_cells, uniq_cells)
    

# Example / basic ParamDefn subclasses

class PositiveParamDefn(ParamDefn):
    lower = 0.0

class ProbabilityParamDefn(PositiveParamDefn):
    upper = 1.0

class RatioParamDefn(PositiveParamDefn):
    lower = 1e-6
    upper = 1e+6
    opt_par_class = LogOptPar

class NonScalarDefn(_InputDefn):
    """Defn for an array or other such object that is an input but
    can not be optimised"""
    
    user_param = False
    numeric = False
    const_by_default = True
    independent_by_default = False
    default = None
    
    def makeDefaultSetting(self):
        if self.default is None:
            return None
        else:
            return ConstVal(self.default)
    
    def checkSettingIsValid(self, setting):
        if not isinstance(setting, ConstVal):
            raise ValueError("%s can only be constant" % self.name)
    
    def makeCells(self, input_soup={}, variable=None):
        if None in self.uniq:
            if [v for v in self.uniq if v is not None]:
                scope = [key for key in self.assignments
                            if self.assignments[key] is None]
                msg = 'Unoptimisable input "%%s" not set for %s' % scope
            else:
                msg = 'Unoptimisable input "%s" not given'
            raise ValueError(msg % self.name)
        uniq_cells = [ConstCell(self.name, v.value) for v in self.uniq]
        return (uniq_cells, uniq_cells)
    
    def getNumFreeParams(self):
        return 0
        
    def updateFromCalculator(self, calc):
        pass # don't reset parallel_context etc.

    

def _proportions(total, params):
    """List of N proportions from N-1 ratios
    
    >>> _proportions(1.0, [3, 1, 1])
    [0.125, 0.125, 0.375, 0.375]"""
    if len(params) == 0:
        return [total]
    half = (len(params)+1) // 2
    part = 1.0 / (params[0] + 1.0) # ratio -> proportion
    return _proportions(total*part, params[1:half]) + \
        _proportions(total*(1.0-part), params[half:])

def _unpack_proportions(values):
    """List of N-1 ratios from N proportions"""
    if len(values) == 1:
        return []
    half = len(values) // 2
    (num, denom) = (sum(values[half:]), sum(values[:half]))
    assert num > 0 and denom > 0
    ratio = num / denom
    return [ratio] + _unpack_proportions(values[:half]) + \
        _unpack_proportions(values[half:])

class PartitionDefn(_InputDefn):
    """A partition such as mprobs can be const or optimised.  Optimised is
    a bit tricky since it isn't just a scalar."""
    
    numeric = False # well, not scalar anyway
    const_by_default = False
    independent_by_default = False
    
    def __init__(self, default=None, name=None, dimensions=None,
            dimension=None, size=None, **kw):
        assert name
        if size is not None:
            pass
        elif default is not None:
            size = len(default)
        elif dimension is not None:
            size = len(dimension[1])
        self.size = size
        if dimension is not None:
            self.internal_dimension = dimension
            (dim_name, dim_cats) = dimension
            self.bin_names = dim_cats
            self.array_template = DictArrayTemplate(dim_cats)
            self.internal_dimensions = (dim_name,)
        if default is None:
            default = self._makeDefaultValue()
        elif self.array_template is not None:
            default = self.array_template.unwrap(default)
        else:
            default = numpy.asarray(default)
        _InputDefn.__init__(self, name=name, default=default,
            dimensions=dimensions, **kw)
        self.checkValueIsValid(default, True)
    
    def _makeDefaultValue(self):
        return numpy.array([1.0/self.size] * self.size)
        
    def makeDefaultSetting(self):
        #return ConstVal(self.default)
        return Var((None, self.default.copy(), None))
    
    def checkSettingIsValid(self, setting):
        value = setting.getDefaultValue()
        return self.checkValueIsValid(value, setting.is_constant)

    def checkValueIsValid(self, value, is_constant):
        if value.shape != (self.size,):
            raise ValueError("Wrong array shape %s for %s, expected (%s,)" % 
                    (value.shape, self.name, self.size))
        for part in value:
            if part < 0:
                raise ValueError("Negative probability in %s" % self.name)                
            if part > 1:
                raise ValueError("Probability > 1 in %s" % self.name)                
            if not is_constant:
                # 0 or 1 leads to log(0) or log(inf) in optimiser code
                if part == 0:
                    raise ValueError("Zeros allowed in %s only when constant" % 
                        self.name)                
                if part == 1:
                    raise ValueError("Ones allowed in %s only when constant" % 
                        self.name)
        if abs(sum(value) - 1.0) > .00001:
            raise ValueError("Elements of %s must sum to 1.0, not %s" %
                (self.name, sum(value)))
    
    def _makePartitionCell(self, name, scope, value):
        # This was originally put in its own function so as to provide a 
        # closure containing the value of sum(value), which is no longer 
        # required since it is now always 1.0.
        N = len(value)
        assert abs(sum(value) - 1.0) < .00001
        ratios = _unpack_proportions(value)
        ratios = [LogOptPar(name+'_ratio', scope, (1e-6,r,1e+6))
                for r in ratios]
        def r2p(*ratios):
            return numpy.asarray(_proportions(1.0, ratios))
        partition = EvaluatedCell(name, r2p, tuple(ratios))
        return (ratios, partition)
    
