Author: bugman
Date: Fri Sep 26 19:14:41 2014
New Revision: 26075
URL: http://svn.gna.org/viewcvs/relax?rev=26075&view=rev
Log:
Merged revisions 26057 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26057 | tlinnet | 2014-09-26 13:06:40 +0200 (Fri, 26 Sep 2014) | 3 lines
Implemented the writing out of parameter values between comparison of NI
level.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Sep 26 19:14:41 2014
@@ -1 +1 @@
-/trunk:1-26017,26043-26056
+/trunk:1-26017,26043-26057
Modified: branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py?rev=26075&r1=26074&r2=26075&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
(original)
+++ branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
Fri Sep 26 19:14:41 2014
@@ -1691,6 +1691,7 @@
res_dic = {}
res_dic['method'] = method
res_dic['selection'] = selection
+ res_dic['analysis'] = analysis
for glob_ini in list_glob_ini:
# Check previous, and get the pipe name.
@@ -1764,7 +1765,7 @@
return res_dic
- def plot_min_corr(self, corr_data, show=False):
+ def plot_min_corr(self, corr_data, show=False, write_stats=False):
# Define figure.
# Nr of columns is number of datasets.
nr_cols = len(corr_data)
@@ -1773,6 +1774,7 @@
glob_ini_0 = glob_inis_0[0]
params_list = data_xy_0[0][str(glob_ini_0)]['params']['params_list']
nr_rows = len(params_list)
+ analysis = data_xy_0[0]['analysis']
# Define figure
fig, axises = plt.subplots(nrows=nr_rows, ncols=nr_cols)
@@ -1780,6 +1782,9 @@
# axises is a tuple with number of elements corresponding to number
of rows.
# Each sub-tuple contains axis for each column.
+
+ # For writing out stats.
+ data_dic = OrderedDict()
# Loop over the rows.
for i, row_axises in enumerate(axises):
@@ -1797,6 +1802,15 @@
y = data_y[str(glob_ini_y)]['params'][param]
np = len(y)
+ # Linear a, with no intercept.
+ a = sum(x * y) / sum(x**2)
+ min_xy = min(concatenate((x,y)))
+ max_xy = max(concatenate((x,y)))
+
+ dx = (max_xy - min_xy) / np
+ x_arange = arange(min_xy, max_xy + dx, dx)
+ y_arange = a * x_arange
+
ax.plot(x, x, 'o', label='%s vs. %s' % (method_x, method_x))
ax.plot(x, y, '.', label='%s vs. %s' % (method_y, method_x) )
@@ -1814,20 +1828,116 @@
ax.ticklabel_format(style='sci', axis='x',
scilimits=(0,0))
ax.ticklabel_format(style='sci', axis='y',
scilimits=(0,0))
- # If r2 or dw parameter, do a straight line:
- if param in PARAMS_R20 + ['dw']:
- # Linear a, with no intercept.
- a = sum(x * y) / sum(x**2)
- min_xy = min(concatenate((x,y)))
- max_xy = max(concatenate((x,y)))
-
- dx = (max_xy - min_xy) / 10
- x_arange = arange(min_xy, max_xy + dx, dx)
- y_arange = a * x_arange
- ax.plot(x_arange, x_arange, 'b--')
- ax.plot(x_arange, y_arange, 'g--')
+ ## If r2 or dw parameter, do a straight line:
+ #if param in PARAMS_R20 + ['dw']:
+
+ # ax.plot(x_arange, x_arange, 'b--')
+ # ax.plot(x_arange, y_arange, 'g--')
+
+ # Do a straight line for all.
+ ax.plot(x_arange, x_arange, 'b--')
+ ax.plot(x_arange, y_arange, 'g--')
+
+ # Store to data dic
+ method_xy_NI = "%s_%s_%s%s_%s%s" % (analysis, param,
method_x, glob_ini_x, method_y, glob_ini_y)
+ data_dic[method_xy_NI] = []
+
+ # Add to data.
+ for k, x_k in enumerate(x):
+ y_k = y[k]
+ x_arange_k = x_arange[k]
+ y_arange_k = y_arange[k]
+ data_dic[method_xy_NI].append(["%3.5f"%x_k, "%3.5f"%y_k,
"%3.5f"%x_arange_k, "%3.5f"%y_arange_k])
plt.tight_layout()
+
+ # Loop over columns for writing data.
