def write_param_files(global_file=None, kex=1500.0, pA=0.95, set_file=None, dir=None, r1=False, force=False):
"""Create the CATIA parameter files.
@keyword global_file: The name of the global parameter file.
@type global_file: str
@keyword set_file: The name of the parameter set file.
@type set_file: str
@keyword dir: The base directory to place the files into.
@type dir: str
@keyword r1: A flag which if True will cause the R1 data to be used for off-resonance effects.
@type r1: bool
@keyword force: A flag which if True will cause a pre-existing file to be overwritten.
@type force: bool
"""
# Open the global parameter file.
param_file = open_write_file(file_name=global_file, dir=dir, force=force)
# Set the starting values.
param_file.write("kex = %s\n" % kex)
param_file.write("pb = %s\n" % (1.0-pA))
# Close the file.
param_file.close()
# Open the 1st parameter set file.
set_file = open_write_file(file_name=set_file, dir=dir, force=force)
# The parameter format.
params = ['Delta0']
values = [0.5]
if r1:
for frq in loop_frq():
params.append("R1iph_%s" % frq_label(frq))
values.append(1.5)
for frq in loop_frq():
params.append("R0iph_%s" % frq_label(frq))
values.append(5.0)
if r1:
params.append("Omega")
values.append(0.0)
# Write out the format.
set_file.write("format = (")
for i in range(len(params)):
if i != 0:
set_file.write(';')
set_file.write(params[i])
set_file.write(")\n")
# Um?!? The average values maybe?
set_file.write("* = (")
for i in range(len(values)):
if i != 0:
set_file.write(';')
set_file.write("%s" % values[i])
set_file.write(")\n")
# Close the file.
set_file.close()
def back_calc_r2eff(spins=None, spin_ids=None, cpmg_frqs=None, spin_lock_offset=None, spin_lock_nu1=None, relax_times_new=None, store_chi2=False):
"""Back-calculation of R2eff/R1rho values for the given spin.
@keyword spins: The list of specific spin data container for cluster.
@type spins: List of SpinContainer instances
@keyword spin_ids: The list of spin ID strings for the spin containers in cluster.
@type spin_ids: list of str
@keyword cpmg_frqs: The CPMG frequencies to use instead of the user loaded values - to enable interpolation.
@type cpmg_frqs: list of lists of numpy rank-1 float arrays
@keyword spin_lock_offset: The spin-lock offsets to use instead of the user loaded values - to enable interpolation.
@type spin_lock_offset: list of lists of numpy rank-1 float arrays
@keyword spin_lock_nu1: The spin-lock field strengths to use instead of the user loaded values - to enable interpolation.
@type spin_lock_nu1: list of lists of numpy rank-1 float arrays
@keyword relax_times_new: The interpolated experiment specific fixed time period for relaxation (in seconds). The dimensions are {Ei, Mi, Oi, Di, Ti}.
@type relax_times_new: rank-4 list of floats
@keyword store_chi2: A flag which if True will cause the spin specific chi-squared value to be stored in the spin container.
@type store_chi2: bool
@return: The back-calculated R2eff/R1rho value for the given spin.
@rtype: numpy rank-1 float array
"""
# Create the initial parameter vector.
param_vector = assemble_param_vector(spins=spins)
# Number of spectrometer fields.
fields = [None]
field_count = 1
if hasattr(cdp, 'spectrometer_frq_count'):
fields = cdp.spectrometer_frq_list
field_count = cdp.spectrometer_frq_count
# Initialise the data structures for the target function.
values, errors, missing, frqs, frqs_H, exp_types, relax_times = return_r2eff_arrays(spins=spins, spin_ids=spin_ids, fields=fields, field_count=field_count)
# The offset and R1 data.
r1_setup()
offsets, spin_lock_fields_inter, chemical_shifts, tilt_angles, Delta_omega, w_eff = return_offset_data(spins=spins, spin_ids=spin_ids, field_count=field_count, spin_lock_offset=spin_lock_offset, fields=spin_lock_nu1)
r1 = return_r1_data(spins=spins, spin_ids=spin_ids, field_count=field_count)
r1_fit = is_r1_optimised(spins[0].model)
# The relaxation times.
if relax_times_new != None:
relax_times = relax_times_new
# The dispersion data.
recalc_tau = True
if cpmg_frqs == None and spin_lock_nu1 == None and spin_lock_offset == None:
cpmg_frqs = return_cpmg_frqs(ref_flag=False)
spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
# Reset the cpmg_frqs if interpolating R1rho models.
elif cpmg_frqs == None and spin_lock_offset != None:
cpmg_frqs = None
spin_lock_nu1 = spin_lock_fields_inter
recalc_tau = False
values = []
errors = []
missing = []
for exp_type, ei in loop_exp(return_indices=True):
values.append([])
errors.append([])
missing.append([])
for si in range(len(spins)):
values[ei].append([])
errors[ei].append([])
missing[ei].append([])
for frq, mi in loop_frq(return_indices=True):
values[ei][si].append([])
errors[ei][si].append([])
missing[ei][si].append([])
for oi, offset in enumerate(offsets[ei][si][mi]):
num = len(spin_lock_nu1[ei][mi][oi])
values[ei][si][mi].append(zeros(num, float64))
errors[ei][si][mi].append(ones(num, float64))
missing[ei][si][mi].append(zeros(num, int32))
# Reconstruct the structures for interpolation.
else:
recalc_tau = False
values = []
errors = []
missing = []
for exp_type, ei in loop_exp(return_indices=True):
values.append([])
errors.append([])
missing.append([])
for si in range(len(spins)):
values[ei].append([])
errors[ei].append([])
missing[ei].append([])
for frq, mi in loop_frq(return_indices=True):
values[ei][si].append([])
errors[ei][si].append([])
missing[ei][si].append([])
for offset, oi in loop_offset(exp_type=exp_type, frq=frq, return_indices=True):
if exp_type in EXP_TYPE_LIST_CPMG:
num = len(cpmg_frqs[ei][mi][oi])
else:
num = len(spin_lock_nu1[ei][mi][oi])
values[ei][si][mi].append(zeros(num, float64))
errors[ei][si][mi].append(ones(num, float64))
missing[ei][si][mi].append(zeros(num, int32))
# Initialise the relaxation dispersion fit functions.
model = Dispersion(model=spins[0].model, num_params=param_num(spins=spins), num_spins=len(spins), num_frq=field_count, exp_types=exp_types, values=values, errors=errors, missing=missing, frqs=frqs, frqs_H=frqs_H, cpmg_frqs=cpmg_frqs, spin_lock_nu1=spin_lock_nu1, chemical_shifts=chemical_shifts, offset=offsets, tilt_angles=tilt_angles, r1=r1, relax_times=relax_times, recalc_tau=recalc_tau, r1_fit=r1_fit)
# Make a single function call. This will cause back calculation and the data will be stored in the class instance.
chi2 = model.func(param_vector)
# Store the chi-squared value.
if store_chi2:
for spin in spins:
spin.chi2 = chi2
# Return the structure.
return model.get_back_calc()
def back_calc_r2eff(spins=None, spin_ids=None, cpmg_frqs=None, spin_lock_offset=None, spin_lock_nu1=None, relax_times_new=None, store_chi2=False):
"""Back-calculation of R2eff/R1rho values for the given spin.
@keyword spins: The list of specific spin data container for cluster.
@type spins: List of SpinContainer instances
@keyword spin_ids: The list of spin ID strings for the spin containers in cluster.
@type spin_ids: list of str
@keyword cpmg_frqs: The CPMG frequencies to use instead of the user loaded values - to enable interpolation.
@type cpmg_frqs: list of lists of numpy rank-1 float arrays
@keyword spin_lock_offset: The spin-lock offsets to use instead of the user loaded values - to enable interpolation.
@type spin_lock_offset: list of lists of numpy rank-1 float arrays
@keyword spin_lock_nu1: The spin-lock field strengths to use instead of the user loaded values - to enable interpolation.
@type spin_lock_nu1: list of lists of numpy rank-1 float arrays
@keyword relax_times_new: The interpolated experiment specific fixed time period for relaxation (in seconds). The dimensions are {Ei, Mi, Oi, Di, Ti}.
@type relax_times_new: rank-4 list of floats
@keyword store_chi2: A flag which if True will cause the spin specific chi-squared value to be stored in the spin container.
@type store_chi2: bool
@return: The back-calculated R2eff/R1rho value for the given spin.
