Author: bugman
Date: Wed May 29 10:56:38 2013
New Revision: 19765
URL: http://svn.gna.org/viewcvs/relax?rev=19765&view=rev
Log:
Large simplification of the Relax_disp system tests using Hansen's CPMG data.
Instead of calculating the R2eff values in the test, these are read from the
high error precision
results files in test_suite/shared_data/dispersion/Hansen. This allows the
model parameters to be
consistently found and to be identical between different runs of the test.
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=19765&r1=19764&r2=19765&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Wed May 29
10:56:38 2013
@@ -63,7 +63,7 @@
"""
# Set the model.
- ds.models = ['R2eff', 'LM63']
+ ds.models = ['LM63']
# Execute the script.
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data.py')
@@ -92,7 +92,7 @@
"""
# Set the model.
- ds.models = ['R2eff', 'CR72']
+ ds.models = ['CR72']
# Execute the script.
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data.py')
Modified:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py?rev=19765&r1=19764&r2=19765&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
Wed May 29 10:56:38 2013
@@ -9,11 +9,8 @@
from status import Status; status = Status()
-# Analysis variables.
-#####################
-
# The dispersion models.
-MODELS = ['R2eff', 'fast 2-site']
+MODELS = ['LM63']
if hasattr(ds, 'models'):
MODELS = ds.models
@@ -25,13 +22,6 @@
-# Set up the data pipe.
-#######################
-
-# The results directory.
-if not hasattr(ds, 'tmpdir'):
- ds.tmpdir = None
-
# Create the data pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
@@ -40,86 +30,12 @@
# The path to the data files.
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
-# Load the sequence.
-sequence.read('fake_sequence.in_trunc', dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen',
res_num_col=1, res_name_col=2)
+# Load the saved base pipe
+results.read(data_path+sep+'base_pipe')
-# Name the spins so they can be matched to the assignments.
-spin.name(name='N')
-
-# Set the relaxation dispersion experiment type.
-relax_disp.exp_type('cpmg fixed')
-
-# The spectral data - spectrum ID, peak list file name, CPMG frequency (Hz),
spectrometer frequency in Hertz.
-data = [
- ['500_reference.in', '500_MHz'+sep+'reference.in_trunc',
None, 500e6],
- ['500_66.667.in', '500_MHz'+sep+'66.667.in_trunc',
66.6666, 500e6],
- ['500_133.33.in', '500_MHz'+sep+'133.33.in_trunc',
133.3333, 500e6],
- ['500_133.33.in.bis', '500_MHz'+sep+'133.33.in.bis_trunc',
133.3333, 500e6],
- ['500_200.in', '500_MHz'+sep+'200.in_trunc',
200.0000, 500e6],
- ['500_266.67.in', '500_MHz'+sep+'266.67.in_trunc',
266.6666, 500e6],
- ['500_333.33.in', '500_MHz'+sep+'333.33.in_trunc',
333.3333, 500e6],
- ['500_400.in', '500_MHz'+sep+'400.in_trunc',
400.0000, 500e6],
- ['500_466.67.in', '500_MHz'+sep+'466.67.in_trunc',
466.6666, 500e6],
- ['500_533.33.in', '500_MHz'+sep+'533.33.in_trunc',
533.3333, 500e6],
- ['500_533.33.in.bis', '500_MHz'+sep+'533.33.in.bis_trunc',
533.3333, 500e6],
- ['500_600.in', '500_MHz'+sep+'600.in_trunc',
600.0000, 500e6],
- ['500_666.67.in', '500_MHz'+sep+'666.67.in_trunc',
666.6666, 500e6],
- ['500_733.33.in', '500_MHz'+sep+'733.33.in_trunc',
733.3333, 500e6],
- ['500_800.in', '500_MHz'+sep+'800.in_trunc',
800.0000, 500e6],
- ['500_866.67.in', '500_MHz'+sep+'866.67.in_trunc',
866.6666, 500e6],
- ['500_933.33.in', '500_MHz'+sep+'933.33.in_trunc',
933.3333, 500e6],
- ['500_933.33.in.bis', '500_MHz'+sep+'933.33.in.bis_trunc',
933.3333, 500e6],
- ['500_1000.in', '500_MHz'+sep+'1000.in_trunc',
1000.0000, 500e6],
