Author: semor
Date: Wed Jan 9 19:20:33 2008
New Revision: 4575
URL: http://svn.gna.org/viewcvs/relax?rev=4575&view=rev
Log:
Changed almost all instances of the 'print_flag' arg to 'verbosity' in the
specific_fns directory.
Exceptions were made for instances in generic_minimise() functions where
'print_flag=print_flag'
becomes 'print_flag=verbosity'.
This was pointed out in a post by Edward d'Auvergne at :
https://mail.gna.org/public/relax-devel/2008-01/msg00021.html (Message-id:
<7f080ed10801090840s341431f2nb75b15b137b46176@xxxxxxxxxxxxxx>)
Modified:
1.3/specific_fns/jw_mapping.py
1.3/specific_fns/noe.py
1.3/specific_fns/relax_fit.py
Modified: 1.3/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=4575&r1=4574&r2=4575&view=diff
==============================================================================
--- 1.3/specific_fns/jw_mapping.py (original)
+++ 1.3/specific_fns/jw_mapping.py Wed Jan 9 19:20:33 2008
@@ -37,7 +37,7 @@
"""Class containing functions specific to reduced spectral density
mapping."""
- def calculate(self, run=None, print_flag=1, sim_index=None):
+ def calculate(self, run=None, verbosity=1, sim_index=None):
"""Calculation of the spectral density values."""
# Run argument.
Modified: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=4575&r1=4574&r2=4575&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py Wed Jan 9 19:20:33 2008
@@ -44,7 +44,7 @@
relax_data_store.res[run][i].sat = intensity
- def calculate(self, run=None, print_flag=1):
+ def calculate(self, run=None, verbosity=1):
"""Function for calculating the NOE and its error.
The error for each peak is calculated using the formula:
Modified: 1.3/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_fit.py?rev=4575&r1=4574&r2=4575&view=diff
==============================================================================
--- 1.3/specific_fns/relax_fit.py (original)
+++ 1.3/specific_fns/relax_fit.py Wed Jan 9 19:20:33 2008
@@ -351,7 +351,7 @@
data.iinf = self.param_vector[2]
- def grid_search(self, run, lower, upper, inc, constraints, print_flag,
sim_index=None):
+ def grid_search(self, run, lower, upper, inc, constraints, verbosity,
sim_index=None):
"""The grid search function."""
# Arguments.
@@ -360,7 +360,7 @@
self.inc = inc
# Minimisation.
- self.minimise(run=run, min_algor='grid', constraints=constraints,
print_flag=print_flag, sim_index=sim_index)
+ self.minimise(run=run, min_algor='grid', constraints=constraints,
verbosity=verbosity, sim_index=sim_index)
def grid_search_setup(self, index=None):
@@ -512,7 +512,7 @@
return A, b
- def mean_and_error(self, run=None, print_flag=0):
+ def mean_and_error(self, run=None, verbosity=0):
"""Function for calculating the average intensity and standard
deviation of all spectra."""
# Arguments.
@@ -534,7 +534,7 @@
# Print out.
print "\nTime point: " +
`relax_data_store.relax_times[self.run][time_index]` + " s"
print "Number of spectra: " +
`relax_data_store.num_spectra[self.run][time_index]`
- if print_flag:
+ if verbosity:
print "%-5s%-6s%-20s%-20s" % ("Num", "Name", "Average", "SD")
# Append zero to the global standard deviation structure.
@@ -590,7 +590,7 @@
data.sd.append(sd)
# Print out.
- if print_flag:
+ if verbosity:
print "%-5i%-6s%-20s%-20s" % (data.num, data.name,
`data.ave_intensities[time_index]`, `data.sd[time_index]`)
# Sum of standard deviations (for average).
@@ -633,12 +633,12 @@
print "\nStandard deviation (averaged over all spectra): " +
`sd`
- def minimise(self, run=None, min_algor=None, min_options=None,
func_tol=None, grad_tol=None, max_iterations=None, constraints=0, scaling=1,
print_flag=0, sim_index=None):
+ def minimise(self, run=None, min_algor=None, min_options=None,
func_tol=None, grad_tol=None, max_iterations=None, constraints=0, scaling=1,
verbosity=0, sim_index=None):
"""Relaxation curve fitting function."""
# Arguments.
self.run = run
- self.print_flag = print_flag
+ self.verbosity = verbosity
# Test if the sequence data for self.run is loaded.
if not relax_data_store.res.has_key(self.run):
@@ -673,9 +673,9 @@
A, b = self.linear_constraints(index=i)
# Print out.
- if self.print_flag >= 1:
+ if self.verbosity >= 1:
# Individual residue print out.
- if self.print_flag >= 2:
+ if self.verbosity >= 2:
print "\n\n"
string = "Fitting to residue: " + `data.num` + " " +
data.name
print "\n\n" + string
@@ -724,9 +724,9 @@
###############
if constraints:
- results = generic_minimise(func=func, dfunc=dfunc,
d2func=d2func, args=(), x0=self.param_vector, min_algor=min_algor,
min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
maxiter=max_iterations, A=A, b=b, full_output=1, print_flag=print_flag)
+ results = generic_minimise(func=func, dfunc=dfunc,
d2func=d2func, args=(), x0=self.param_vector, min_algor=min_algor,
min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
maxiter=max_iterations, A=A, b=b, full_output=1, print_flag=verbosity)
else:
- results = generic_minimise(func=func, dfunc=dfunc,
d2func=d2func, args=(), x0=self.param_vector, min_algor=min_algor,
min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
maxiter=max_iterations, full_output=1, print_flag=print_flag)
+ results = generic_minimise(func=func, dfunc=dfunc,
d2func=d2func, args=(), x0=self.param_vector, min_algor=min_algor,
min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
maxiter=max_iterations, full_output=1, print_flag=verbosity)
if results == None:
return
self.param_vector, self.func, self.iter_count, self.f_count,
self.g_count, self.h_count, self.warning = results
r4575 - in /1.3/specific_fns: jw_mapping.py noe.py relax_fit.py