def cut_transitions_square(filename, start, end, outfile, count="cut"):
"""Read transitions from file and cut out the piece start->end,
so size NxN with N=end-start, row/col end is not included
counting starts from 0"""
#from mcdiff.reading import read_transition_square, read_transition_header
from mcdiff.tools.functionsextract import write_Tmat_square
dim_trans = guess_dim_transition_square(filename)
header = read_transition_header(filename)
transmatrix = read_transition_square(filename, dim_trans)
#L = end-start+1
if 'edges' in header:
edges = header['edges']
edges = edges[start:end + 1]
else:
edges = None
#count = header['count']
lt = header['lt']
dt = header['dt']
dn = header['dn']
A = transmatrix[start:end, start:end]
assert filename != outfile # do not overwrite
write_Tmat_square(A, outfile, lt, count, edges=edges, dt=dt, dn=dn)
def read_transition(self, filename, reduction=False):
dim_trans = guess_dim_transition_square(filename)
header = read_transition_header(filename)
transmatrix = read_transition_square(filename, dim_trans)
if reduction:
dim_trans, header, transmatrix = reduce_Tmat(
dim_trans, header, transmatrix)
if not self.started: # initialize settings
self.started = True
self.count = header['count']
self.dim_trans = dim_trans
if 'edges' in header:
self.edges = header['edges']
else:
self.edges = np.arange(self.dim_trans + 1.)
else: # assert same settings
assert self.count == header['count']
assert self.dim_trans == dim_trans
if 'edges' in header:
assert (self.edges == header['edges']).all()
self.list_lt.append(header['lt'])
self.list_dt.append(header['dt'])
self.list_dn.append(header['dn'])
self.list_trans.append(transmatrix)
def cyclic_permuation_transitions_square(
filename,
shift,
outfile,
): #count=None):
"""Shift indices periodically
Read transitions from file and cut out the piece [shift:] and paste it behind [:shift],
counting starts from 0"""
#from mcdiff.reading import read_transition_square, read_transition_header
from mcdiff.tools.functionsextract import write_Tmat_square
dim_trans = guess_dim_transition_square(filename)
header = read_transition_header(filename)
transmatrix = read_transition_square(filename, dim_trans)
if 'edges' in header:
edges = header['edges']
else:
edges = None
count = header['count']
lt = header['lt']
dt = header['dt']
dn = header['dn']
n = dim_trans
A = np.zeros(transmatrix.shape, int)
A[:(n - shift), :(n - shift)] = transmatrix[shift:, shift:]
A[(n - shift):, :(n - shift)] = transmatrix[:shift, shift:]
A[:(n - shift), (n - shift):] = transmatrix[shift:, :shift]
A[(n - shift):, (n - shift):] = transmatrix[:shift, :shift]
assert filename != outfile # do not overwrite
write_Tmat_square(A, outfile, lt, count, edges=edges, dt=dt, dn=dn)
def cut_transitions_square(filename,start,end,outfile,count="cut"):
"""Read transitions from file and cut out the piece start->end,
so size NxN with N=end-start, row/col end is not included
counting starts from 0"""
#from mcdiff.reading import read_transition_square, read_transition_header
from mcdiff.tools.functionsextract import write_Tmat_square
dim_trans = guess_dim_transition_square(filename)
header = read_transition_header(filename)
transmatrix = read_transition_square(filename,dim_trans)
#L = end-start+1
if 'edges' in header:
edges = header['edges']
edges = edges[start:end+1]
else:
edges = None
#count = header['count']
lt = header['lt']
dt = header['dt']
dn = header['dn']
A = transmatrix[start:end,start:end]
assert filename != outfile # do not overwrite
write_Tmat_square(A,outfile,lt,count,edges=edges,dt=dt,dn=dn)
def read_transition(self,filename,reduction=False):
dim_trans = guess_dim_transition_square(filename)
header = read_transition_header(filename)
transmatrix = read_transition_square(filename,dim_trans)
if reduction:
dim_trans,header,transmatrix = reduce_Tmat(dim_trans,header,transmatrix)
if not self.started: # initialize settings
self.started = True
self.count = header['count']
self.dim_trans = dim_trans
if 'edges' in header:
self.edges = header['edges']
else:
self.edges = np.arange(self.dim_trans+1.)
else: # assert same settings
assert self.count == header['count']
assert self.dim_trans == dim_trans
if 'edges' in header:
assert (self.edges == header['edges']).all()
self.list_lt.append(header['lt'])
self.list_dt.append(header['dt'])
self.list_dn.append(header['dn'])
self.list_trans.append(transmatrix)
def cyclic_permuation_transitions_square(filename,shift,outfile,): #count=None):
"""Shift indices periodically
Read transitions from file and cut out the piece [shift:] and paste it behind [:shift],
counting starts from 0"""
#from mcdiff.reading import read_transition_square, read_transition_header
from mcdiff.tools.functionsextract import write_Tmat_square
dim_trans = guess_dim_transition_square(filename)
header = read_transition_header(filename)
transmatrix = read_transition_square(filename,dim_trans)
if 'edges' in header:
edges = header['edges']
else:
edges = None
count = header['count']
lt = header['lt']
dt = header['dt']
dn = header['dn']
n = dim_trans
A = np.zeros(transmatrix.shape,int)
A[:(n-shift),:(n-shift)] = transmatrix[shift:,shift:]
A[(n-shift):,:(n-shift)] = transmatrix[:shift,shift:]
A[:(n-shift),(n-shift):] = transmatrix[shift:,:shift]
A[(n-shift):,(n-shift):] = transmatrix[:shift,:shift]
assert filename != outfile # do not overwrite
write_Tmat_square(A,outfile,lt,count,edges=edges,dt=dt,dn=dn)