def plot_compare(args):
cwd = os.getcwd()
subdir = args.subdir
os.chdir(subdir)
FRETfile = args.trace
FRETr = np.loadtxt(FRETfile)
# Load full experimental transition matrix
TMfile = args.TMfile
T_matrix = np.loadtxt(TMfile)
# Calculate and unflatten transition matrix
tmatrix = tmcalc.get_T_matrix(FRETr,
spacing=args.spacing,
framestep=args.fstep)
if tmcalc.check_matrix(tmatrix):
tmatrix = tmcalc.unflatten_matrix(tmatrix)
# Calculate experimental matrix
bin_size = np.size(tmatrix)**0.5
spacing = 0.1
lower_ran = spacing * (np.floor(10 * np.min(FRETr)))
upper_ran = spacing * (np.ceil(10 * np.max(FRETr)))
ran_size = (lower_ran, upper_ran)
tmatrix_exp = xtm.tmatrix_exp_calc(T_matrix, bin_size, ran_size, spacing)
if tmcalc.check_matrix(tmatrix_exp):
tmatrix_exp = tmcalc.unflatten_matrix(tmatrix_exp)
# Difference matrix
diff_matrix = tmatrix - tmatrix_exp
diff_squared = np.mean(np.abs(diff_matrix))
print "Average absolute difference is: "
print diff_squared
# Generate plots
if "color" in args.plot_type:
ptm.plot_matrix(tmatrix, "Simulated Transition Matrix", 0, 0.5)
ptm.plot_matrix(tmatrix_exp, "Experimental Transition Matrix", 0, 0.5)
ptm.plot_matrix(diff_matrix,
"Transition Probability Differences",
-0.5,
0.5,
diff=True)
if "spy" in args.plot_type:
ptm.spy_matrix(tmatrix, "Non-zero entries, simulated")
ptm.spy_matrix(tmatrix_exp, "Non-zero entries, experimental")
ptm.spy_matrix(diff_matrix, "Non-zero entries, difference")
def plot_single_matrix(args):
cwd = os.getcwd()
subdir = args.subdir
os.chdir(subdir)
FRETfile = args.trace
FRETr = np.loadtxt(FRETfile)
# Calculate transition matrix
tmatrix = tmcalc.get_T_matrix(FRETr,
spacing=args.spacing,
framestep=args.fstep)
# Unflatten matrix if necessary
if tmcalc.check_matrix(tmatrix):
tmatrix = tmcalc.unflatten_matrix(tmatrix)
# Plot matrix
if "color" in args.plot_type:
diff = False
ptm.plot_matrix(tmatrix, "Transition Matrix", 0, 0.5, diff)
if "spy" in args.plot_type:
ptm.spy_matrix(tmatrix, "Non-Zero Transitions")
def plot_compare(args):
cwd = os.getcwd()
subdir = args.subdir
os.chdir(subdir)
FRETfile = args.trace
FRETr = np.loadtxt(FRETfile)
# Load full experimental transition matrix
TMfile = args.TMfile
T_matrix = np.loadtxt(TMfile)
# Calculate and unflatten transition matrix
tmatrix = tmcalc.get_T_matrix(FRETr, spacing=args.spacing, framestep=args.fstep)
if tmcalc.check_matrix(tmatrix):
tmatrix = tmcalc.unflatten_matrix(tmatrix)
# Calculate experimental matrix
bin_size = np.size(tmatrix)**0.5
spacing=0.1
lower_ran = spacing*(np.floor(10*np.min(FRETr)))
upper_ran = spacing*(np.ceil(10*np.max(FRETr)))
ran_size = (lower_ran, upper_ran)
tmatrix_exp = xtm.tmatrix_exp_calc(T_matrix, bin_size, ran_size, spacing)
if tmcalc.check_matrix(tmatrix_exp):
tmatrix_exp = tmcalc.unflatten_matrix(tmatrix_exp)
# Difference matrix
diff_matrix = tmatrix - tmatrix_exp
diff_squared = np.mean(np.abs(diff_matrix))
print "Average absolute difference is: "
print diff_squared
# Generate plots
if "color" in args.plot_type:
ptm.plot_matrix(tmatrix, "Simulated Transition Matrix", 0, 0.5)
