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from numpy import asarray
import numpy as np
import copy
ListType = list
TupleType = tuple
StringType = str
def abut(source, *args):
# comment: except for the repetition, this is equivalent to hstack.
"""\nLike the |Stat abut command. It concatenates two arrays column-wise
and returns the result. CAUTION: If one array is shorter, it will be
repeated until it is as long as the other.
Format: abut (source, args) where args=any # of arrays
Returns: an array as long as the LONGEST array past, source appearing on the
'left', arrays in <args> attached on the 'right'.\n"""
source = asarray(source)
if len(source.shape)==1:
width = 1
source = np.resize(source,[source.shape[0],width])
else:
width = source.shape[1]
for addon in args:
if len(addon.shape)==1:
width = 1
addon = np.resize(addon,[source.shape[0],width])
else:
width = source.shape[1]
if len(addon) < len(source):
addon = np.resize(addon,[source.shape[0],addon.shape[1]])
elif len(source) < len(addon):
source = np.resize(source,[addon.shape[0],source.shape[1]])
source = np.concatenate((source,addon),1)
return source
def unique(inarray):
"""Returns unique items in the FIRST dimension of the passed array. Only
works on arrays NOT including string items (e.g., type 'O' or 'c').
"""
inarray = asarray(inarray)
uniques = np.array([inarray[0]])
if len(uniques.shape) == 1: # IF IT'S A 1D ARRAY
for item in inarray[1:]:
if np.add.reduce(np.equal(uniques,item).flat) == 0:
try:
uniques = np.concatenate([uniques,np.array[np.newaxis,:]])
except TypeError:
uniques = np.concatenate([uniques,np.array([item])])
else: # IT MUST BE A 2+D ARRAY
if inarray.dtype.char != 'O': # not an Object array
for item in inarray[1:]:
if not np.sum(np.alltrue(np.equal(uniques,item),1),axis=0):
try:
uniques = np.concatenate( [uniques,item[np.newaxis,:]] )
except TypeError: # the item to add isn't a list
uniques = np.concatenate([uniques,np.array([item])])
else:
pass # this item is already in the uniques array
else: # must be an Object array, alltrue/equal functions don't work
for item in inarray[1:]:
newflag = 1
for unq in uniques: # NOTE: cmp --> 0=same, -1=<, 1=>
test = np.sum(abs(np.array(map(cmp,item,unq))),axis=0)
if test == 0: # if item identical to any 1 row in uniques
newflag = 0 # then not a novel item to add
break
if newflag == 1:
try:
uniques = np.concatenate( [uniques,item[np.newaxis,:]] )
except TypeError: # the item to add isn't a list
uniques = np.concatenate([uniques,np.array([item])])
return uniques
def colex(a, indices, axis=1):
"""\nExtracts specified indices (a list) from passed array, along passed
axis (column extraction is default). BEWARE: A 1D array is presumed to be a
column-array (and that the whole array will be returned as a column).
Returns: the columns of a specified by indices\n"""
if type(indices) not in [ListType,TupleType,np.ndarray]:
indices = [indices]
if len(np.shape(a)) == 1:
cols = np.resize(a,[a.shape[0],1])
else:
cols = np.take(a,indices,axis)
return cols
def adm(a, criterion):
"""\nReturns rows from the passed list of lists that meet the criteria in
the passed criterion expression (a string).
Format: adm (a,criterion) where criterion is like 'x[2]==37'\n"""
lines = eval('filter(lambda x: '+criterion+',a)')
try:
lines = np.array(lines)
except:
lines = np.array(lines,'O')
return lines
def linexand(a, columnlist, valuelist):
"""Returns the rows of an array where col (from columnlist) = val
(from valuelist). One value is required for each column in columnlist.
