Author: bugman
Date: Thu Nov 21 17:04:56 2013
New Revision: 21584
URL: http://svn.gna.org/viewcvs/relax?rev=21584&view=rev
Log:
Large improvements to the relax_disp.plot_disp_curves user function including
MMQ model support.
This user function now handles multiple dispersion data sets better by
placing each into a new
graph. All graphs have also been improved by matching the colours of the
sets for each field
strength and using different symbols and line styles to emphasize the data.
Modified:
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=21584&r1=21583&r2=21584&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Thu Nov 21
17:04:56 2013
@@ -1106,57 +1106,66 @@
@type force: bool
"""
- # Test if the current pipe exists.
+ # Checks.
pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Initalise.
+ check_mol_res_spin_data()
# 1H MMQ flag.
proton_mmq_flag = has_proton_mmq_cpmg()
- # Loop over each experiment type.
- for exp_type, exp_type_index in loop_exp(return_indices=True):
- # Loop over each spin.
- for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
- # Skip protons for MMQ data.
- if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
- continue
-
- # Get the attached proton.
- proton = None
- if proton_mmq_flag:
- proton = return_attached_protons(spin_id)[0]
+ # Default hardcoded colours (one colour for each magnetic field
strength).
+ color_order = [4, 15, 2, 13, 11, 1, 3, 5, 6, 7, 8, 9, 10, 12, 14]
+
+ # Loop over each spin.
+ for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+ # Skip protons for MMQ data.
+ if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
+ continue
+
+ # Initialise some data structures.
+ data = []
+ set_labels = []
+ x_err_flag = False
+ y_err_flag = False
+ set_colours = []
+ symbols = []
+ linetype = []
+ linestyle = []
+
+ # The unique file name.
+ file_name = "disp%s.agr" % spin_id.replace('#', '_').replace(':',
'_').replace('@', '_')
+
+ # Open the file for writing.
+ file_path = get_file_path(file_name, dir)
+ file = open_write_file(file_name, dir, force)
+
+ # Get the attached proton.
+ proton = None
+ if proton_mmq_flag:
+ proton = return_attached_protons(spin_id)[0]
+
+ # Loop over each experiment type.
+ graph_index = 0
+ for exp_type, exp_type_index in loop_exp(return_indices=True):
+ # Update the structures.
+ data.append([])
+ set_labels.append([])
+ set_colours.append([])
+ symbols.append([])
+ linetype.append([])
+ linestyle.append([])
# Alias the correct spin.
current_spin = spin
if exp_type in [EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_PROTON_MQ]:
current_spin = proton
- # The unique file name.
- file_name = "disp%s.agr" % spin_id.replace('#',
'_').replace(':', '_').replace('@', '_')
- if num_exp_types() > 1:
- file_name = "%s_%s" % (exp_type.replace(' ', '_'), file_name)
-
- # Open the file for writing.
- file_path = get_file_path(file_name, dir)
- file = open_write_file(file_name, dir, force)
-
- # Initialise some data structures.
- data = []
- set_labels = []
- x_err_flag = False
- y_err_flag = False
-
# Loop over the spectrometer frequencies.
- graph_index = 0
+ set_index = 0
err = False
for frq, frq_index in loop_frq(return_indices=True):
# Add a new set for the data at each frequency.
- data.append([])
+ data[graph_index].append([])
# Add a new label.
if exp_type in EXP_TYPE_LIST_CPMG:
@@ -1167,6 +1176,12 @@
label += " (%.1f MHz)" % (frq / 1e6)
set_labels.append(label)
+ # The other settings.
+ set_colours[graph_index].append(color_order[frq_index])
+ symbols[graph_index].append(1)
+ linetype[graph_index].append(0)
+ linestyle[graph_index].append(0)
+
# Loop over the dispersion points.
for point, point_index in
loop_point(exp_type_index=exp_type_index, frq_index=frq_index,
return_indices=True):
# The data key.
@@ -1177,17 +1192,20 @@
continue
# Add the data.
- data[-1].append([point, current_spin.r2eff[key]])
+ data[graph_index][set_index].append([point,
current_spin.r2eff[key]])
# Add the error.
if hasattr(current_spin, 'r2eff_err') and key in
current_spin.r2eff_err:
err = True
- data[-1][-1].append(current_spin.r2eff_err[key])
+
data[graph_index][set_index][-1].append(current_spin.r2eff_err[key])
+
+ # Increment the graph set index.
+ set_index += 1
# Add the back-calculated data.
for frq, frq_index in loop_frq(return_indices=True):
# Add a new set for the data at each frequency.
- data.append([])
+ data[graph_index].append([])
# Add a new label.
if exp_type in EXP_TYPE_LIST_CPMG:
@@ -1198,6 +1216,12 @@
label += " (%.1f MHz)" % (frq / 1e6)
set_labels.append(label)
+ # The other settings.