+ # Write to file.
+ if write_stats:
+ # Re-order the data.
+ headings_all = []
+ method_xy_NI_all = []
+ # Loop over the columns.
+ for j in range(nr_cols):
+ headings_j = []
+ method_xy_NI_j = []
+ # Loop over rows
+ for i in range(nr_rows):
+ # Extract from lists.
+ data, methods, glob_inis = corr_data[j]
+ method_x, method_y = methods
+ glob_ini_x, glob_ini_y = glob_inis
+ param = params_list[i]
+
+ # Add to headings
+ method_x_NI = "%s_%s_%s%s" % (analysis, param, method_x,
glob_ini_x)
+ method_y_NI = "%s_%s_%s%s" % (analysis, param, method_y,
glob_ini_y)
+ method_x_NI_lin = "%s_%s_lin_%s%s" % (analysis, param,
method_x, glob_ini_x)
+ method_y_NI_lin = "%s_%s_lin_%s%s" % (analysis, param,
method_y, glob_ini_y)
+ headings_j = headings_j + [method_x_NI, method_y_NI,
method_x_NI_lin, method_y_NI_lin]
+
+ method_xy_NI = "%s_%s_%s%s_%s%s" % (analysis, param,
method_x, glob_ini_x, method_y, glob_ini_y)
+ method_xy_NI_j.append(method_xy_NI)
+
+ headings_all.append(headings_j)
+ method_xy_NI_all.append(method_xy_NI_j)
+
+ # Loop over the columns.
+ for j, headings_j in enumerate(headings_all):
+ method_xy_NI_j = method_xy_NI_all[j]
+
+ data_w = []
+ method_xy_NI_r2 = method_xy_NI_j[0]
+ data_r2 = data_dic[method_xy_NI_r2]
+
+ # Loop over the rows of data.
+ for k, data_r2_k in enumerate(data_r2):
+ data_row = data_r2_k
+ # Loop over the columns.
+ for method_xy_NI in method_xy_NI_j[1:]:
+ data_param = data_dic[method_xy_NI]
+
+ try:
+ data_param_row = data_param[k]
+ except IndexError:
+ data_param_row = len(data_param[0]) * ['0.0']
+
+ data_row = data_row + data_param_row
+
+ data_w.append(data_row)
+
+ # Define file name.
+ data, methods, glob_inis = corr_data[j]
+ data_x, data_y = data
+ method_x, method_y = methods
+ glob_ini_x, glob_ini_y = glob_inis
+
+ # Get the spin selection for correlation.
+ selection = data_x['selection']
+
+ file_name_ini = '%s_%s_%s_%s_%s' % (analysis, method_x,
glob_ini_x, method_y, glob_ini_y)
+ if selection == None:
+ file_name_ini = file_name_ini + '_all'
+ else:
+ file_name_ini = file_name_ini + '_sel'
+
+ file_name = file_name_ini + '.txt'
+ path = self.results_dir
+
+ # save figure
+ # Write png.
+ png_file_name = file_name_ini + '.png'
+ png_file_path = get_file_path(file_name=png_file_name,
dir=path)
+ plt.savefig(png_file_path, bbox_inches='tight')
+
+ # Write file
+ 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_j, data=data_w)
+
+ # Close file.
+ file_obj.close()
if show:
plt.show()
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=26075&r1=26074&r2=26075&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py Fri
Sep 26 19:14:41 2014
@@ -6123,8 +6123,97 @@
for i, data_i in enumerate(data):
print(i, data_i)
- # Do minimisation.
- if False:
+
+ # Do minimisation individual.
+ if True:
+ methods = ['FT', 'MDD']
+ # Now calculate R2eff.
+ RDR.calc_r2eff(methods=methods, list_glob_ini=[128, 126])
+
+ min_methods = [['FT'], ['MDD']]
+ min_list_glob_ini = [[128], range(126, 130, 2)[::-1]]
+
+ #min_methods = [['FT']]
+ #min_list_glob_ini = [[128]]
+ #selection = ':2,3'
+ selection = None
+
+ for i, methods in enumerate(min_methods):
+ list_glob_ini = min_list_glob_ini[i]
+
+ if True:
+ # First get data.
+ if True:
+ # First load all data.