Returns: the rows of a where columnlist[i]=valuelist[i] for ALL i\n"""
a = asarray(a)
if type(columnlist) not in [ListType,TupleType,np.ndarray]:
columnlist = [columnlist]
if type(valuelist) not in [ListType,TupleType,np.ndarray]:
valuelist = [valuelist]
criterion = ''
for i in range(len(columnlist)):
if type(valuelist[i])==StringType:
critval = '\'' + valuelist[i] + '\''
else:
critval = str(valuelist[i])
criterion = criterion + ' x['+str(columnlist[i])+']=='+critval+' and'
criterion = criterion[0:-3] # remove the "and" after the last crit
return adm(a,criterion)
def collapse(a, keepcols, collapsecols, stderr=0, ns=0, cfcn=None):
"""Averages data in collapsecol, keeping all unique items in keepcols
(using unique, which keeps unique LISTS of column numbers), retaining
the unique sets of values in keepcols, the mean for each. If the sterr or
N of the mean are desired, set either or both parameters to 1.
Returns: unique 'conditions' specified by the contents of columns specified
by keepcols, abutted with the mean(s,axis=0) of column(s) specified by
collapsecols
Examples
--------
import numpy as np
from scipy import stats
xx = np.array([[ 0., 0., 1.],
[ 1., 1., 1.],
[ 2., 2., 1.],
[ 0., 3., 1.],
[ 1., 4., 1.],
[ 2., 5., 1.],
[ 0., 6., 1.],
[ 1., 7., 1.],
[ 2., 8., 1.],
[ 0., 9., 1.]])
>>> stats._support.collapse(xx, (0), (1,2), stderr=0, ns=0, cfcn=None)
array([[ 0. , 4.5, 1. ],
[ 0. , 4.5, 1. ],
[ 1. , 4. , 1. ],
[ 1. , 4. , 1. ],
[ 2. , 5. , 1. ],
[ 2. , 5. , 1. ]])
>>> stats._support.collapse(xx, (0), (1,2), stderr=1, ns=1, cfcn=None)
array([[ 0. , 4.5 , 1.93649167, 4. , 1. ,
0. , 4. ],
[ 0. , 4.5 , 1.93649167, 4. , 1. ,
0. , 4. ],
[ 1. , 4. , 1.73205081, 3. , 1. ,
0. , 3. ],
[ 1. , 4. , 1.73205081, 3. , 1. ,
0. , 3. ],
[ 2. , 5. , 1.73205081, 3. , 1. ,
0. , 3. ],
[ 2. , 5. , 1.73205081, 3. , 1. ,
0. , 3. ]])
"""
if cfcn is None:
cfcn = lambda(x): np.mean(x, axis=0)
a = asarray(a)
if keepcols == []:
avgcol = colex(a,collapsecols)
means = cfcn(avgcol)
return means
else:
if type(keepcols) not in [ListType,TupleType,np.ndarray]:
keepcols = [keepcols]
values = colex(a,keepcols) # so that "item" can be appended (below)
uniques = unique(values).tolist() # get a LIST, so .sort keeps rows intact
uniques.sort()
newlist = []
for item in uniques:
if type(item) not in [ListType,TupleType,np.ndarray]:
item =[item]
tmprows = linexand(a,keepcols,item)
for col in collapsecols:
avgcol = colex(tmprows,col)
item.append(cfcn(avgcol))
if stderr:
if len(avgcol)>1:
item.append(compute_stderr(avgcol))
else:
item.append('N/A')
if ns:
item.append(len(avgcol))
newlist.append(item)
try:
new_a = np.array(newlist)
except TypeError:
new_a = np.array(newlist,'O')
return new_a
def _chk_asarray(a, axis):
if axis is None:
a = np.ravel(a)
outaxis = 0
else:
a = np.asarray(a)
outaxis = axis
return a, outaxis
def _chk2_asarray(a, b, axis):
if axis is None:
a = np.ravel(a)
b = np.ravel(b)
outaxis = 0
else:
a = np.asarray(a)
b = np.asarray(b)
outaxis = axis
return a, b, outaxis
def compute_stderr(a, axis=0, ddof=1):
a, axis = _chk_asarray(a, axis)
return np.std(a,axis,ddof=1) / float(np.sqrt(a.shape[axis]))
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