python-biom-format 1.1.2-1 / usr / share / pyshared / biom / sparsedict.py

#!/usr/bin/env python

from numpy import array, ndarray
from operator import itemgetter
from biom.util import flatten

__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2012, BIOM-Format Project"
__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso", 
               "Jose Clemente", "Justin Kuczynski"]
__license__ = "GPL"
__url__ = "http://biom-format.org"
__version__ = "1.1.2"
__maintainer__ = "Daniel McDonald"
__email__ = "daniel.mcdonald@colorado.edu"

class SparseDict(dict):
    """Support for sparse dicts

    Must specify rows and columns in advance

    Object cannot "grow" in shape

    There is additional overhead on inserts in order to support rapid lookups
    across rows or columns
    """

    def __init__(self, rows, cols, dtype=float, enable_indices=True):
        self.shape = (rows, cols) 
        self.dtype = dtype # casting is minimal, trust the programmer...

        if enable_indices:
            self._index_rows = [set() for i in range(rows)]
            self._index_cols = [set() for i in range(cols)]
        else:
            self._index_rows = None
            self._index_rows = None
        self._indices_enabled = enable_indices

    def copy(self):
        """Return a copy of self"""
        new_self = self.__class__(self.shape[0], self.shape[1], self.dtype, \
                                  self._indices_enabled)
        new_self.update(self)
        return new_self

    def __setitem__(self,args,value):
        """Wrap setitem, complain if out of bounds"""
        try:
            row,col = args
        except:
            # fast support foo[5] = 10, like numpy 1d vectors
            col = args
            row = 0
            args = (row,col) # passed onto update_internal_indices
    
        in_self_rows, in_self_cols = self.shape

        if row >= in_self_rows or row < 0:
            raise KeyError, "The specified row is out of bounds"
        if col >= in_self_cols or col < 0:
            raise KeyError, "The specified col is out of bounds"

        if value == 0:
            if args in self:
                self._update_internal_indices(args, value)
                del self[args]
            else:
                return
        else:
            self._update_internal_indices(args, value)
            super(SparseDict, self).__setitem__(args, value)

    def __getitem__(self,args):
        """Wrap getitem to handle slices"""
        try:
            row,col = args
        except TypeError:
            raise IndexError, "Must specify (row, col)"

        if isinstance(row, slice): 
            if row.start is None and row.stop is None:
                return self.getCol(col)
            else:
                raise AttributeError, "Can only handle full : slices per axis"
        elif isinstance(col, slice):
            if col.start is None and col.stop is None:
                return self.getRow(row)
            else:
                raise AttributeError, "Can only handle full : slices per axis"
        else:
            # boundary check
            self_rows, self_cols = self.shape
            if row >= self_rows or row < 0:
                raise IndexError, "Row index out of range"
            if col >= self_cols or col < 0:
                raise IndexError, "Col index out of range"

            # return dtype(0) if args don't exist
            if args not in self:
                return self.dtype(0)
            
            return super(SparseDict, self).__getitem__(args)

    def _update_internal_indices(self, args, value):
        """Update internal row,col indices"""
        if not self._indices_enabled:
            return
            
        row,col = args
        if value == 0:
            if args in self:
                self._index_rows[row].remove(args)
                self._index_cols[col].remove(args)
            else:
                return # short circuit, no point in setting 0
        else:
            self._index_rows[row].add(args)
            self._index_cols[col].add(args)

    def getRow(self, row):
        """Returns a row: {((row,col):value}"""
        in_self_rows, in_self_cols = self.shape
        if row >= in_self_rows or row < 0:
            raise IndexError, "The specified row is out of bounds"
    
        new_row = SparseDict(1, in_self_cols, enable_indices=False)
        
        d = {}
        for r,c in self._index_rows[row]:
            d[(0,c)] = super(SparseDict, self).__getitem__((r,c))
        new_row.update(d)
        return new_row

    def getCol(self, col):
        """Return a col: {((row,col):value}"""
        in_self_rows, in_self_cols = self.shape
        if col >= in_self_cols or col < 0:
            raise IndexError, "The specified col is out of bounds"

        new_col = SparseDict(in_self_rows, 1, enable_indices=False)
        d = {}
        for r,c in self._index_cols[col]:
            d[(r,0)] = super(SparseDict, self).__getitem__((r,c))
        new_col.update(d)
        return new_col

    def transpose(self):
        """Transpose self"""
        new_self = self.__class__(*self.shape[::-1], \
                enable_indices=self._indices_enabled)
        new_self.update(dict([((c,r),v) for (r,c),v in self.iteritems()]))
        return new_self
    T = property(transpose)

    def _get_size(self):
        """Returns the number of nonzero elements stored"""
        return len(self)
    size = property(_get_size)

    def update(self, update_dict):
        """Update self"""
        in_self_rows, in_self_cols = self.shape
    
