def add_sample_space(self, samples):
"Adds space for n samples, where n can also be negative (deletes space). New space is filled up with \"0\""
if not self.cont_data:
print "Warning ADC-Result: Tried to resize empty array!"
return
length = len(self.y[0])
self.x = numarray.resize(self.x, (length+samples))
for i in range(self.get_number_of_channels()):
self.y[i] = numarray.resize(self.y[i], (length+samples))
self.index.append((length, len(self.y[0])-1))
def notes_roc(la, lb, eps):
from numarray import transpose, add, resize
""" creates a matrix of size len(la)*len(lb) then look for hit and miss
in it within eps tolerance windows """
gdn, fpw, fpg, fpa, fdo, fdp = 0, 0, 0, 0, 0, 0
m = len(la)
n = len(lb)
x = resize(la[:][0], (n, m))
y = transpose(resize(lb[:][0], (m, n)))
teps = (abs(x - y) <= eps[0])
x = resize(la[:][1], (n, m))
y = transpose(resize(lb[:][1], (m, n)))
tpitc = (abs(x - y) <= eps[1])
res = teps * tpitc
res = add.reduce(res, axis=0)
for i in range(len(res)):
if res[i] > 1:
gdn += 1
fdo += res[i] - 1
elif res[i] == 1:
gdn += 1
fpa = n - gdn - fpa
return gdn, fpw, fpg, fpa, fdo, fdp
def notes_roc (la, lb, eps):
from numarray import transpose, add, resize
""" creates a matrix of size len(la)*len(lb) then look for hit and miss
in it within eps tolerance windows """
gdn,fpw,fpg,fpa,fdo,fdp = 0,0,0,0,0,0
m = len(la)
n = len(lb)
x = resize(la[:][0],(n,m))
y = transpose(resize(lb[:][0],(m,n)))
teps = (abs(x-y) <= eps[0])
x = resize(la[:][1],(n,m))
y = transpose(resize(lb[:][1],(m,n)))
tpitc = (abs(x-y) <= eps[1])
res = teps * tpitc
res = add.reduce(res,axis=0)
for i in range(len(res)) :
if res[i] > 1:
gdn+=1
fdo+=res[i]-1
elif res [i] == 1:
gdn+=1
fpa = n - gdn - fpa
return gdn,fpw,fpg,fpa,fdo,fdp
def normalize(self, dim=-1):
""" If dim=-1 all elements sum to 1. Otherwise sum to specific dimension, such that
sum(Pr(x=i|Pa(x))) = 1 for all values of i and a specific set of values for Pa(x)
"""
if dim == -1 or len(self.cpt.shape) == 1:
self.cpt /= self.cpt.sum()
else:
ndim = self.assocdim[dim]
order = range(len(self.names_list))
order[0] = ndim
order[ndim] = 0
tcpt = na.transpose(self.cpt, order)
t1cpt = na.sum(tcpt, axis=0)
t1cpt = na.resize(t1cpt,tcpt.shape)
tcpt = tcpt/t1cpt
self.cpt = na.transpose(tcpt, order)
def file2matrix(fileName):
"""
Given a file "fileName", this script converts the contents of the
file to a numarray matrix of size (m,) or (m,n).
"""
# Open the file
open1 = open(fileName, 'r')
line = open1.readline()
# A single line from the file is read. This should be the number
# of columns. Spliting "line" results in a list, the length of
# which is the number of columns: cols
cols = len(line.split())
# x is the placeholder for the data.
# The placeholder matrix is made of concatenating
# every line that is read from the file.
# The type code is float.
x = numarray.zeros(cols, type='f')
while (line):
temp = []
list_elements = line.split()
for e in list_elements:
temp.append(float(e))
x = numarray.concatenate((x, numarray.array(temp)))
line = open1.readline()
open1.close()
# concatenate((x,x)) is along the dimension 1,
# each new addition is an increase in columns,
# the total length of x gives m*n. We determine
# the rows as
rows = len(x) / cols
# We have added an aritifical row, so if row == 2
# the file has tuple, hence the data consists of
# everything after our artificial set of columns
if rows == 2:
return x[cols:]
else:
# If there are m+1 rows, we resize the data to (m+1)xn
# and return everything other than the artificial first
# row of zeros
x = numarray.resize(x, (rows, cols))
return x[1:, :]
def __init__(self, baseAddr, size = None, endAddr = None, openTime = None):
if self.vertices is None:
self.__class__.vertices = numarray.resize(0.0,(4,3))
self.order = self.newOrder()
if openTime is None:
self.openTime = time()
else:
self.openTime = openTime
self.closeTime = None
self.baseAddr = baseAddr
if size is None:
if endAddr is None:
raise Exception, 'Either size or endAddr must have a value'
else:
self.endAddr = endAddr
else:
self.endAddr = baseAddr + size
def GetPHTitration(prefix):
from numarray import resize, array
inputfile = "%s%s" % (prefix,'.sinout')
outputfile = "%s%s" % (prefix,'.pHtitr')
f = open(inputfile)
all_lines = f.readlines()
f.close()
IS = []; pH = []
for line_counter, line in enumerate(all_lines):
if line[0:12] == 'IONIC. STRN.':
i = 1
current_line = all_lines[line_counter + i ]
while current_line != '\n':
IS.append("%5.3F" % float(current_line[2:13]))
i += 1
current_line = all_lines[line_counter + i]
if line[0:19] == ' IONIC STRN.':
number_IS = len(IS)
j = 4; number_pH = 0
current_line = all_lines[line_counter + j]
while current_line != '\n':
pH.append("%5.2F" % float(current_line[0:6]))
j += 1
current_line = all_lines[line_counter + j]
number_pH = len(pH)
all_data = resize(array(0.0),[number_IS,number_pH,4])
break
i = 0
for line_counter, line in enumerate(all_lines):
if line[0:19] == ' IONIC STRN.':
j = 4
current_line = all_lines[line_counter + j]
while current_line != '\n':
tmp_H = current_line[36:44]
tmp_q = current_line[44:52]
if tmp_H == ' ****** ': tmp_H = 0
if tmp_q == ' ****** ': tmp_q = 0
all_data[i,j-4,0] = float(tmp_H)
all_data[i,j-4,1] = float(tmp_q)
all_data[i,j-4,2] = float(current_line[54:62])
all_data[i,j-4,3] = float(current_line[63:71])
j += 1
current_line = all_lines[line_counter + j]
i += 1
out = ["%s%s%s" % ('#pH titration of ',prefix,' at IS values:\n')]
for i in range(number_IS):
out.append("%s%s%s" % ('#\t',IS[i],'\n'))
out.append('\tpH\t')
for i in range(number_IS):
out.append("%s%s%s%s" % ('IS',i,'_boundH','\t'))
out.append("%s%s%s%s" % ('IS',i,'_charge','\t'))
out.append("%s%s%s%s" % ('IS',i,'_dGtot','\t'))
out.append("%s%s%s%s" % ('IS',i,'_dGH','\t'))
out.append('\n')
for i in range(number_pH):
out.append("%s%s" % (str(i),'\t'))
out.append("%s%s" % (pH[i],'\t'))
for j in range(number_IS):
for k in range(4):
out.append("%5.3F%s" % (all_data[j,i,k],'\t'))
out.append('\n')
g = open(outputfile,'w')
g.write("".join(out))
g.close()
print outputfile, 'written.'
