Author: bugman
Date: Wed Oct 9 18:01:30 2013
New Revision: 21027
URL: http://svn.gna.org/viewcvs/relax?rev=21027&view=rev
Log:
Merged revisions 21025-21026 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r21025 | bugman | 2013-10-09 18:00:30 +0200 (Wed, 09 Oct 2013) | 6 lines
Updated the spectrum.error_analysis user function backend to use the
lib.statistics.std() function.
This simplifies the code. It affects only the peak intensity error
analysis when spectra have been
replicated.
........
r21026 | bugman | 2013-10-09 18:00:57 +0200 (Wed, 09 Oct 2013) | 3 lines
Updated the test suite with slight changes needed due to r21025.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/pipe_control/spectrum.py
branches/relax_disp/test_suite/gui_tests/rx.py
branches/relax_disp/test_suite/system_tests/relax_fit.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Oct 9 18:01:30 2013
@@ -1,1 +1,1 @@
-/trunk:1-21015
+/trunk:1-21026
Modified: branches/relax_disp/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/spectrum.py?rev=21027&r1=21026&r2=21027&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/spectrum.py (original)
+++ branches/relax_disp/pipe_control/spectrum.py Wed Oct 9 18:01:30 2013
@@ -34,6 +34,7 @@
from lib.errors import RelaxError, RelaxImplementError, RelaxNoSpectraError
from lib.io import write_data
from lib.spectrum.peak_list import read_peak_list
+from lib.statistics import std
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
from pipe_control import pipes
from pipe_control.mol_res_spin import check_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_loop
@@ -110,14 +111,14 @@
# Number of spectra.
num_spectra = len(spectra)
- # Print out.
+ # Printout.
print("\nReplicated spectra: " + repr(spectra))
if verbosity:
- print("%-5s%-6s%-20s%-20s" % ("Num", "Name", "Average", "SD"))
+ print("%-20s%-20s" % ("Spin_ID", "SD"))
# Calculate the mean value.
count = 0
- for spin in spin_loop():
+ for spin, spin_id in spin_loop(return_id=True):
# Skip deselected spins.
if not spin.select:
continue
@@ -135,33 +136,22 @@
if missing:
continue
- # Average intensity.
- ave_intensity = 0.0
+ # The peak intensities.
+ values = []
for j in range(num_spectra):
- ave_intensity = ave_intensity + spin.intensities[spectra[j]]
- ave_intensity = ave_intensity / num_spectra
-
- # Sum of squared errors.
- SSE = 0.0
- for j in range(num_spectra):
- SSE = SSE + (spin.intensities[spectra[j]] - ave_intensity)
** 2
-
- # Variance.
- #
- # 1
- # sigma^2 = ----- * sum({Xi - Xav}^2)]
- # n - 1
- #
- var_I = 1.0 / (num_spectra - 1.0) * SSE
-
- # Print out.
+ values.append(spin.intensities[spectra[j]])
+
+ # The standard deviation.
+ sd = std(values=values, dof=1)
+
+ # Printout.
if verbosity:
- print("%-5i%-6s%-20s%-20s" % (spin.num, spin.name,
repr(ave_intensity), repr(var_I)))
+ print("%-20s%-20s" % (spin_id, sd))
# Sum of variances (for average).
if not id in cdp.var_I:
cdp.var_I[id] = 0.0
- cdp.var_I[id] = cdp.var_I[id] + var_I
+ cdp.var_I[id] = cdp.var_I[id] + sd**2
count = count + 1
# No data catch.
Modified: branches/relax_disp/test_suite/gui_tests/rx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/gui_tests/rx.py?rev=21027&r1=21026&r2=21027&view=diff
==============================================================================
--- branches/relax_disp/test_suite/gui_tests/rx.py (original)
+++ branches/relax_disp/test_suite/gui_tests/rx.py Wed Oct 9 18:01:30 2013
@@ -72,8 +72,8 @@
# Check the errors.
for key in cdp.sigma_I:
- self.assertEqual(cdp.sigma_I[key], 10578.03948242143)
- self.assertEqual(cdp.var_I[key], 111894919.29166666)
+ self.assertEqual(cdp.sigma_I[key], 10578.039482421433)
+ self.assertEqual(cdp.var_I[key], 111894919.29166669)
# Spin data check.
i = 0
Modified: branches/relax_disp/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_fit.py?rev=21027&r1=21026&r2=21027&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_fit.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_fit.py Wed Oct 9
18:01:30 2013
@@ -82,8 +82,8 @@
# Check the errors.
for key in cdp.sigma_I:
- self.assertEqual(cdp.sigma_I[key], 10578.03948242143)
- self.assertEqual(cdp.var_I[key], 111894919.29166666)
+ self.assertEqual(cdp.sigma_I[key], 10578.039482421433)
+ self.assertEqual(cdp.var_I[key], 111894919.29166669)
# Spin data check.
i = 0
r21027 - in /branches/relax_disp: ./ pipe_control/spectrum.py test_suite/gui_tests/rx.py test_suite/system_tests/relax_fit.py