        # handle zero values different and dont pass them to update
        scrubbed = {}
        for (row,col),value in update_dict.items():
            if row >= in_self_rows or row < 0:
                raise KeyError, "The specified row is out of bounds"
            if col >= in_self_cols or col < 0:
                raise KeyError, "The specified col is out of bounds"
            if value == 0:
                self.__setitem__((row,col), 0)
            else:
                scrubbed[(row,col)] = value
            
            if self._indices_enabled:
                self._update_internal_indices((row,col), value)

        super(SparseDict, self).update(scrubbed)

def to_sparsedict(values, transpose=False, dtype=float):
    """Tries to returns a populated SparseDict object

    NOTE: assumes the max value observed in row and col defines the size of the
    matrix
    """
    # if it is a vector
    if isinstance(values, ndarray) and len(values.shape) == 1:
        if transpose:
            mat = nparray_to_sparsedict(values[:,newaxis], dtype)
        else:
            mat = nparray_to_sparsedict(values, dtype)
        return mat
    if isinstance(values, ndarray):
        if transpose:
            mat = nparray_to_sparsedict(values.T, dtype)
        else:
            mat = nparray_to_sparsedict(values, dtype)
        return mat 
    # the empty list
    elif isinstance(values, list) and len(values) == 0:
        mat = SparseDict(0,0)
        return mat
    # list of np vectors
    elif isinstance(values, list) and isinstance(values[0], ndarray):
        mat = list_nparray_to_sparsedict(values, dtype)
        if transpose:
            mat = mat.T
        return mat
    # list of dicts, each representing a row in row order
    elif isinstance(values, list) and isinstance(values[0], dict):
        mat = list_dict_to_sparsedict(values, dtype)
        if transpose:
            mat = mat.T
        return mat
    elif isinstance(values, dict):
        mat = dict_to_sparsedict(values, dtype)
        if transpose:
            mat = mat.T
        return mat
    else:
        raise TableException, "Unknown input type"
        
def list_list_to_sparsedict(data, dtype=float, shape=None):
    """Convert a list of lists into a sparsedict

    [[row, col, value], ...]
    """
    d = dict([((r,c),dtype(v)) for r,c,v in data if v != 0])

    if shape is None:
        n_rows = 0
        n_cols = 0
        for (r,c) in d:
            if r >= n_rows:
                n_rows = r + 1 # deal with 0-based indexes
            if c >= n_cols:
                n_cols = c + 1

        mat = SparseDict(n_rows, n_cols)
    else:
        mat = SparseDict(*shape)

    mat.update(d)
    return mat

def nparray_to_sparsedict(data, dtype=float):
    """Convert a numpy array to a dict"""
    if len(data.shape) == 1:
        mat = SparseDict(1, data.shape[0], dtype=dtype,enable_indices=False)

        for idx,v in enumerate(data):
            if v != 0:
                mat[(0,idx)] = dtype(v)
    else:
        mat = SparseDict(*data.shape)
        for row_idx, row in enumerate(data):
            for col_idx, value in enumerate(row):
                if value != 0:
                    mat[(row_idx, col_idx)] = dtype(value)
    return mat

def list_nparray_to_sparsedict(data, dtype=float):
    """Takes a list of numpy arrays and creates a dict"""
    mat = SparseDict(len(data), len(data[0]))
    for row_idx, row in enumerate(data):
        if len(row.shape) != 1:
            raise TableException, "Cannot convert non-1d vectors!"
        if len(row) != mat.shape[1]:
            raise TableException, "Row vector isn't the correct length!"

        for col_idx, val in enumerate(row):
            mat[row_idx, col_idx] = dtype(val)
    return mat

def list_dict_to_sparsedict(data, dtype=float):
    """Takes a list of dict {(0,col):val} and creates a full dict"""
    if isinstance(data[0], SparseDict):
        if data[0].shape[0] > data[0].shape[1]:
            is_col = True
            n_cols = len(data)
            n_rows = data[0].shape[0]
        else:
            is_col = False
            n_rows = len(data)
            n_cols = data[0].shape[1]
    else:
        all_keys = flatten([d.keys() for d in data])
        n_rows = max(all_keys, key=itemgetter(0))[0] + 1
        n_cols = max(all_keys, key=itemgetter(1))[1] + 1
        if n_rows > n_cols:
            is_col = True
            n_cols = len(data)
        else:
            is_col = False
            n_rows = len(data)

    mat = SparseDict(n_rows, n_cols)
    for row_idx,row in enumerate(data):
        for (foo,col_idx),val in row.items():
            if is_col:
                mat[foo,row_idx] = dtype(val)
            else:
                mat[row_idx,col_idx] = dtype(val)

    return mat

def dict_to_sparsedict(data, dtype=float):
    """takes a dict {(row,col):val} and creates a SparseDict"""
    n_rows = max(data.keys(), key=itemgetter(0))[0] + 1
    n_cols = max(data.keys(), key=itemgetter(1))[1] + 1
    mat = SparseDict(n_rows, n_cols)
    mat.update(data)
    return mat