Author: tlinnet
Date: Tue Sep 16 13:19:38 2014
New Revision: 25856
URL: http://svn.gna.org/viewcvs/relax?rev=25856&view=rev
Log:
Implemented writing out of statistics to file.
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=25856&r1=25855&r2=25856&view=diff
==============================================================================
--- trunk/auto_analyses/relax_disp_repeat_cpmg.py (original)
+++ trunk/auto_analyses/relax_disp_repeat_cpmg.py Tue Sep 16 13:19:38
2014
@@ -38,7 +38,7 @@
# relax module imports.
import dep_check
-from lib.io import extract_data, get_file_path, sort_filenames, write_data
+from lib.io import extract_data, get_file_path, open_write_file,
sort_filenames, write_data
from lib.text.sectioning import section, subsection, subtitle, title
from lib.warnings import RelaxWarning
from pipe_control.mol_res_spin import display_spin, generate_spin_string,
return_spin, spin_loop
@@ -1016,6 +1016,7 @@
# Loop over the glob ini:
res_dic = {}
res_dic['method'] = method
+ res_dic['selection'] = selection
for glob_ini in list_glob_ini:
# Store under glob_ini
res_dic[str(glob_ini)] = {}
@@ -1146,11 +1147,15 @@
r2eff_dic_ref = list_r2eff_dics[0]
method_ref = r2eff_dic_ref['method']
res_dic['method_ref'] = method_ref
+ glob_ini_ref = str(list_glob_ini[0])
+ res_dic['glob_ini_ref'] = glob_ini_ref
+ selection = r2eff_dic_ref['selection']
+ res_dic['selection'] = selection
# Let the reference R2eff array be the initial glob.
- r2eff_arr_ref = r2eff_dic_ref[str(list_glob_ini[0])]['r2eff_arr']
+ r2eff_arr_ref = r2eff_dic_ref[glob_ini_ref]['r2eff_arr']
res_dic['r2eff_arr_ref'] = r2eff_arr_ref
- r2eff_err_arr_ref =
r2eff_dic_ref[str(list_glob_ini[0])]['r2eff_err_arr']
+ r2eff_err_arr_ref = r2eff_dic_ref[glob_ini_ref]['r2eff_err_arr']
res_dic['r2eff_err_arr_ref'] = r2eff_err_arr_ref
# Get the current method
@@ -1267,26 +1272,37 @@
return res_dic
- def plot_r2eff_stat(self, r2eff_stat_dic=None, methods=[],
list_glob_ini=[], show=False):
-
- # Loop over the methods.
+ def plot_r2eff_stat(self, r2eff_stat_dic=None, methods=[],
list_glob_ini=[], show=False, write_stats=False):
# Define figure
fig, axises = plt.subplots(nrows=2, ncols=1)
fig.suptitle('Stats per NI')
ax1, ax2 = axises
+ # Catch min and max values for all methods.
min_a = 1.0
max_a = 0.0
min_r_xy2 = 1.0
max_r_xy2 = 0.0
+
+ # Prepare header for writing.
+ selection = r2eff_stat_dic['selection']
+
+ # For writing out stats.
+ headings = []
+ data_dic = OrderedDict()
+ i_max = 0
for method in methods:
if method not in r2eff_stat_dic:
continue
+ # Use NI as x.
x = r2eff_stat_dic[method]['glob_ini']
+
+ # Add to headings.
+ headings = headings + ['method', 'NI', 'slope', 'rxy2']
# Get stats.
# Linear regression slope, without intercept
@@ -1306,9 +1322,32 @@
if min(r_xy2) < min_r_xy2:
min_r_xy2 = min(r_xy2)
+ # Add to data.
+ data_dic[method] = OrderedDict()
+ for i, x_i in enumerate(x):
+ a_i = a[i]
+ r_xy2_i = r_xy2[i]
+ data_dic[method][str(i)] = ["%i"%x_i, "%3.5f"%a_i,
"%3.5f"%r_xy2_i]
+ if i > i_max:
+ i_max = i
+
ax1.plot(x, a, ".-", label='%s LR'%method)
ax2.plot(x, r_xy2, "o--", label='%s SC'%method)
+ # Loop over methods for writing data.
+ data = []
+ for i in range(0, i_max):
+ data_i = []
+ for method, data_dic_m in data_dic.iteritems():
+ # Loop over all possible data points.
+ if str(i) in data_dic_m:
+ data_i = data_i + [method] + data_dic_m[str(i)]
+ else:
+ data_i = data_i + [method] + ["0", "0", "0"]
+
+ data.append(data_i)
+
+ # Set legends.
ax1.legend(loc='lower left', shadow=True, prop = fontP)
ax1.set_xlabel('NI')
#ax1.set_ylabel(r'$\sigma ( R_{2,\mathrm{eff}} )$')
@@ -1322,6 +1361,23 @@
ax2.set_xticks(x)
ax2.set_ylim(min_r_xy2*0.95, max_r_xy2*1.05)
ax2.invert_xaxis()
+
+ # Write to file.
+ if write_stats:
+ if selection == None:
+ file_name = 'r2eff_stat_all.txt'
+ else:
+ file_name = 'r2eff_stat_sel.txt'
+ path = self.results_dir
+ file_obj, file_path = open_write_file(file_name=file_name,
dir=path, force=True, compress_type=0, verbosity=1, return_path=True)
+
+ # Write data.
+ write_data(out=file_obj, headings=headings, data=data)
+
+ # Close file.
+ file_obj.close()
+
+ # Plot data.
if show:
plt.show()
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=25856&r1=25855&r2=25856&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Sep 16 13:19:38 2014
@@ -36,7 +36,7 @@
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
from lib.errors import RelaxError
-from lib.io import extract_data, get_file_path
+from lib.io import extract_data, get_file_path, open_read_file
from lib.spectrum.nmrpipe import show_apod_extract, show_apod_rmsd,
show_apod_rmsd_dir_to_files, show_apod_rmsd_to_file
from pipe_control.mol_res_spin import display_spin, generate_spin_string,
return_spin, spin_loop
from pipe_control.minimise import assemble_scaling_matrix
@@ -6058,7 +6058,21 @@
r2eff_stat_dic =
RDR.get_r2eff_stat_dic(list_r2eff_dics=[r2eff_ft_sel, r2eff_mdd_sel],
list_glob_ini=[128, 126])
## Plot R2eff stats
- RDR.plot_r2eff_stat(r2eff_stat_dic=r2eff_stat_dic,
methods=['FT', 'MDD'], list_glob_ini=[128, 126, 6], show=True)
+ write_stats = True
+ RDR.plot_r2eff_stat(r2eff_stat_dic=r2eff_stat_dic,
methods=['FT', 'MDD'], list_glob_ini=[128, 126, 6], show=False,
write_stats=write_stats)
+
+ # Open stat file.
+ if write_stats:
+ if selection == None:
+ file_name = 'r2eff_stat_all.txt'
+ else:
+ file_name = 'r2eff_stat_sel.txt'
+ path = RDR.results_dir
+ data = extract_data(file=file_name, dir=path)
+
+ # Loop over the lines.
+ for i, data_i in enumerate(data):
+ print(i, data_i)
# Do minimisation
r25856 - in /trunk: auto_analyses/relax_disp_repeat_cpmg.py test_suite/system_tests/relax_disp.py