Author: tlinnet
Date: Sun Sep 7 19:31:30 2014
New Revision: 25678
URL: http://svn.gna.org/viewcvs/relax?rev=25678&view=rev
Log:
Further extended methods in the tclass for repeated analysis of dispersion
data.
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=25678&r1=25677&r2=25678&view=diff
==============================================================================
--- trunk/auto_analyses/relax_disp_repeat_cpmg.py (original)
+++ trunk/auto_analyses/relax_disp_repeat_cpmg.py Sun Sep 7 19:31:30
2014
@@ -30,6 +30,7 @@
from datetime import datetime
from glob import glob
from os import F_OK, access, getcwd, sep
+from numpy import asarray, std
import sys
# relax module imports.
@@ -37,7 +38,7 @@
from lib.text.sectioning import section, subsection, subtitle, title
from pipe_control import pipes
from prompt.interpreter import Interpreter
-from specific_analyses.relax_disp.data import has_exponential_exp_type,
is_r1_optimised, return_param_key_from_data
+from specific_analyses.relax_disp.data import has_exponential_exp_type,
is_r1_optimised, 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
from status import Status; status = Status()
@@ -211,7 +212,7 @@
# Read the intensity per spectrum id and set the RMSD error.
# Switch to the pipe.
- if pipes.get_pipe() != pipe_name:
+ if pipes.cdp_name() != pipe_name:
self.interpreter.pipe.switch(pipe_name)
# Loop over spectrometer frequencies.
@@ -265,7 +266,7 @@
# Switch to the pipe.
- if pipes.get_pipe() != pipe_name:
+ if pipes.cdp_name() != pipe_name:
self.interpreter.pipe.switch(pipe_name)
# Loop over spectrometer frequencies.
@@ -295,7 +296,7 @@
self.interpreter.spectrum.error_analysis(subset=spectrum_ids)
- def set_int(self, list_glob_ini=[0]):
+ def set_int(self, list_glob_ini=[0], force=False):
"""Call both the setup of data and the error analysis"""
# Define model
@@ -306,10 +307,12 @@
# Check previous, and get the pipe name.
found, pipe_name, resfile, path =
self.check_previous_result(model=model, glob_ini=glob_ini,
method=self.method, clusterid='', bundle=self.method)
- # If found, then pass, else calculate it.
- if found:
- pass
- else:
+ if not found:
+ calculate = True
+ elif found:
+ calculate = False
+
+ if calculate:
# Create the data pipe, by copying setup pipe.
self.interpreter.pipe.copy(pipe_from=self.base_setup_pipe_name,
pipe_to=pipe_name, bundle_to=self.method)
self.interpreter.pipe.switch(pipe_name)
@@ -319,6 +322,12 @@
# Call error analysis.
self.do_spectrum_error_analysis(pipe_name=pipe_name,
glob_ini=glob_ini)
+
+ # Save results, and store the current settings dic to pipe.
+ cdp.settings = self.settings
+ self.interpreter.results.write(file=resfile, dir=path,
force=force)
+
+
def calc_r2eff(self, list_glob_ini=[0], force=False):
@@ -331,11 +340,12 @@
# Check previous, and get the pipe name.
found, pipe_name, resfile, path =
self.check_previous_result(model=model, glob_ini=glob_ini,
method=self.method, clusterid='', bundle=self.method)
- # If found, then pass, else calculate it.
- if found:
- pass
-
- else:
+ if not found:
+ calculate = True
+ elif found:
+ calculate = False
+
+ if calculate:
# Create the data pipe by copying the intensity pipe, then
switching to it.
# If not intensity pipe name pipe exists, then calculate it.
intensity_pipe_name = self.name_pipe(model='int',
glob_ini=glob_ini, method=self.method, clusterid='')
@@ -356,8 +366,10 @@
if model == MODEL_R2EFF and not has_exponential_exp_type():
self.interpreter.minimise.calculate()
- # Finally save the R2eff results.
+ # Save results, and store the current settings dic to pipe.
