Author: bugman
Date: Fri May 24 17:39:43 2013
New Revision: 19738
URL: http://svn.gna.org/viewcvs/relax?rev=19738&view=rev
Log:
The relaxation dispersion specific code now uses the changes of the
spectrometer.frequency user function.
This simplifies the handling of magnetic field strength data.
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19738&r1=19737&r2=19738&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Fri May 24
17:39:43 2013
@@ -120,19 +120,11 @@
# Create a scaling matrix.
scaling_matrix = assemble_scaling_matrix(spins=[spin], scaling=False)
- # The number of spectrometer field strengths.
- field_count = 1
- fields = []
- if hasattr(cdp, 'frq'):
- fields = unique_elements(cdp.frq.values())
- fields.sort()
- field_count = len(fields)
-
# Initialise the data structures for the target function.
- values, errors, missing = return_r2eff_arrays(spins=[spin],
spin_ids=[spin_id], fields=fields, field_count=field_count)
+ values, errors, missing = return_r2eff_arrays(spins=[spin],
spin_ids=[spin_id], fields=cdp.spectrometer_frq_list,
field_count=cdp.spectrometer_frq_count)
# Initialise the relaxation dispersion fit functions.
- model = Dispersion(model=cdp.model,
num_params=param_num(spins=[spin]), num_spins=1, num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
missing=missing, frqs=fields, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
+ model = Dispersion(model=cdp.model,
num_params=param_num(spins=[spin]), num_spins=1,
num_frq=cdp.spectrometer_frq_count, num_disp_points=cdp.dispersion_points,
values=values, errors=errors, missing=missing,
frqs=cdp.spectrometer_frq_list, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
# Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
model.func(param_vector)
@@ -1014,14 +1006,6 @@
# Exit the method.
return
- # The number of spectrometer field strengths.
- field_count = 1
- fields = []
- if hasattr(cdp, 'frq'):
- fields = unique_elements(cdp.frq.values())
- fields.sort()
- field_count = len(fields)
-
# The number of time points for the exponential curves (if present).
num_time_pts = 1
if hasattr(cdp, 'num_time_pts'):
@@ -1030,7 +1014,7 @@
# Loop over the spin blocks.
for spins, spin_ids in self.model_loop():
# The R2eff/R1rho data.
- values, errors, missing = return_r2eff_arrays(spins=spins,
spin_ids=spin_ids, fields=fields, field_count=field_count)
+ values, errors, missing = return_r2eff_arrays(spins=spins,
spin_ids=spin_ids, fields=cdp.spectrometer_frq_list,
field_count=cdp.spectrometer_frq_count)
# Create the initial parameter vector.
param_vector = assemble_param_vector(spins=spins)
@@ -1063,7 +1047,7 @@
print("Unconstrained grid search size: %s (constraints
may decrease this size).\n" % grid_size)
# Initialise the function to minimise.
- model = Dispersion(model=cdp.model,
num_params=param_num(spins=spins), num_spins=len(spins), num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
missing=missing, frqs=fields, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
+ model = Dispersion(model=cdp.model,
num_params=param_num(spins=spins), num_spins=len(spins),
num_frq=cdp.spectrometer_frq_count, num_disp_points=cdp.dispersion_points,
values=values, errors=errors, missing=missing,
frqs=cdp.spectrometer_frq_list, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
# Grid search.
if search('^[Gg]rid', min_algor):
Modified: branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py?rev=19738&r1=19737&r2=19738&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py Fri May 24
17:39:43 2013
@@ -190,12 +190,7 @@
file.write("title %s\n" % spin_id)
# The proton frequencies.
- frq = get_frequencies()
-
- # Loop over each frequency.
- for i in range(len(frq)):
- # Convert to Tesla.
- frq[i] = frq[i] * 2.0 * pi / g1H
+ frq = get_frequencies(units='T')
# The frequency info.
file.write("fields %s" % len(frq))
@@ -234,7 +229,6 @@
continue
# Tesla units.
- print frq
B0 = frq * 2.0 * pi / g1H
# Write out the data and error.
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=19738&r1=19737&r2=19738&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Fri May 24
17:39:43 2013
@@ -157,8 +157,8 @@
for id in cdp.spectrum_ids:
# The spectrometer frequency.
frq2 = None
- if hasattr(cdp, 'frq'):
- frq2 = cdp.frq[id]
+ if hasattr(cdp, 'spectrometer_frq'):
+ frq2 = cdp.spectrometer_frq[id]
if frq2 == frq and disp_data[id] == point and cdp.relax_times[id] ==
time:
ids.append(id)
@@ -178,16 +178,8 @@
@rtype: float
"""
- # The number of spectrometer field strengths.
- field_count = 1
- fields = [None]
- if hasattr(cdp, 'frq'):
- field_count = count_unique_elements(cdp.frq.values())
- fields = unique_elements(cdp.frq.values())
- fields.sort()
-
# Yield each unique spectrometer field strength.
- for field in fields:
+ for field in cdp.spectrometer_frq_list:
yield field
@@ -370,17 +362,8 @@
@rtype: int
"""
- # Initialise.
- index = 0
-
- # Find the index if the frequency has been set.
- if hasattr(cdp, 'frq'):
- fields = unique_elements(cdp.frq.values())
- fields.sort()
- index = fields.index(value)
-
# Return the index.
- return index
+ return cdp.spectrometer_frq_list.index(value)
def return_index_from_disp_point_key(key):
@@ -597,15 +580,11 @@
"""
# No data.
- if not hasattr(cdp, 'frq'):
+ if not hasattr(cdp, 'spectrometer_frq'):
return None
- # The number of spectrometer field strengths.
- fields = unique_elements(cdp.frq.values())
- fields.sort()
-
# Return the field.
- return fields[frq_index]
+ return cdp.spectrometer_frq[frq_index]
def spin_lock_field(spectrum_id=None, field=None):
r19738 - in /branches/relax_disp/specific_analyses/relax_disp: __init__.py cpmgfit.py disp_data.py