+ set_colours[graph_index].append(color_order[frq_index])
+ symbols[graph_index].append(0)
+ linetype[graph_index].append(1)
+ linestyle[graph_index].append(1)
+
# Loop over the dispersion points.
for point, point_index in
loop_point(exp_type_index=exp_type_index, frq_index=frq_index,
return_indices=True):
# The data key.
@@ -1208,16 +1232,19 @@
continue
# Add the data.
- data[-1].append([point, current_spin.r2eff_bc[key]])
+ data[graph_index][set_index].append([point,
current_spin.r2eff_bc[key]])
# Handle the errors.
if err:
- data[-1][-1].append(None)
+ data[graph_index][set_index][-1].append(None)
+
+ # Increment the graph set index.
+ set_index += 1
# Add the residuals for statistical comparison.
for frq, frq_index in loop_frq(return_indices=True):
# Add a new set for the data at each frequency.
- data.append([])
+ data[graph_index].append([])
# Add a new label.
label = "Residuals"
@@ -1225,6 +1252,12 @@
label += " (%.1f MHz)" % (frq / 1e6)
set_labels.append(label)
+ # The other settings.
+ set_colours[graph_index].append(color_order[frq_index])
+ symbols[graph_index].append(9)
+ linetype[graph_index].append(1)
+ linestyle[graph_index].append(2)
+
# Loop over the dispersion points.
for point, point_index in
loop_point(exp_type_index=exp_type_index, frq_index=frq_index,
return_indices=True):
# The data key.
@@ -1235,34 +1268,47 @@
continue
# Add the data.
- data[-1].append([point, current_spin.r2eff[key] -
current_spin.r2eff_bc[key]])
+ data[graph_index][set_index].append([point,
current_spin.r2eff[key] - current_spin.r2eff_bc[key]])
# Handle the errors.
if err:
err = True
- data[-1][-1].append(current_spin.r2eff_err[key])
-
- # The axis labels.
- if exp_type in EXP_TYPE_LIST_CPMG:
- axis_labels = ['\\qCPMG pulse train frequency (Hz)\\Q',
'\\qR\\s2,eff\\N\\Q (rad.s\\S-1\\N)']
- else:
- axis_labels = ['\\qSpin-lock field strength (Hz)\\Q',
'\\qR\\s1\\xr\\B\\N\\Q (rad.s\\S-1\\N)']
-
- # Write the header.
- title = "Relaxation dispersion plot"
- write_xy_header(file=file, title=title, sets=len(data),
set_names=set_labels, axis_labels=axis_labels, legend_box_fill_pattern=0,
legend_char_size=0.8)
-
- # Write the data.
- graph_type = 'xy'
- if err:
- graph_type = 'xydy'
- write_xy_data([data], file=file, graph_type=graph_type)
-
- # Close the file.
- file.close()
-
- # Add the file to the results file list.
- add_result_file(type='grace', label='Grace', file=file_path)
+
data[graph_index][set_index][-1].append(current_spin.r2eff_err[key])
+
+ # Increment the graph set index.
+ set_index += 1
+
+ # Increment the graph index.
+ graph_index += 1
+
+ # The axis labels.
+ if exp_type in EXP_TYPE_LIST_CPMG:
+ axis_labels = ['\\qCPMG pulse train frequency (Hz)\\Q',
'\\qR\\s2,eff\\N\\Q (rad.s\\S-1\\N)']
+ else:
+ axis_labels = ['\\qSpin-lock field strength (Hz)\\Q',
'\\qR\\s1\\xr\\B\\N\\Q (rad.s\\S-1\\N)']
+
+ # Write the header.
+ title = "Relaxation dispersion plot"
+ graph_num = len(data)
+ sets = []
+ legend = []
+ for gi in range(len(data)):
+ sets.append(len(data[gi]))
+ legend.append(False)
+ legend[0] = True
+ write_xy_header(file=file, title=title, graph_num=graph_num,
sets=sets, set_names=[set_labels]*graph_num, set_colours=set_colours,
symbols=symbols, linetype=linetype, linestyle=linestyle,
axis_labels=[axis_labels]*graph_num, legend=legend,
legend_box_fill_pattern=[0]*graph_num, legend_char_size=[0.8]*graph_num)
+
+ # Write the data.
+ graph_type = 'xy'
+ if err:
+ graph_type = 'xydy'
+ write_xy_data(data, file=file, graph_type=graph_type)
+
+ # Close the file.
+ file.close()
+
+ # Add the file to the results file list.
+ add_result_file(type='grace', label='Grace', file=file_path)
# Write a python "grace to PNG/EPS/SVG..." conversion script.
# Open the file for writing.
@@ -1372,13 +1418,16 @@
axis_labels = ['Relaxation time period (s)', 'Peak intensities']
# Write the header.
- write_xy_header(sets=len(data[0]), file=file, set_names=set_labels,
axis_labels=axis_labels, norm=norm)
+ sets = []
+ for gi in range(len(data)):
+ sets.append(len(data[gi]))
+ write_xy_header(sets=sets, file=file, set_names=[set_labels],
axis_labels=[axis_labels], norm=[norm])
# Write the data.
graph_type = 'xy'
if err:
graph_type = 'xydy'
- write_xy_data(data, file=file, graph_type=graph_type, norm=norm)
+ write_xy_data(data, file=file, graph_type=graph_type, norm=[norm])
# Close the file.
file.close()
r21584 - /branches/relax_disp/specific_analyses/relax_disp/disp_data.py