@rtype: numpy rank-1 float array
"""
# Create the initial parameter vector.
param_vector = assemble_param_vector(spins=spins)
# Number of spectrometer fields.
fields = [None]
field_count = 1
if hasattr(cdp, 'spectrometer_frq_count'):
fields = cdp.spectrometer_frq_list
field_count = cdp.spectrometer_frq_count
# Initialise the data structures for the target function.
values, errors, missing, frqs, frqs_H, exp_types, relax_times = return_r2eff_arrays(spins=spins, spin_ids=spin_ids, fields=fields, field_count=field_count)
# The offset and R1 data.
r1_setup()
offsets, spin_lock_fields_inter, chemical_shifts, tilt_angles, Delta_omega, w_eff = return_offset_data(spins=spins, spin_ids=spin_ids, field_count=field_count, spin_lock_offset=spin_lock_offset, fields=spin_lock_nu1)
r1 = return_r1_data(spins=spins, spin_ids=spin_ids, field_count=field_count)
r1_fit = is_r1_optimised(spins[0].model)
# The relaxation times.
if relax_times_new != None:
relax_times = relax_times_new
# The dispersion data.
recalc_tau = True
if cpmg_frqs == None and spin_lock_nu1 == None and spin_lock_offset == None:
cpmg_frqs = return_cpmg_frqs(ref_flag=False)
spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
# Reset the cpmg_frqs if interpolating R1rho models.
elif cpmg_frqs == None and spin_lock_offset != None:
cpmg_frqs = None
spin_lock_nu1 = spin_lock_fields_inter
recalc_tau = False
values = []
errors = []
missing = []
for exp_type, ei in loop_exp(return_indices=True):
values.append([])
errors.append([])
missing.append([])
for si in range(len(spins)):
values[ei].append([])
errors[ei].append([])
missing[ei].append([])
for frq, mi in loop_frq(return_indices=True):
values[ei][si].append([])
errors[ei][si].append([])
missing[ei][si].append([])
for oi, offset in enumerate(offsets[ei][si][mi]):
num = len(spin_lock_nu1[ei][mi][oi])
values[ei][si][mi].append(zeros(num, float64))
errors[ei][si][mi].append(ones(num, float64))
missing[ei][si][mi].append(zeros(num, int32))
# Reconstruct the structures for interpolation.
else:
recalc_tau = False
values = []
errors = []
missing = []
for exp_type, ei in loop_exp(return_indices=True):
values.append([])
errors.append([])
missing.append([])
for si in range(len(spins)):
values[ei].append([])
errors[ei].append([])
missing[ei].append([])
for frq, mi in loop_frq(return_indices=True):
values[ei][si].append([])
errors[ei][si].append([])
missing[ei][si].append([])
for offset, oi in loop_offset(exp_type=exp_type, frq=frq, return_indices=True):
if exp_type in EXP_TYPE_LIST_CPMG:
num = len(cpmg_frqs[ei][mi][oi])
else:
num = len(spin_lock_nu1[ei][mi][oi])
values[ei][si][mi].append(zeros(num, float64))
errors[ei][si][mi].append(ones(num, float64))
missing[ei][si][mi].append(zeros(num, int32))
# Initialise the relaxation dispersion fit functions.
model = Dispersion(model=spins[0].model, num_params=param_num(spins=spins), num_spins=len(spins), num_frq=field_count, exp_types=exp_types, values=values, errors=errors, missing=missing, frqs=frqs, frqs_H=frqs_H, cpmg_frqs=cpmg_frqs, spin_lock_nu1=spin_lock_nu1, chemical_shifts=chemical_shifts, offset=offsets, tilt_angles=tilt_angles, r1=r1, relax_times=relax_times, recalc_tau=recalc_tau, r1_fit=r1_fit)
# Make a single function call. This will cause back calculation and the data will be stored in the class instance.
chi2 = model.func(param_vector)
# Store the chi-squared value.
if store_chi2:
for spin in spins:
spin.chi2 = chi2
# Return the structure.
return model.get_back_calc()
def write_r2eff_files(input_dir=None, base_dir=None, force=False):
"""Create the CATIA R2eff input files.
@keyword input_dir: The special directory for the R2eff input files.
@type input_dir: str
@keyword base_dir: The base directory to place the files into.
@type base_dir: str
@keyword force: A flag which if True will cause a pre-existing file to be overwritten.
@type force: bool
"""
# Create the directory for the R2eff files for each field and spin.
dir = base_dir + sep + input_dir
mkdir_nofail(dir, verbosity=0)
# Determine the isotope information.
isotope = None
for spin in spin_loop(skip_desel=True):
if hasattr(spin, 'isotope'):
if isotope == None:
isotope = spin.isotope
elif spin.isotope != isotope:
raise RelaxError("CATIA only supports one spin type.")
if isotope == None:
raise RelaxError("The spin isotopes have not been specified.")