+ RDR.calc_r2eff(methods=methods,
list_glob_ini=list_glob_ini)
+
+ # Then set R20
+ if True:
+ # Set R20 from min R2eff in preparation for Grid
search.
+ RDR.r20_from_min_r2eff(methods=methods,
model=MODEL_CR72, model_from=MODEL_R2EFF, analysis='grid_setup_ind',
analysis_from='int', list_glob_ini=list_glob_ini, force=True)
+
+ # Check and print parameters.
+ if True:
+ # Print for pipe name
+ method = methods[0]
+ glob_ini = list_glob_ini[0]
+
+ test_pipe_name = RDR.name_pipe(method=method,
model=MODEL_CR72, analysis='grid_setup_ind', glob_ini=glob_ini)
+ RDR.spin_display_params(pipe_name=test_pipe_name)
+
+ # Then Grid search.
+ if True:
+ # Do Grid search.
+ RDR.minimise_grid_search(inc=4, verbosity=1,
methods=methods, model=MODEL_CR72, analysis='grid_setup_ind',
list_glob_ini=list_glob_ini, force=True)
+
+ # Then Minimise.
+ if True:
+ # Minimise
+ RDR.opt_max_iterations = int(1e2)
+ RDR.minimise_execute(methods=methods, model=MODEL_CR72,
analysis='min_ind', analysis_from='grid_setup_ind',
list_glob_ini=list_glob_ini, force=True)
+
+ #print asd
+
+ # Plot statistics.
+ # Try plot some minimisation correlations.
+ if True:
+ selection = None
+ # Collect param values.
+ analysis = 'min_ind'
+ min_ft_sel = RDR.col_min(method='FT', model=MODEL_CR72,
analysis=analysis, list_glob_ini=[128], selection=selection)
+ min_mdd_sel = RDR.col_min(method='MDD', model=MODEL_CR72,
analysis=analysis, list_glob_ini=range(126, 130, 2)[::-1],
selection=selection)
+
+ fig1 = [[min_ft_sel, min_mdd_sel], ['FT', 'MDD'], [128, 128]]
+ fig2 = [[min_ft_sel, min_mdd_sel], ['FT', 'MDD'], [128, 126]]
+ corr_data = [fig1, fig2]
+
+ write_stats = True
+ RDR.plot_min_corr(corr_data=corr_data, show=False,
write_stats=write_stats)
+
+ # Open stat file.
+ if write_stats:
+ for i, corr_data_i in enumerate(corr_data):
+ data, methods, glob_inis = corr_data[i]
+ data_x, data_y = data
+ method_x, method_y = methods
+ glob_ini_x, glob_ini_y = glob_inis
+
+ file_name_ini = '%s_%s_%s_%s_%s' % (analysis, method_x,
glob_ini_x, method_y, glob_ini_y)
+
+ if selection == None:
+ file_name = file_name_ini + '_all.txt'
+ else:
+ file_name = file_name_ini + '_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 clustered.
+ if True:
methods = ['FT', 'MDD']
# Now calculate R2eff.
RDR.calc_r2eff(methods=methods, list_glob_ini=[128, 126])
@@ -6148,23 +6237,19 @@
# Then select spins.
if True:
# Deselect all spins.
- #RDR.deselect_all(methods=methods, model='setup',
model_from=MODEL_R2EFF, analysis='grid_setup', analysis_from='int',
list_glob_ini=list_glob_ini)
RDR.deselect_all(methods=methods, model='setup',
model_from=MODEL_R2EFF, analysis='grid_setup', analysis_from='int',
list_glob_ini=list_glob_ini, force=True)
- #RDR.select_spin(spin_id=selection, methods=methods,
model='setup', analysis='grid_setup', list_glob_ini=list_glob_ini)
RDR.select_spin(spin_id=selection, methods=methods,
model='setup', analysis='grid_setup', list_glob_ini=list_glob_ini, force=True)
# Then preset values.
if True:
# Set k_AB for Grid search.
- #RDR.value_set(methods=methods, val=1000.,
param='kex', model=MODEL_CR72, model_from='setup', analysis='grid_setup',
list_glob_ini=list_glob_ini)
RDR.value_set(methods=methods, val=1000.,
param='kex', model=MODEL_CR72, model_from='setup', analysis='grid_setup',
list_glob_ini=list_glob_ini, force=True)
RDR.value_set(methods=methods, val=0.95, param='pA',
model=MODEL_CR72, model_from='setup', analysis='grid_setup',
list_glob_ini=list_glob_ini, force=True)
# Then set R20
if True:
# Set R20 from min R2eff in preparation for Grid
search.
