Author: bugman
Date: Tue Sep 30 17:16:15 2008
New Revision: 7458
URL: http://svn.gna.org/viewcvs/relax?rev=7458&view=rev
Log:
Converted the relax_curve_diff.py sample script to the new design.
This was identified by the unnecessary import of the relax data storage
object.
Modified:
branches/pipe_refs/sample_scripts/relax_curve_diff.py
Modified: branches/pipe_refs/sample_scripts/relax_curve_diff.py
URL:
http://svn.gna.org/viewcvs/relax/branches/pipe_refs/sample_scripts/relax_curve_diff.py?rev=7458&r1=7457&r2=7458&view=diff
==============================================================================
--- branches/pipe_refs/sample_scripts/relax_curve_diff.py (original)
+++ branches/pipe_refs/sample_scripts/relax_curve_diff.py Tue Sep 30 17:16:15
2008
@@ -1,7 +1,25 @@
-# Script: relax_curve_diff.py
-# Author: Edward d'Auvergne
-# Email: edward at nmr-relax dot com
-#
+###############################################################################
+#
#
+# Copyright (C) 2007-2008 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
# This script creates a Grace plot of Ix - Ix(theta), the difference between
the measured peak
# intensity and the back calculated peak intensity for each spin system x.
Ix(theta) is back
# calculated using the parameter vector theta = [Rx, I0], where Rx is either
the R1 or R2 relaxation
@@ -18,7 +36,7 @@
# extensions). The file name of the saved state can be changed at the
bottom of this script. It is
# important to note that the same version of relax should be used for
creating the saved state as
# reading the program state, these files are neither backwards nor forwards
compatible. The name of
-# the run using in the curve fitting is expected to be 'rx' but this can
also be changed at the
+# the data pipe using in the curve fitting is expected to be 'rx' but this
can also be changed at
# bottom of the script. Only the two parameter exponential fit is currently
supported.
@@ -26,21 +44,26 @@
from numpy import float64, array, identity, sqrt, zeros
# relax module imports.
-from data import Relax_data_store; ds = Relax_data_store()
+from generic_fns.mol_res_spin import spin_loop
+from generic_fns import pipes
from maths_fns.relax_fit import back_calc_I, func, setup
-# The relax data storage object.
-
-
-def back_calc(name):
+# The name of the save file generated by 'relax_fit.py'.
+SAVE_FILE = 'rx.save'
+
+
+def back_calc():
"""Back calculate the peak intensities.
The simple two parameter exponential curve (Rx, I0) is assumed.
"""
+ # Get the current data pipe.
+ cdp = pipes.get_pipe()
+
# Loop over the spins.
- for spin in ds.res[name]:
+ for spin in spin_loop()
# Skip deselected spins.
if not spin.select:
continue
@@ -49,7 +72,7 @@
param_vector = array([spin.rx, spin.i0], float64)
# Initialise the relaxation fit functions.
- setup(num_params=len(spin.params),
num_times=len(ds.relax_times[name]), values=spin.ave_intensities,
sd=ds.sd[name], relax_times=ds.relax_times[name], scaling_matrix=identity(2,
float64))
+ setup(num_params=len(spin.params), num_times=len(cdp.relax_times),
values=spin.ave_intensities, sd=cdp.sd, relax_times=cdp.relax_times,
scaling_matrix=identity(2, float64))
# Make a single function call. This will cause back calculation and
the data will be stored in the C module.
func(param_vector)
@@ -71,9 +94,12 @@
and Xav is the peak intensity difference averaged across all spins.
"""
+ # Get the current data pipe.