# Isotope translation.
if isotope == '1H':
isotope = 'H1'
elif isotope == '13C':
isotope = 'C13'
elif isotope == '15N':
isotope = 'N15'
# Loop over the frequencies.
for frq, mi in loop_frq(return_indices=True):
# The frequency string in MHz.
frq_string = int(frq * 1e-6)
# The set files.
file_name = "data_set_%i.inp" % frq_string
set_file = open_write_file(file_name=file_name,
dir=base_dir,
force=force)
id = frq_string
set_file.write("ID=%s\n" % id)
set_file.write("Sfrq = %s\n" % frq_string)
set_file.write("Temperature = %s\n" % 0.0)
set_file.write("Nucleus = %s\n" % isotope)
set_file.write("Couplednucleus = %s\n" % 'H1')
set_file.write("Time_equil = %s\n" % 0.0)
set_file.write("Pwx_cp = %s\n" % 0.0)
set_file.write("Taub = %s\n" % 0.0)
set_file.write("Time_T2 = %s\n" % cdp.relax_time_list[0])
set_file.write("Xcar = %s\n" % 0.0)
set_file.write("Seqfil = %s\n" % 'CW_CPMG')
set_file.write("Minerror = %s\n" % "(2.%;0.5/s)")
set_file.write("Basis = (%s)\n" % "Iph_7")
set_file.write("Format = (%i;%i;%i)\n" % (0, 1, 2))
set_file.write("DataDirectory = %s\n" % (dir + sep))
set_file.write("Data = (\n")
# Loop over the spins.
for spin, mol_name, res_num, res_name, spin_id in spin_loop(
full_info=True, return_id=True, skip_desel=True):
# The file.
file_name = "spin%s_%i.cpmg" % (spin_id.replace('#', '_').replace(
':', '_').replace('@', '_'), frq_string)
spin_file = open_write_file(file_name=file_name,
dir=dir,
force=force)
# Write the header.
spin_file.write("# %18s %20s %20s\n" %
("nu_cpmg(Hz)", "R2(1/s)", "Esd(R2)"))
# Loop over the dispersion points.
for offset, point, oi, di in loop_offset_point(
exp_type=EXP_TYPE_CPMG_SQ, frq=frq, return_indices=True):
# The key.
key = return_param_key_from_data(exp_type=EXP_TYPE_CPMG_SQ,
frq=frq,
offset=offset,
point=point)
# No data.
if key not in spin.r2eff:
continue
# Write out the data.
spin_file.write("%20.15f %20.15f %20.15f\n" %
(point, spin.r2eff[key], spin.r2eff_err[key]))
# Close the file.
spin_file.close()
# Add the file name to the set.
catia_spin_id = "%i%s" % (res_num, spin.name)
set_file.write(" [%s;%s];\n" % (catia_spin_id, file_name))
# Terminate the set file.
set_file.write(")\n")
set_file.close()
def write_param_files(global_file=None,
kex=1500.0,
pA=0.95,
set_file=None,
dir=None,
r1=False,
force=False):
"""Create the CATIA parameter files.
@keyword global_file: The name of the global parameter file.
@type global_file: str
@keyword set_file: The name of the parameter set file.
@type set_file: str
@keyword dir: The base directory to place the files into.
@type dir: str
@keyword r1: A flag which if True will cause the R1 data to be used for off-resonance effects.
@type r1: bool
@keyword force: A flag which if True will cause a pre-existing file to be overwritten.
@type force: bool
"""
# Open the global parameter file.
param_file = open_write_file(file_name=global_file, dir=dir, force=force)
# Set the starting values.
param_file.write("kex = %s\n" % kex)
param_file.write("pb = %s\n" % (1.0 - pA))
# Close the file.
param_file.close()
# Open the 1st parameter set file.
set_file = open_write_file(file_name=set_file, dir=dir, force=force)
# The parameter format.
params = ['Delta0']
values = [0.5]
if r1:
for frq in loop_frq():
params.append("R1iph_%s" % frq_label(frq))
values.append(1.5)
for frq in loop_frq():
params.append("R0iph_%s" % frq_label(frq))
values.append(5.0)
if r1:
params.append("Omega")
values.append(0.0)
# Write out the format.
set_file.write("format = (")
for i in range(len(params)):
if i != 0:
set_file.write(';')
set_file.write(params[i])
set_file.write(")\n")
# Um?!? The average values maybe?
set_file.write("* = (")
for i in range(len(values)):
if i != 0:
set_file.write(';')
set_file.write("%s" % values[i])
set_file.write(")\n")
# Close the file.
set_file.close()
def write_main_file(file=None,
dir=None,
output_dir=None,
f_tol=1e-25,
max_iter=10000000,
r1=False,
force=False):
"""Create the main CATIA execution file.