- #RDR.r20_from_min_r2eff(methods=methods,
model=MODEL_CR72, analysis='grid_setup', list_glob_ini=list_glob_ini)
RDR.r20_from_min_r2eff(methods=methods,
model=MODEL_CR72, analysis='grid_setup', list_glob_ini=list_glob_ini,
force=True)
# Check and print parameters.
@@ -6179,38 +6264,54 @@
# Then Grid search.
if True:
# Do Grid search.
- #RDR.minimise_grid_search(inc=200, verbosity=1,
methods=methods, model=MODEL_CR72, analysis='grid',
analysis_from='grid_setup', list_glob_ini=list_glob_ini)
RDR.minimise_grid_search(inc=200, verbosity=1,
methods=methods, model=MODEL_CR72, analysis='grid',
analysis_from='grid_setup', list_glob_ini=list_glob_ini, force=True)
# Then cluster spins.
if True:
- #RDR.cluster_spins(spin_id=selection,
methods=methods, model=MODEL_CR72, analysis='grid',
list_glob_ini=list_glob_ini)
RDR.cluster_spins(spin_id=selection,
methods=methods, model=MODEL_CR72, analysis='grid',
list_glob_ini=list_glob_ini, force=True)
# Then Minimise.
if True:
# Minimise
RDR.opt_max_iterations = int(1e2)
- #RDR.minimise_execute(methods=methods, model=MODEL_CR72,
analysis='min', analysis_from='grid', list_glob_ini=list_glob_ini, force=True)
RDR.minimise_execute(methods=methods, model=MODEL_CR72,
analysis='min', analysis_from='grid', list_glob_ini=list_glob_ini,
force=False)
-
- #print asd
# Plot statistics.
# Try plot some minimisation correlations.
- if False:
- # Collect r2eff values.
- min_ft_sel = RDR.col_min(method='FT', model=MODEL_CR72,
analysis='min', list_glob_ini=[128], selection=None)
- min_mdd_sel = RDR.col_min(method='MDD', model=MODEL_CR72,
analysis='min', list_glob_ini=range(126, 130, 2)[::-1], selection=None)
-
- fig1 = [[min_ft_sel, min_mdd_sel], ['FT', 'MDD'], [128, 126]]
- fig2 = [[min_mdd_sel, min_mdd_sel], ['MDD', 'MDD'], [128, 126]]
+ if True:
+ selection = ':2,3'
+ # Collect param values.
+ analysis = 'min'
+ min_ft_sel = RDR.col_min(method='FT', model=MODEL_CR72,
analysis=analysis, list_glob_ini=[128], selection=selection)
+ min_mdd_sel = RDR.col_min(method='MDD', model=MODEL_CR72,
analysis=analysis, list_glob_ini=range(126, 130, 2)[::-1],
selection=selection)
+
+ fig1 = [[min_ft_sel, min_mdd_sel], ['FT', 'MDD'], [128, 128]]
+ fig2 = [[min_ft_sel, min_mdd_sel], ['FT', 'MDD'], [128, 126]]
corr_data = [fig1, fig2]
- RDR.plot_min_corr(corr_data=corr_data, show=False)
-
- # Print the pipes.
- #display(sort=True, rev=True)
+ write_stats = True
+ RDR.plot_min_corr(corr_data=corr_data, show=False,
write_stats=write_stats)
+
+ # Open stat file.
+ if write_stats:
+ for i, corr_data_i in enumerate(corr_data):
+ data, methods, glob_inis = corr_data[i]
+ data_x, data_y = data
+ method_x, method_y = methods
+ glob_ini_x, glob_ini_y = glob_inis
+
+ file_name_ini = '%s_%s_%s_%s_%s' % (analysis, method_x,
glob_ini_x, method_y, glob_ini_y)
+
+ if selection == None:
+ file_name = file_name_ini + '_all.txt'
+ else:
+ file_name = file_name_ini + '_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)
def test_r1rho_kjaergaard_auto(self):
r26075 - in /branches/frame_order_cleanup: ./ auto_analyses/relax_disp_repeat_cpmg.py test_suite/system_tests/relax_disp.py