ptm.plot_matrix(tmatrix_exp, "Experimental Transition Matrix", 0, 0.5)
ptm.plot_matrix(diff_matrix, "Transition Probability Differences", -0.5, 0.5, diff=True)
if "spy" in args.plot_type:
ptm.spy_matrix(tmatrix, "Non-zero entries, simulated")
ptm.spy_matrix(tmatrix_exp, "Non-zero entries, experimental")
ptm.spy_matrix(diff_matrix, "Non-zero entries, difference")
def plot_double(args):
# Plot two matrices along with a difference matrix
if args.iter != None:
import os
subdir = args.subdir
iter = args.iter
file_location = "%s/iteration_%d" % (subdir, iter)
os.chdir(file_location)
print os.getcwd()
##ASSUMES SIMULATED MATRIX FED FIRST
(sim_file, exp_file) = args.tmatrix
sim_matrix = np.loadtxt(sim_file)
exp_matrix = np.loadtxt(exp_file)
if check_matrix(sim_matrix):
sim_matrix = unflatten_matrix(sim_matrix)
if check_matrix(exp_matrix):
exp_matrix = unflatten_matrix(exp_matrix)
# Subtract matrices to determine difference matrix
diff_matrix = sim_matrix - exp_matrix
##PRINT AVERAGE ABSOLUTE DIFFERENCE
print "Average absolute difference is: "
print np.mean(np.abs(diff_matrix))
if "color" in args.plot_type:
plot_matrix(sim_matrix, "Simulated Transition Matrix", 0, 0.5)
plot_matrix(exp_matrix, "Experimental Transition Matrix", 0, 0.5)
plot_matrix(diff_matrix,
"Transition Probability Differences",
-0.5,
0.5,
diff=True)
if "spy" in args.plot_type:
spy_matrix(sim_matrix, "Non-zero entries, simulated")
spy_matrix(exp_matrix, "Non-zero entries, experimental")
spy_matrix(diff_matrix, "Non-zero entries, difference")
return
def plot_double(args):
# Plot two matrices along with a difference matrix
if args.iter != None:
import os
subdir = args.subdir
iter = args.iter
file_location = "%s/iteration_%d" % (subdir, iter)
os.chdir(file_location)
print os.getcwd()
##ASSUMES SIMULATED MATRIX FED FIRST
(sim_file, exp_file) = args.tmatrix
sim_matrix = np.loadtxt(sim_file)
exp_matrix = np.loadtxt(exp_file)
if check_matrix(sim_matrix):
sim_matrix = unflatten_matrix(sim_matrix)
if check_matrix(exp_matrix):
exp_matrix = unflatten_matrix(exp_matrix)
# Subtract matrices to determine difference matrix
diff_matrix = sim_matrix - exp_matrix
##PRINT AVERAGE ABSOLUTE DIFFERENCE
print "Average absolute difference is: "
print np.mean(np.abs(diff_matrix))
if "color" in args.plot_type:
plot_matrix(sim_matrix, "Simulated Transition Matrix", 0, 0.5)
plot_matrix(exp_matrix, "Experimental Transition Matrix", 0, 0.5)
plot_matrix(diff_matrix, "Transition Probability Differences", -0.5, 0.5, diff=True)
if "spy" in args.plot_type:
spy_matrix(sim_matrix, "Non-zero entries, simulated")
spy_matrix(exp_matrix, "Non-zero entries, experimental")
spy_matrix(diff_matrix, "Non-zero entries, difference")
return
def plot_all(args):
cwd = os.getcwd()
subdir = args.subdir
os.chdir("%s/%s"%(cwd, subdir))
if args.compare:
T_matrix_1 = np.loadtxt(args.files[0])
if check_matrix(T_matrix_1):
T_matrix_1 = unflatten_matrix(T_matrix_1)
bins_1, avg_j_1 = find_avg_transition(T_matrix_1)
T_matrix_2 = np.loadtxt(args.files[1])
if check_matrix(T_matrix_2):