+ cdp = pipes.get_pipe()
+
# Diff array, std deviation array, and number of spins.
- diff_array = zeros(sum(ds.num_spectra[name]), float64)
- sd_array = zeros(sum(ds.num_spectra[name]), float64)
+ diff_array = zeros(sum(cdp.num_spectra), float64)
+ sd_array = zeros(sum(cdp.num_spectra), float64)
num_spins = 0
@@ -81,7 +107,7 @@
###################################
# Loop over the spins.
- for spin in ds.res[name]:
+ for spin in spin_loop()
# Skip deselected spins.
if not spin.select:
continue
@@ -107,7 +133,7 @@
####################################
# Loop over the spins.
- for spin in ds.res[name]:
+ for spin in spin_loop()
# Skip deselected spins.
if not spin.select:
continue
@@ -185,8 +211,11 @@
file.write("@ s2 line linestyle 3\n")
-def grace_plot(ave, sd, name):
+def grace_plot(ave, sd):
"""Grace plot of the intensity differences."""
+
+ # Get the current data pipe.
+ cdp = pipes.get_pipe()
# Open the file.
file = open('differences.agr', 'w')
@@ -196,7 +225,7 @@
ymax = 2.5*max(ave + sd)
# Grace header.
- grace_header(file, xmin=0, xmax=ds.relax_times[name][-1], ymin=ymin,
ymax=ymax)
+ grace_header(file, xmin=0, xmax=cdp.relax_times[-1], ymin=ymin,
ymax=ymax)
# First time point difference distributions.
@@ -207,15 +236,15 @@
file.write("@type xy\n")
# Loop over the individual time points.
- for i in xrange(len(ds.num_spectra[name])):
+ for i in xrange(len(cdp.num_spectra)):
# Loop over the spins.
- for spin in ds.res[name]:
+ for spin in spin_loop():
# Skip deselected spins.
if not spin.select:
continue
# Grace data point.
- file.write("%-30s%-30s\n" % (`ds.relax_times[name][i]`,
`spin.intensities[i][0] - spin.fit_int[i]`))
+ file.write("%-30s%-30s\n" % (`cdp.relax_times[i]`,
`spin.intensities[i][0] - spin.fit_int[i]`))
# End the graph.
file.write("&\n")
@@ -229,16 +258,16 @@
file.write("@type xy\n")
# Loop over the individual time points.
- for i in xrange(len(ds.num_spectra[name])):
+ for i in xrange(len(cdp.num_spectra)):
# Loop over the spins.
- for spin in ds.res[name]:
+ for spin in spin_loop():
# Skip deselected spins.
if not spin.select:
continue
# Grace data point.
if len(spin.intensities[i]) == 2:
- file.write("%-30s%-30s\n" % (`ds.relax_times[name][i]`,
`spin.intensities[i][1] - spin.fit_int[i]`))
+ file.write("%-30s%-30s\n" % (`cdp.relax_times[i]`,
`spin.intensities[i][1] - spin.fit_int[i]`))
# End the graph.
file.write("&\n")
@@ -253,10 +282,10 @@
# Loop over the data.
index = 0
- for i in xrange(len(ds.num_spectra[name])):
- for j in xrange(ds.num_spectra[name][i]):
+ for i in xrange(len(cdp.num_spectra)):
+ for j in xrange(cdp.num_spectra[i]):
# Grace data point.
- file.write("%-30s%-30s%-30s\n" % (`ds.relax_times[name][i]`,
`ave[index]`, `sd[index]`))
+ file.write("%-30s%-30s%-30s\n" % (`cdp.relax_times[i]`,
`ave[index]`, `sd[index]`))
# Increment the index.
index = index + 1
@@ -269,19 +298,16 @@
# Load the program state containing saved by the 'relax_fit.py' sample
script.
-state.load('rx.save')
-
-# The name of the run from the 'relax_fit.py' sample script.
-name = 'rx'
+state.load(SAVE_FILE)
# Back calculate the peak intensities from the fitted parameters.
-back_calc(name)
+back_calc()
# Calculate the average difference and standard deviations for each time
point.
ave, sd = calc_ave_sd()
# Create a Grace plot of the differences.
-grace_plot(ave, sd, name)
+grace_plot(ave, sd)
# View the graph.
grace.view(file='differences.agr', dir=None)
r7458 - /branches/pipe_refs/sample_scripts/relax_curve_diff.py