    def makeCells(self, input_soup={}, variable=None):
        uniq_cells = []
        all_cells = []
        for (i, v) in enumerate(self.uniq):
            if v is None:
                raise ValueError("input %s not set" % self.name)
            assert hasattr(v, 'getDefaultValue'), v
            value = v.getDefaultValue()
            assert hasattr(value, 'shape'), value
            assert value.shape == (self.size,)
            scope = [key for key in self.assignments
                    if self.assignments[key] is v]
            assert value is not None
            if v.is_constant or (variable is not None and variable is not v):
                partition = ConstCell(self.name, value)
            else:
                (ratios, partition) = self._makePartitionCell(
                        self.name, scope, value)
                all_cells.extend(ratios)
            all_cells.append(partition)
            uniq_cells.append(partition)
        return (all_cells, uniq_cells)
    
def NonParamDefn(name, dimensions=None, **kw):
    # Just to get 2nd arg as dimensions
    return NonScalarDefn(name=name, dimensions=dimensions, **kw)

class ConstDefn(NonScalarDefn):
    # This isn't really needed - just use NonParamDefn
    name_required = False
    
    def __init__(self, value, name=None, **kw):
        NonScalarDefn.__init__(self, default=value, name=name, **kw)
    
    def checkSettingIsValid(self, setting):
        if setting is not None and setting.value is not self.default:
            raise ValueError("%s is constant" % self.name)


class SelectForDimension(_Defn):
    """A special kind of Defn used to bridge from Defns where a particular
    dimension is wrapped up inside an array to later Defns where each
    value has its own Defn, eg: gamma distributed rates"""
    
    name = 'select'
    user_param = True
    numeric=True # not guarenteed!
    internal_dimensions = ()
    
    def __init__(self, arg, dimension, name=None):
        assert not arg.activated, arg.name
        if name is not None:
            self.name = name
        _Defn.__init__(self)
        self.args = (arg,)
        self.arg = arg
        self.valid_dimensions = arg.valid_dimensions
        if dimension not in self.valid_dimensions:
            self.valid_dimensions =  self.valid_dimensions + (dimension,)
        self.dimension = dimension
        arg.addClient(self)
    
    def update(self):
        for scope_t in self.assignments:
            scope = dict(zip(self.valid_dimensions, scope_t))
            scope2 = dict((n,v) for (n,v) in scope.items() if n!=self.dimension)
            input_num = self.arg.outputOrdinalFor(scope2)
            pos = self.arg.bin_names.index(scope[self.dimension])
            self.assignments[scope_t] = (input_num, pos)
        self._update_from_assignments()
        self.values = [self.arg.values[i][p] for (i,p) in self.uniq]
    
    def _select(self, arg, p):
        return arg[p]
    
    def makeCells(self, input_soup, variable=None):
        cells = []
        distribs = input_soup[id(self.arg)]
        for (input_num, bin_num) in self.uniq:
            cell = EvaluatedCell(
                self.name, (lambda x,p=bin_num:x[p]), (distribs[input_num],))
            cells.append(cell)
        return (cells, cells)
    

# Some simple CalcDefns

#SumDefn = CalcDefn(lambda *args:sum(args), 'sum')
#ProductDefn = CalcDefn(lambda *args:numpy.product(args), 'product')
#CallDefn = CalcDefn(lambda func,*args:func(*args), 'call')
#ParallelSumDefn = CalcDefn(lambda comm,local:comm.sum(local), 'parallel_sum')

class SwitchDefn(CalculationDefn):
    name = 'switch'
    def calc(self, condition, *args):
        return args[condition]

    def getShortcutCell(self, condition, *args):
        if condition.is_constant:
            return self.calc(self, condition.value, *args)

class VectorMatrixInnerDefn(CalculationDefn):
    name = 'evolve'
    def calc(self, pi, psub):
        return numpy.inner(pi, psub)
        
    def getShortcutCell(self, pi, psub):
        if psub.is_stationary:
            return pi
    
class SumDefn(CalculationDefn):
    name = 'sum'
    def calc(self, *args):
        return sum(args)
    

class ProductDefn(CalculationDefn):
    name = 'product'
    def calc(self, *args):
        return numpy.product(args)
    

class CallDefn(CalculationDefn):
    name = 'call'
    def calc(self, func, *args):
        return func(*args)
    

class ParallelSumDefn(CalculationDefn):
    name = 'parallel_sum'
    def calc(self, comm, local):
        return comm.allreduce(local)  # default MPI op is SUM
    

__all__ = ['ConstDefn', 'NonParamDefn', 'CalcDefn', 'SumDefn', 'ProductDefn',
        'CallDefn', 'ParallelSumDefn'] + [
        n for (n,c) in vars().items()
        if (isinstance(c, type) and issubclass(c, _Defn) and n[0] != '_')
        or isinstance(c, CalcDefn)]