T_matrix_2 = unflatten_matrix(T_matrix_2)
bins_2, avg_j_2 = find_avg_transition(T_matrix_2)
labels = args.labels
plot_compare(bins_1, avg_j_1, bins_2, avg_j_2, labels)
else:
T_matrix = np.loadtxt(args.files[0])
if check_matrix(T_matrix):
T_matrix = unflatten_matrix(T_matrix)
bins, avg_j = find_avg_transition(T_matrix)
plot_single_vec(bins, avg_j)
def plot_difference_matrix(args):
subdir = args.subdir
cwd = os.getcwd()
os.chdir("%s/%s" % (cwd, subdir[0]))
T_matrix_1 = np.loadtxt(args.files[0])
if check_matrix(T_matrix_1):
T_matrix_1 = unflatten_matrix(T_matrix_1)
os.chdir(cwd)
os.chdir("%s/%s" % (cwd, subdir[1]))
T_matrix_2 = np.loadtxt(args.files[1])
if check_matrix(T_matrix_2):
T_matrix_2 = unflatten_matrix(T_matrix_2)
os.chdir(cwd)
c_direc = "%s/tmatrix_compare" % (cwd)
if not os.path.isdir(c_direc):
os.mkdir(c_direc)
os.chdir(c_direc)
diff_matrix = T_matrix_1 - T_matrix_2
if args.iter != None:
iter = args.iter
title = "Transition Differences Iter %d and %d" % (iter[0], iter[1])
else:
title = "Transition Differences"
ptm.plot_matrix(diff_matrix, title, -0.5, 0.5, diff=True)
def plot_difference_matrix(args):
subdir = args.subdir
cwd = os.getcwd()
os.chdir("%s/%s"%(cwd,subdir[0]))
T_matrix_1 = np.loadtxt(args.files[0])
if check_matrix(T_matrix_1):
T_matrix_1 = unflatten_matrix(T_matrix_1)
os.chdir(cwd)
os.chdir("%s/%s"%(cwd,subdir[1]))
T_matrix_2 = np.loadtxt(args.files[1])
if check_matrix(T_matrix_2):
T_matrix_2 = unflatten_matrix(T_matrix_2)
os.chdir(cwd)
c_direc = "%s/tmatrix_compare"%(cwd)
if not os.path.isdir(c_direc):
os.mkdir(c_direc)
os.chdir(c_direc)
diff_matrix = T_matrix_1 - T_matrix_2
if args.iter != None:
iter = args.iter
title = "Transition Differences Iter %d and %d"%(iter[0], iter[1])
else:
title = "Transition Differences"
ptm.plot_matrix(diff_matrix, title, -0.5, 0.5, diff=True)
def plot_single(args):
# Plot a single matrix
matrix_file = args.tmatrix
T_matrix = np.loadtxt(matrix_file)
if check_matrix(T_matrix):
T_matrix = unflatten_matrix(T_matrix)
if "color" in args.plot_type:
plot_matrix(T_matrix, "Transition Matrix", 0, 0.5)
if "spy" in args.plot_type:
spy_matrix(T_matrix, "Non-Zero Transitions")
return
def plot_single(args):
# Plot a single matrix
matrix_file = args.tmatrix
T_matrix = np.loadtxt(matrix_file)
if check_matrix(T_matrix):
T_matrix = unflatten_matrix(T_matrix)
if "color" in args.plot_type:
plot_matrix(T_matrix, "Transition Matrix", 0, 0.5)
if "spy" in args.plot_type:
spy_matrix(T_matrix, "Non-Zero Transitions")
return
def plot_single_matrix(args):
cwd = os.getcwd()
subdir = args.subdir
os.chdir(subdir)
FRETfile = args.trace
FRETr = np.loadtxt(FRETfile)
# Calculate transition matrix
tmatrix = tmcalc.get_T_matrix(FRETr, spacing=args.spacing, framestep=args.fstep)
# Unflatten matrix if necessary
if tmcalc.check_matrix(tmatrix):
tmatrix = tmcalc.unflatten_matrix(tmatrix)
# Plot matrix
if "color" in args.plot_type:
diff = False
ptm.plot_matrix(tmatrix, "Transition Matrix", 0, 0.5, diff)
if "spy" in args.plot_type:
ptm.spy_matrix(tmatrix, "Non-Zero Transitions")