@keyword file: The main CATIA execution file.
@type file: str
@keyword dir: The directory to place the files into.
@type dir: str or None
@keyword output_dir: The CATIA output directory, located within the directory specified by the dir argument. This directory will be created.
@type output_dir: str
@keyword r1: A flag which if True will cause the R1 data to be used for off-resonance effects.
@type r1: bool
@keyword force: A flag which if True will cause a pre-existing file to be overwritten.
@type force: bool
"""
# The file.
catia_in = open_write_file(file_name=file, dir=dir, force=force)
# The R2eff input sets.
for frq in loop_frq():
frq_label = int(frq * 1e-6)
file_name = "data_set_%i.inp" % frq_label
catia_in.write("ReadDataset(%s)\n" % file_name)
# Write out the data.
catia_in.write("ReadParam_Global(ParamGlobal.inp)\n")
catia_in.write("ReadParam_Local(ParamSet1.inp)\n")
catia_in.write("\n")
# The R1 data for off-resonance effects.
if r1:
catia_in.write("ReadParam(Omega;%s;0;1)\n" % shift_file)
for frq in loop_frq():
frq_label = int(frq * 1e-6)
param = "R1iph_%s" % frq_label
r1_file = "R1_%s.out" % frq_label
catia_in.write("ReadParam(%s;%s;0;1)\n" % (param, r1_file))
catia_in.write("\n")
# Fix these off-resonance parameters.
catia_in.write("FreeLocalParam(all;Omega;false)\n")
for frq in loop_frq():
frq_label = int(frq * 1e-6)
param = "R1iph_%s" % frq_label
catia_in.write("FreeLocalParam(all;%s;false)\n" % param)
catia_in.write("\n")
# Minimisation.
catia_in.write("Minimize(print=y;tol=%s;maxiter=%i)\n" % (f_tol, max_iter))
catia_in.write("\n")
# Plotting.
catia_in.write("PrintParam(%s/GlobalParam.fit;global)\n" % output_dir)
catia_in.write("PrintParam(%s/DeltaOmega.fit;DeltaO)\n" % output_dir)
catia_in.write("PrintData(%s/)\n" % output_dir)
catia_in.write("\n")
# Calculate the chi-squared value (not sure why, it's calculated in the minimisation).
catia_in.write("ChiSq(all;all)\n")
# Exit the program.
catia_in.write("exit(0)\n")
# Close the file.
catia_in.close()
def write_r2eff_files(input_dir=None, base_dir=None, force=False):
"""Create the CATIA R2eff input files.
@keyword input_dir: The special directory for the R2eff input files.
@type input_dir: str
@keyword base_dir: The base directory to place the files into.
@type base_dir: str
@keyword force: A flag which if True will cause a pre-existing file to be overwritten.
@type force: bool
"""
# Create the directory for the R2eff files for each field and spin.
dir = base_dir + sep + input_dir
mkdir_nofail(dir, verbosity=0)
# Determine the isotope information.
isotope = None
for spin in spin_loop(skip_desel=True):
if hasattr(spin, 'isotope'):
if isotope == None:
isotope = spin.isotope
elif spin.isotope != isotope:
raise RelaxError("CATIA only supports one spin type.")
if isotope == None:
raise RelaxError("The spin isotopes have not been specified.")
# Isotope translation.
if isotope == '1H':
isotope = 'H1'
elif isotope == '13C':
isotope = 'C13'
elif isotope == '15N':
isotope = 'N15'
# Loop over the frequencies.
for frq, mi in loop_frq(return_indices=True):
# The frequency string in MHz.
frq_string = int(frq*1e-6)
