r28130 - /trunk/test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/1_tutorial_prepare_data.py -- November 28, 2015 - 23:56

Author: tlinnet
Date: Sat Nov 28 23:56:54 2015
New Revision: 28130

URL: http://svn.gna.org/viewcvs/relax?rev=28130&view=rev
Log:
Adding a tutorial script.

Added:
    
trunk/test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/1_tutorial_prepare_data.py

Added: 
trunk/test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/1_tutorial_prepare_data.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/1_tutorial_prepare_data.py?rev=28130&view=auto
==============================================================================
--- 
trunk/test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/1_tutorial_prepare_data.py
    (added)
+++ 
trunk/test_suite/shared_data/dispersion/Paul_Schanda_2015_Nov/1_tutorial_prepare_data.py
    Sat Nov 28 23:56:54 2015
@@ -0,0 +1,98 @@
+import os
+from scipy.io import loadmat
+import numpy as np
+
+# Set path
+cwd  = os.getcwd()
+outdir = cwd + os.sep
+
+fields = [600, 950]
+file_names = ['residues', 'rates', 'errorbars_rate', 'RFfields']
+
+# Store data in dictionary
+all_data = {}
+all_data['fields'] = fields
+all_data['file_names'] = file_names
+
+# Make list of residues and make unique
+all_res = []
+
+# Loop over the experiments, collect all data
+for field in fields:
+    print("%s"%field,)
+
+    # Make a dic inside
+    all_data['%s'%field] = {}
+
+    # Construct the path to the data
+    path = cwd + os.sep
+
+    # Collect all filename paths
+    field_file_name_paths = []
+    for file_name in file_names:
+        # Create path name
+        file_name_path = path + "%s_%s.mat"%(field, file_name)
+        field_file_name_paths.append(file_name_path)
+
+        # Load the data
+        file_name_path_data = loadmat(file_name_path)
+        # Extract as numpy
+        file_name_path_data_np = file_name_path_data[file_name]
+        # And store
+        all_data['%s'%field]['%s'%file_name] = file_name_path_data
+        all_data['%s'%field]['np_%s'%file_name] = file_name_path_data_np
+
+        print(file_name, file_name_path_data_np.shape)
+
+        # Collect residues
+        if file_name == "residues":
+            all_res += list(file_name_path_data_np.flatten())
+
+    # Store
+    all_data['%s'%field]['field_file_name_paths'] = field_file_name_paths
+
+
+# Make list of residues and make unique
+all_res_uniq = sorted(list(set(all_res)))
+all_data['all_res_uniq'] = all_res_uniq
+
+# Write a sequence file for relax
+f = open(outdir + "residues.txt", "w")
+f.write("# Residue_i\n")
+for res in all_res_uniq:
+    f.write("%s\n"%res)
+f.close()
+
+f_exp = open(outdir + "exp_settings.txt", "w")
+f_exp.write("# sfrq_MHz RFfield_kHz file_name\n")
+
+# Then write the files for the rates
+k = 1
+for field in all_data['fields']:
+    resis = all_data['%s'%field]['np_residues'][0]
+    rates = all_data['%s'%field]['np_rates']
+    errorbars_rate = all_data['%s'%field]['np_errorbars_rate']
+    RFfields = all_data['%s'%field]['np_RFfields'][0]
+
+    print("\nfield: %3.3f"%field)
+    for i, RF_field_strength_kHz in enumerate(RFfields):
+        #print "RF_field_strength_kHz: %3.3f"%RF_field_strength_kHz
+        # Generate file name
+        f_name = outdir + "sfrq_%i_MHz_RFfield_%1.3f_kHz_%03d.in"%(field, 
RF_field_strength_kHz, k)
+        cur_file = open(f_name, "w")
+        cur_file.write("# resi rate        rate_err\n")
+
+        exp_string = "%11.7f %11.7f %s\n"%(field, RF_field_strength_kHz, 
f_name)
+        print("%s"%exp_string,)
+        f_exp.write(exp_string)
+
+        for j, resi in enumerate(resis):
+            rate = rates[j, i]
+            error = errorbars_rate[j, i]
+            string = "%4d %11.7f %11.7f\n"%(resi, rate, error)
+            cur_file.write(string)
+
+        cur_file.close()
+        k += 1
+
+f_exp.close()