+ cdp.settings = self.settings
self.interpreter.results.write(file=resfile, dir=path,
force=force)
+
def minimise_model(self, model=None, list_glob_ini=[0], force=False,
redo=False):
@@ -368,12 +380,16 @@
# Check previous, and get the pipe name.
found, pipe_name, resfile, path =
self.check_previous_result(model=model, glob_ini=glob_ini,
method=self.method, clusterid='', bundle=self.method)
- # If found, then pass, else calculate it.
- if found:
- pass
-
- else:
-
+ if not found:
+ calculate = True
+
+ elif found and redo == False:
+ calculate = False
+
+ elif found and redo == True:
+ calculate = True
+
+ if calculate:
# Get the pipe name for R2eff values.
r2eff_pipe_name = self.name_pipe(model=MODEL_R2EFF,
glob_ini=glob_ini, method=self.method, clusterid='')
@@ -383,6 +399,7 @@
# Copy pipe from base setup.
self.interpreter.pipe.copy(pipe_from=self.base_setup_pipe_name,
pipe_to=pipe_name, bundle_to=self.method)
+ self.interpreter.pipe.switch(pipe_name)
# Now copy the R2eff values.
self.interpreter.value.copy(pipe_from=r2eff_pipe_name,
pipe_to=pipe_name, param='r2eff')
@@ -396,7 +413,8 @@
# Now optimise.
self.optimise(model=model)
- # Finally save the model results.
+ # Save results, and store the current settings dic to pipe.
+ cdp.settings = self.settings
self.interpreter.results.write(file=resfile, dir=path,
force=force)
@@ -536,6 +554,119 @@
return list_dub_mapping
+ def col_r2eff(self, method=None, list_glob_ini=[0]):
+
+ # Loop over the glob ini:
+ res_dic = {}
+ res_dic['method'] = method
+ for glob_ini in list_glob_ini:
+ # Store under glob_ini
+ res_dic[str(glob_ini)] = {}
+
+ # Get the pipe name for R2eff values.
+ pipe_name = self.name_pipe(model=MODEL_R2EFF, glob_ini=glob_ini,
method=method, clusterid='')
+
+ # Check if pipe exists, or else calculate.
+ if not pipes.has_pipe(pipe_name):
+ self.calc_r2eff(list_glob_ini=[glob_ini])
+
+ if pipes.get_pipe() != pipe_name:
+ self.interpreter.pipe.switch(pipe_name)
+
+ # Results dictionary.
+ res_dic[str(glob_ini)] = {}
+ res_dic[str(glob_ini)]['r2eff'] = {}
+ res_dic[str(glob_ini)]['r2eff_err'] = {}
+ spin_point_r2eff_list = []
+ spin_point_r2eff_err_list = []
+
+ # Loop over the spins.
+ for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ # Make spin dic.
+ res_dic[str(glob_ini)]['r2eff'][spin_id] = {}
+ res_dic[str(glob_ini)]['r2eff_err'][spin_id] = {}
+
+ # Loop over the R2eff points
+ for exp_type, frq, offset, point, ei, mi, oi, di in
loop_exp_frq_offset_point(return_indices=True):
+ # Define the key.
+ data_key =
return_param_key_from_data(exp_type=self.exp_type, frq=frq, offset=offset,
point=point)
+
+ # Check for bad data has skipped r2eff points
+ if data_key in cur_spin.r2eff:
+ r2eff_point = cur_spin.r2eff[data_key]
+ r2eff_err_point = cur_spin.r2eff_err[data_key]
+
+ res_dic[str(glob_ini)]['r2eff'][spin_id][data_key] =
r2eff_point
+
res_dic[str(glob_ini)]['r2eff_err'][spin_id][data_key] = r2eff_err_point
+ spin_point_r2eff_list.append(r2eff_point)
+ spin_point_r2eff_err_list.append(r2eff_err_point)
+
+ res_dic[str(glob_ini)]['r2eff_arr'] =
asarray(spin_point_r2eff_list)
+ res_dic[str(glob_ini)]['r2eff_err_arr'] =
asarray(spin_point_r2eff_err_list)
+
+ return res_dic
+
+ def get_r2eff_stat_dic(self, list_r2eff_dics=None, list_glob_ini=[0]):
+
+ # Loop over the result dictionaries:
+ res_dic = {}
+ for i, r2eff_dic in enumerate(list_r2eff_dics):
+ # Let the reference dic be initial dic
+ r2eff_dic_ref = list_r2eff_dics[0]
+ method_ref = r2eff_dic_ref['method']
+ res_dic['method_ref'] = method_ref
+
+ # Let the reference R2eff array be the initial glob.
