Author: bugman
Date: Wed May 29 17:53:30 2013
New Revision: 19777
URL: http://svn.gna.org/viewcvs/relax?rev=19777&view=rev
Log:
Implemented a basic graph for the relax_disp.plot_disp_curves user function.
This simply plots out the nu_CPMG value or spin-lock field verses the
R2eff/R1rho values from the
experiment. The graph of the back calculated R2eff/R1rho values from the
model fit is still to be
added.
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19777&r1=19776&r2=19777&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Wed May 29
17:53:30 2013
@@ -604,6 +604,86 @@
self.data_init(spin)
+ def _plot_disp_curves(self, dir=None, force=None):
+ """Custom 2D Grace plotting function for the dispersion curves.
+
+ One file will be created per spin system.
+
+
+ @keyword dir: The optional directory to place the file
into.
+ @type dir: str
+ @param force: Boolean argument which if True causes the
files to be overwritten if it already exists.
+ @type force: bool
+ """
+
+ # Test if the current pipe exists.
+ pipes.test()
+
+ # Test if the sequence data is loaded.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # Loop over each spin.
+ for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+ # Open the file for writing.
+ file_name = "disp_%s.agr" % spin_id
+ 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
+
+ # Add a new set for the measured data.
+ data.append([])
+
+ # Loop over the spectrometer frequencies.
+ graph_index = 0
+ err = False
+ for frq in loop_frq():
+ # Loop over the dispersion points.
+ for disp_point in loop_point():
+ # The data key.
+ key = return_param_key_from_data(frq=frq,
point=disp_point)
+
+ # No data present.
+ if key not in spin.r2eff:
+ continue
+
+ # Add the data.
+ data[-1].append([disp_point, spin.r2eff[key]])
+
+ # Add the error.
+ if hasattr(spin, 'r2eff_err') and key in spin.r2eff_err:
+ err = True
+ data[-1][-1].append(spin.r2eff_err[key])
+
+ # FIXME: Add the back-calculated data as a second set.
+
+ # The axis labels.
+ if cdp.exp_type == '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.
+ write_xy_header(sets=len(data), file=file, set_names=set_labels,
axis_labels=axis_labels)
+
+ # 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)
+
+
def _plot_exp_curves(self, file=None, dir=None, force=None, norm=None):
"""Custom 2D Grace plotting function for the exponential curves.
@@ -625,7 +705,6 @@
raise RelaxNoSequenceError
# Open the file for writing.
-
file_path = get_file_path(file, dir)
file = open_write_file(file, dir, force)
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=19777&r1=19776&r2=19777&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Wed May 29 17:53:30 2013
@@ -303,6 +303,36 @@
uf.wizard_size = (800, 600)
uf.wizard_apply_button = False
uf.wizard_image = WIZARD_IMAGE_PATH + 'nessy.png'
+
+
+# The relax_disp.plot_disp_curves user function.
+uf = uf_info.add_uf('relax_disp.plot_disp_curves')
+uf.title = "Create 2D Grace plots of the dispersion curves for each spin
system."
+uf.title_short = "Dispersion curve plotting."
+uf.add_keyarg(
+ name = "dir",
+ default = "grace",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory name to place all of the spin system files into.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "force",
+ default = False,
+ py_type = "bool",
+ desc_short = "force flag",
+ desc = "A flag which, if set to True, will cause the files to be
overwritten."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This is used to created 2D Grace plots of the
dispersion curves of the spin-lock field strength or nu_CPMG frequencies
verses R2eff/R1rho. One file will be created per spin system with the name
'disp_x.agr', where x is the spin ID string.")
+uf.backend = relax_disp_obj._plot_disp_curves
+uf.menu_text = "&plot_disp_curves"
+uf.gui_icon = "oxygen.actions.document-save"
+uf.wizard_size = (700, 500)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'grace.png'
# The relax_disp.plot_exp_curves user function.
r19777 - in /branches/relax_disp: specific_analyses/relax_disp/__init__.py user_functions/relax_disp.py