- ['800_reference.in', '800_MHz'+sep+'reference.in_trunc',
None, 800e6],
- ['800_66.667.in', '800_MHz'+sep+'66.667.in_trunc',
66.6666, 800e6],
- ['800_133.33.in', '800_MHz'+sep+'133.33.in_trunc',
133.3333, 800e6],
- ['800_133.33.in.bis', '800_MHz'+sep+'133.33.in.bis_trunc',
133.3333, 800e6],
- ['800_200.in', '800_MHz'+sep+'200.in_trunc',
200.0000, 800e6],
- ['800_266.67.in', '800_MHz'+sep+'266.67.in_trunc',
266.6666, 800e6],
- ['800_333.33.in', '800_MHz'+sep+'333.33.in_trunc',
333.3333, 800e6],
- ['800_400.in', '800_MHz'+sep+'400.in_trunc',
400.0000, 800e6],
- ['800_466.67.in', '800_MHz'+sep+'466.67.in_trunc',
466.6666, 800e6],
- ['800_533.33.in', '800_MHz'+sep+'533.33.in_trunc',
533.3333, 800e6],
- ['800_533.33.in.bis', '800_MHz'+sep+'533.33.in.bis_trunc',
533.3333, 800e6],
- ['800_600.in', '800_MHz'+sep+'600.in_trunc',
600.0000, 800e6],
- ['800_666.67.in', '800_MHz'+sep+'666.67.in_trunc',
666.6666, 800e6],
- ['800_733.33.in', '800_MHz'+sep+'733.33.in_trunc',
733.3333, 800e6],
- ['800_800.in', '800_MHz'+sep+'800.in_trunc',
800.0000, 800e6],
- ['800_866.67.in', '800_MHz'+sep+'866.67.in_trunc',
866.6666, 800e6],
- ['800_933.33.in', '800_MHz'+sep+'933.33.in_trunc',
933.3333, 800e6],
- ['800_933.33.in.bis', '800_MHz'+sep+'933.33.in.bis_trunc',
933.3333, 800e6],
- ['800_1000.in', '800_MHz'+sep+'1000.in_trunc',
1000.0000, 800e6]
-]
-
-# Loop over the spectra.
-for id, file, cpmg_frq, H_frq in data:
- # Load the peak intensities.
- spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id,
int_method='height')
-
- # Set the relaxation dispersion CPMG frequencies.
- relax_disp.cpmg_frq(spectrum_id=id, cpmg_frq=cpmg_frq)
-
- # Set the NMR field strength of the spectrum.
- spectrometer.frequency(id=id, frq=H_frq)
-
- # Relaxation dispersion CPMG constant time delay T (in s).
- relax_disp.relax_time(spectrum_id=id, time=0.030)
-
-# Specify the duplicated spectra.
-spectrum.replicated(spectrum_ids=['500_133.33.in', '500_133.33.in.bis'])
-spectrum.replicated(spectrum_ids=['500_533.33.in', '500_533.33.in.bis'])
-spectrum.replicated(spectrum_ids=['500_933.33.in', '500_933.33.in.bis'])
-spectrum.replicated(spectrum_ids=['800_133.33.in', '800_133.33.in.bis'])
-spectrum.replicated(spectrum_ids=['800_533.33.in', '800_533.33.in.bis'])
-spectrum.replicated(spectrum_ids=['800_933.33.in', '800_933.33.in.bis'])
-
-# Peak intensity error analysis.
-spectrum.error_analysis(subset=['500_reference.in', '500_66.667.in',
'500_133.33.in', '500_133.33.in.bis', '500_200.in', '500_266.67.in',
'500_333.33.in', '500_400.in', '500_466.67.in', '500_533.33.in',
'500_533.33.in.bis', '500_600.in', '500_666.67.in', '500_733.33.in',
'500_800.in', '500_866.67.in', '500_933.33.in', '500_933.33.in.bis',
'500_1000.in'])
-spectrum.error_analysis(subset=['800_reference.in', '800_66.667.in',
'800_133.33.in', '800_133.33.in.bis', '800_200.in', '800_266.67.in',
'800_333.33.in', '800_400.in', '800_466.67.in', '800_533.33.in',
'800_533.33.in.bis', '800_600.in', '800_666.67.in', '800_733.33.in',
'800_800.in', '800_866.67.in', '800_933.33.in', '800_933.33.in.bis',
'800_1000.in'])
-
-# Deselect unresolved spins.
-deselect.read(file='unresolved', dir=data_path+sep+'500_MHz', res_num_col=1)
-deselect.read(file='unresolved', dir=data_path+sep+'800_MHz', res_num_col=1)
+# Create the R2eff data pipe and load the results.
+pipe.create(pipe_name='R2eff', bundle=pipe_bundle, pipe_type='relax_disp')
+results.read(data_path+sep+'r2eff_pipe')
# Auto-analysis execution.
r19765 - in /branches/relax_disp/test_suite/system_tests: relax_disp.py scripts/relax_disp/hansen_data.py