+ r2eff_arr_ref = r2eff_dic_ref[str(list_glob_ini[0])]['r2eff_arr']
+ res_dic['r2eff_arr_ref'] = r2eff_arr_ref
+
+ # Get the current method
+ method_cur = r2eff_dic['method']
+ res_dic[method_cur] = {}
+ res_dic[method_cur]['method'] = method_cur
+
+ # Now loop over glob_ini:
+ for glob_ini in list_glob_ini:
+ # Get the array, if it exists.
+ if str(glob_ini) not in r2eff_dic:
+ continue
+
+ r2eff_arr = r2eff_dic[str(glob_ini)]['r2eff_arr']
+
+ # Make a normalised R2eff array according to reference.
+ # This require that all number of points are equal.
+ if len(r2eff_arr) != len(r2eff_arr_ref):
+ continue
+
+ # Get the normalised array.
+ r2eff_norm_arr = r2eff_arr/r2eff_arr_ref
+
+ # Calculate the standard deviation
+ r2eff_norm_std = std(r2eff_norm_arr, ddof=1)
+
+ # Get the diff, then norm
+ r2eff_diff_norm_arr = (r2eff_arr - r2eff_arr_ref) /
r2eff_arr_ref
+ r2eff_diff_norm_std = std(r2eff_diff_norm_arr, ddof=1)
+
+ # 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
+
+
+ return res_dic
+
+ def plot_r2eff_stat(self, r2eff_stat_dic=None, methods=[],
list_glob_ini=[], show=False):
+
+ # Loop over the methods.
+ for method in methods:
+ if method not in r2eff_stat_dic:
+ continue
+
+ print method
+
def interpreter_start(self):
# Load the interpreter.
self.interpreter = Interpreter(show_script=False,
raise_relax_error=True)
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=25678&r1=25677&r2=25678&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Sun Sep 7 19:31:30 2014
@@ -5950,7 +5950,7 @@
sdic[e_2]['rmsd_folder'] = rmsd_folder_2
# Define temporary folder.
- sdic['results_dir'] = self.tmpdir
+ #sdic['results_dir'] = self.tmpdir
# Setup class with data.
RDR = Relax_disp_rep(sdic)
@@ -5962,10 +5962,37 @@
#RDR.set_int(list_glob_ini=[128, 126])
# Now calculate R2eff.
- #RDR.calc_r2eff(list_glob_ini=[128, 126])
-
- RDR.minimise_model(model=MODEL_CR72, list_glob_ini=[128])
-
+ RDR.calc_r2eff(list_glob_ini=[128, 126, 6])
+
+ # Minimise.
+ #RDR.minimise_model(model=MODEL_CR72, list_glob_ini=[128, 126])
+
+ # Try for bad data.
+ #RDR.calc_r2eff(list_glob_ini=[6, 4])
+
+ # Change method.
+ RDR.set_self(key='method', value='MDD')
+
+ # Now calculate R2eff.
+ RDR.calc_r2eff(list_glob_ini=[128, 126])
+
+ # Minimise.
+ #RDR.minimise_model(model=MODEL_CR72, list_glob_ini=[128, 126])
+
+ # Collect r2eff values.
+ r2eff_ft = RDR.col_r2eff(method='FT', list_glob_ini=[128, 126, 6])
+
+ # Collect r2eff values.
+ r2eff_mdd = RDR.col_r2eff(method='MDD', list_glob_ini=[128, 126])
+
+ # Get R2eff stats.
+ 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)
+
+ # Print the pipes.
+ self.interpreter.pipe.display()
def test_r1rho_kjaergaard_auto(self):
r25678 - in /trunk: auto_analyses/relax_disp_repeat_cpmg.py test_suite/system_tests/relax_disp.py