Author: tlinnet
Date: Mon Sep 8 22:23:07 2014
New Revision: 25709
URL: http://svn.gna.org/viewcvs/relax?rev=25709&view=rev
Log:
Initial try to implement plotting in the repeated auto analysis protocol.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
Modified:
trunk/auto_analyses/relax_disp_repeat_cpmg.py
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp_repeat_cpmg.py?rev=25709&r1=25708&r2=25709&view=diff
==============================================================================
--- trunk/auto_analyses/relax_disp_repeat_cpmg.py (original)
+++ trunk/auto_analyses/relax_disp_repeat_cpmg.py Mon Sep 8 22:23:07
2014
@@ -36,6 +36,7 @@
from warnings import warn
# relax module imports.
+import dep_check
from lib.io import extract_data, get_file_path, sort_filenames, write_data
from lib.text.sectioning import section, subsection, subtitle, title
from lib.warnings import RelaxWarning
@@ -45,6 +46,9 @@
from specific_analyses.relax_disp.data import generate_r20_key,
has_exponential_exp_type, is_r1_optimised, loop_exp_frq_offset,
loop_exp_frq_offset_point, return_param_key_from_data, spin_loop
from specific_analyses.relax_disp.variables import MODEL_NOREX,
MODEL_PARAMS, MODEL_R2EFF, PARAMS_R20
from status import Status; status = Status()
+
+if dep_check.matplotlib_module:
+ import matplotlib.pyplot as plt
# Define sfrq key to dic.
@@ -868,11 +872,11 @@
res_dic[str(glob_ini)] = {}
# Get the pipe name for R2eff values.
- pipe_name = self.name_pipe(method=method, model=MODEL_R2EFF,
analysis=analysis, glob_ini=glob_ini)
+ pipe_name = self.name_pipe(method=method, model=MODEL_R2EFF,
analysis='int', glob_ini=glob_ini)
# Check if pipe exists, or else calculate.
if not pipes.has_pipe(pipe_name):
- self.calc_r2eff(list_glob_ini=[glob_ini])
+ self.calc_r2eff(methods=[method], list_glob_ini=[glob_ini])
if pipes.get_pipe() != pipe_name:
self.interpreter.pipe.switch(pipe_name)
@@ -929,6 +933,8 @@
method_cur = r2eff_dic['method']
res_dic[method_cur] = {}
res_dic[method_cur]['method'] = method_cur
+ res_dic[method_cur]['glob_ini'] = []
+ res_dic[method_cur]['r2eff_norm_std'] = []
# Now loop over glob_ini:
for glob_ini in list_glob_ini:
@@ -953,12 +959,22 @@
r2eff_diff_norm_arr = (r2eff_arr - r2eff_arr_ref) /
r2eff_arr_ref
r2eff_diff_norm_std = std(r2eff_diff_norm_arr, ddof=1)
+ # Store x
+ res_dic[method_cur]['glob_ini'].append(glob_ini)
+
# Store to result dic.
- res_dic[method_cur]['r2eff_arr'] = r2eff_arr
- res_dic[method_cur]['r2eff_norm_arr'] = r2eff_norm_arr
- res_dic[method_cur]['r2eff_norm_std'] = r2eff_norm_std
- res_dic[method_cur]['r2eff_diff_norm_arr'] =
r2eff_diff_norm_arr
- res_dic[method_cur]['r2eff_diff_norm_std'] =
r2eff_diff_norm_std
+ res_dic[method_cur][str(glob_ini)] = {}
+ res_dic[method_cur][str(glob_ini)]['r2eff_arr'] = r2eff_arr
+ res_dic[method_cur][str(glob_ini)]['r2eff_norm_arr'] =
r2eff_norm_arr
+ res_dic[method_cur][str(glob_ini)]['r2eff_norm_std'] =
r2eff_norm_std
+ res_dic[method_cur]['r2eff_norm_std'].append(r2eff_norm_std)
+
+ res_dic[method_cur][str(glob_ini)]['r2eff_diff_norm_arr'] =
r2eff_diff_norm_arr
+ res_dic[method_cur][str(glob_ini)]['r2eff_diff_norm_std'] =
r2eff_diff_norm_std
+
+
+ res_dic[method_cur]['glob_ini'] =
asarray(res_dic[method_cur]['glob_ini'])
+ res_dic[method_cur]['r2eff_norm_std'] =
asarray(res_dic[method_cur]['r2eff_norm_std'])
return res_dic
@@ -971,7 +987,16 @@
if method not in r2eff_stat_dic:
continue
- print method
+ if not dep_check.matplotlib_module:
+ continue
+
+ fig = plt.figure()
+ x = r2eff_stat_dic[method]['glob_ini']
+ y = r2eff_stat_dic[method]['r2eff_norm_std']
+ plt.plot(x, y)
+
+ if show:
+ plt.show()
def interpreter_start(self):
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=25709&r1=25708&r2=25709&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Sep 8 22:23:07 2014
@@ -5959,8 +5959,8 @@
# Setup base information.
RDR.set_base_cpmg(glob_ini=128)
- #methods = ['FT', 'MDD']
- methods = ['FT']
+ methods = ['FT', 'MDD']
+ #methods = ['FT']
# Set the intensity.
#RDR.set_int(methods=methods, list_glob_ini=[128, 126])
@@ -5972,7 +5972,7 @@
# Try for bad data.
#RDR.calc_r2eff(methods=['FT'], list_glob_ini=[6, 4])
- if False:
+ if True:
# Collect r2eff values.
r2eff_ft = RDR.col_r2eff(method='FT', list_glob_ini=[128,
126, 6])
@@ -5983,10 +5983,10 @@
r2eff_stat_dic =
RDR.get_r2eff_stat_dic(list_r2eff_dics=[r2eff_ft, r2eff_mdd],
list_glob_ini=[128, 126, 6])
# Plot R2eff stats
- RDR.plot_r2eff_stat(r2eff_stat_dic=r2eff_stat_dic,
methods=['FT'], list_glob_ini=[128, 126, 6], show=True)
+ RDR.plot_r2eff_stat(r2eff_stat_dic=r2eff_stat_dic,
methods=['FT'], list_glob_ini=[128, 126, 6], show=False)
# Do minimisation
- if True:
+ if False:
# Deselect all spins.
#self.interpreter.spin.display()
RDR.deselect_all(methods=methods, model='setup',
model_from=MODEL_R2EFF, analysis='grid setup', analysis_from='int',
list_glob_ini=[128, 126])
r25709 - in /trunk: auto_analyses/relax_disp_repeat_cpmg.py test_suite/system_tests/relax_disp.py