# The set files.
file_name = "data_set_%i.inp" % frq_string
set_file = open_write_file(file_name=file_name, dir=base_dir, force=force)
id = frq_string
set_file.write("ID=%s\n" % id)
set_file.write("Sfrq = %s\n" % frq_string)
set_file.write("Temperature = %s\n" % 0.0)
set_file.write("Nucleus = %s\n" % isotope)
set_file.write("Couplednucleus = %s\n" % 'H1')
set_file.write("Time_equil = %s\n" % 0.0)
set_file.write("Pwx_cp = %s\n" % 0.0)
set_file.write("Taub = %s\n" % 0.0)
set_file.write("Time_T2 = %s\n"% cdp.relax_time_list[0])
set_file.write("Xcar = %s\n" % 0.0)
set_file.write("Seqfil = %s\n" % 'CW_CPMG')
set_file.write("Minerror = %s\n" % "(2.%;0.5/s)")
set_file.write("Basis = (%s)\n" % "Iph_7")
set_file.write("Format = (%i;%i;%i)\n" % (0, 1, 2))
set_file.write("DataDirectory = %s\n" % (dir+sep))
set_file.write("Data = (\n")
# Loop over the spins.
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
# The file.
file_name = "spin%s_%i.cpmg" % (spin_id.replace('#', '_').replace(':', '_').replace('@', '_'), frq_string)
spin_file = open_write_file(file_name=file_name, dir=dir, force=force)
# Write the header.
spin_file.write("# %18s %20s %20s\n" % ("nu_cpmg(Hz)", "R2(1/s)", "Esd(R2)"))
# Loop over the dispersion points.
for offset, point, oi, di in loop_offset_point(exp_type=EXP_TYPE_CPMG_SQ, frq=frq, return_indices=True):
# The key.
key = return_param_key_from_data(exp_type=EXP_TYPE_CPMG_SQ, frq=frq, offset=offset, point=point)
# No data.
if key not in spin.r2eff:
continue
# Write out the data.
spin_file.write("%20.15f %20.15f %20.15f\n" % (point, spin.r2eff[key], spin.r2eff_err[key]))
# Close the file.
spin_file.close()
# Add the file name to the set.
catia_spin_id = "%i%s" % (res_num, spin.name)
set_file.write(" [%s;%s];\n" % (catia_spin_id, file_name))
# Terminate the set file.
set_file.write(")\n")
set_file.close()
def write_main_file(file=None, dir=None, output_dir=None, f_tol=1e-25, max_iter=10000000, r1=False, force=False):
"""Create the main CATIA execution file.
@keyword file: The main CATIA execution file.
@type file: str
@keyword dir: The directory to place the files into.
@type dir: str or None
@keyword output_dir: The CATIA output directory, located within the directory specified by the dir argument. This directory will be created.
@type output_dir: str
@keyword r1: A flag which if True will cause the R1 data to be used for off-resonance effects.
@type r1: bool
@keyword force: A flag which if True will cause a pre-existing file to be overwritten.
@type force: bool
"""
# The file.
catia_in = open_write_file(file_name=file, dir=dir, force=force)
# The R2eff input sets.
for frq in loop_frq():
frq_label = int(frq*1e-6)
file_name = "data_set_%i.inp" % frq_label
catia_in.write("ReadDataset(%s)\n" % file_name)
# Write out the data.
catia_in.write("ReadParam_Global(ParamGlobal.inp)\n")
catia_in.write("ReadParam_Local(ParamSet1.inp)\n")
catia_in.write("\n")
# The R1 data for off-resonance effects.
if r1:
catia_in.write("ReadParam(Omega;%s;0;1)\n" % shift_file)
for frq in loop_frq():
frq_label = int(frq*1e-6)
param = "R1iph_%s" % frq_label
r1_file = "R1_%s.out" % frq_label
catia_in.write("ReadParam(%s;%s;0;1)\n" % (param, r1_file))
catia_in.write("\n")
# Fix these off-resonance parameters.
catia_in.write("FreeLocalParam(all;Omega;false)\n")
for frq in loop_frq():
frq_label = int(frq*1e-6)
param = "R1iph_%s" % frq_label
catia_in.write("FreeLocalParam(all;%s;false)\n" % param)
catia_in.write("\n")
# Minimisation.
catia_in.write("Minimize(print=y;tol=%s;maxiter=%i)\n" % (f_tol, max_iter))
catia_in.write("\n")
# Plotting.
catia_in.write("PrintParam(%s/GlobalParam.fit;global)\n" % output_dir)
catia_in.write("PrintParam(%s/DeltaOmega.fit;DeltaO)\n" % output_dir)
catia_in.write("PrintData(%s/)\n" % output_dir)
catia_in.write("\n")
# Calculate the chi-squared value (not sure why, it's calculated in the minimisation).
catia_in.write("ChiSq(all;all)\n")
# Exit the program.
catia_in.write("exit(0)\n")
# Close the file.
catia_in.close()
