Author: bugman
Date: Thu Apr 18 14:31:29 2013
New Revision: 19492
URL: http://svn.gna.org/viewcvs/relax?rev=19492&view=rev
Log:
Created the relax_disp.plot_exp_curves user function.
This is to be used to create 2D graphs of the exponential curves (relaxation
time verses peak
intensity) as the grace.write user function plots are not very nice - the
curves from each
spectrometer field strength and dispersion point are mixed into one curve.
Modified:
branches/relax_disp/specific_analyses/relax_disp.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp.py?rev=19492&r1=19491&r2=19492&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Thu Apr 18 14:31:29
2013
@@ -35,10 +35,14 @@
# relax module imports.
from dep_check import C_module_exp_fn
from lib.errors import RelaxError, RelaxFuncSetupError, RelaxLenError,
RelaxNoModelError, RelaxNoSequenceError, RelaxNoSpectraError
+from lib.io import get_file_path, open_write_file
+from lib.list import count_unique_elements, unique_elements
+from lib.software.grace import write_xy_data, write_xy_header
from lib.text.sectioning import subsection
from lib.list import count_unique_elements, unique_elements
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
+from pipe_control.result_files import add_result_file
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
from target_functions.relax_disp import Dispersion
@@ -547,6 +551,27 @@
# Increment the parameter index.
param_index = param_index + 1
+
+
+ def _dispersion_point_loop(self):
+ """Generator method for looping over all dispersion points (either
spin-lock field or nu_CPMG points).
+
+ @return: Either the spin-lock field strength in Hz or the nu_CPMG
frequency in Hz.
+ @rtype: float
+ """
+
+ # CPMG type data.
+ if cdp.exp_type in ['cpmg']:
+ fields = unique_elements(cdp.cpmg_frqs_list.values())
+ elif cdp.exp_type in ['r1rho']:
+ fields = unique_elements(cdp.spin_lock_nu1.values())
+ else:
+ raise RelaxError("The experiment type '%s' is unknown.")
+ fields.sort()
+
+ # Yield each unique field strength or frequency.
+ for field in fields:
+ yield field
def _exp_curve_index_from_key(self, key):
@@ -1207,6 +1232,86 @@
return num
+ def _plot_exp_curves(self, file=None, dir=None, force=None, norm=None):
+ """Custom 2D Grace plotting function for the exponential curves.
+
+ @keyword file: The name of the Grace file to create.
+ @type file: str
+ @keyword dir: The optional directory to place the file
into.
+ @type dir: str
+ @param force: Boolean argument which if True causes the
file to be overwritten if it already exists.
+ @type force: bool
+ @keyword norm: The normalisation flag which if set to True
will cause all graphs to be normalised to a starting value of 1.
+ @type norm: 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
+
+ # Open the file for writing.
+ file_path = get_file_path(file, dir)
+ file = open_write_file(file, 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
+ err = False
+ for field in self._spectrometer_loop():
+ # Loop over the dispersion points.
+ for disp_point in self._dispersion_point_loop():
+ # Create a new graph.
+ data.append([])
+
+ # Loop over each spin.
+ for spin, id in spin_loop(return_id=True, skip_desel=True):
+ # Append a new set structure and set the name to the
spin ID.
+ data[graph_index].append([])
+ if graph_index == 0:
+ set_labels.append("Spin %s" % id)
+
+ # Loop over the relaxation time periods.
+ for time in cdp.relax_time_list:
+ # The key.
+ key = self._intensity_key(exp_key=disp_point,
relax_time=time)
+
+ # Add the data.
+ if hasattr(spin, 'intensity_err'):
+ data[graph_index][-1].append([time,
spin.intensities[key], spin.intensity_err[key]])
+ err = True
+ else:
+ data[graph_index][-1].append([time,
spin.intensities[key]])
+
+ # Increment the field index.
+ graph_index += 1
+
+ # The axis labels.
+ 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)
+
+ # Write the data.
+ graph_type = 'xy'
+ if err:
+ graph_type = 'xydy'
+ write_xy_data(data, file=file, graph_type=graph_type, norm=norm)
+
+ # Close the file.
+ file.close()
+
+ # Add the file to the results file list.
+ add_result_file(type='grace', label='Grace', file=file_path)
+
+
def _relax_time(self, time=0.0, spectrum_id=None):
"""Set the relaxation time period associated with a given spectrum.
@@ -1285,6 +1390,26 @@
# Set up the model.
self._model_setup(model, params)
+
+
+ def _spectrometer_loop(self):
+ """Generator method for looping over all spectrometer field data.
+
+ @return: The field strength in Hz.
+ @rtype: float
+ """
+
+ # The number of spectrometer field strengths.
+ field_count = 1
+ fields = [None]
+ if hasattr(cdp, 'frq'):
+ field_count = count_unique_elements(cdp.frq.values())
+ fields = unique_elements(cdp.frq.values())
+ fields.sort()
+
+ # Yield each unique spectrometer field strength.
+ for field in fields:
+ yield field
def _spin_lock_field(self, spectrum_id=None, field=None):
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=19492&r1=19491&r2=19492&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Thu Apr 18 14:31:29 2013
@@ -22,6 +22,14 @@
# Module docstring.
"""The relax_disp user function definitions."""
+
+# Python module imports.
+import dep_check
+if dep_check.wx_module:
+ from wx import FD_OPEN, FD_SAVE
+else:
+ FD_OPEN = -1
+ FD_SAVE = -1
# relax module imports.
from pipe_control import spectrum
@@ -261,6 +269,52 @@
uf.wizard_apply_button = False
+# The relax_disp.plot_exp_curves user function.
+uf = uf_info.add_uf('relax_disp.plot_exp_curves')
+uf.title = "Create 2D Grace plots of the exponential curves."
+uf.title_short = "Exponential curve plotting."
+uf.add_keyarg(
+ name = "file",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "file name",
+ desc = "The name of the file.",
+ wiz_filesel_wildcard = "Grace files (*.agr)|*.agr;*.AGR",
+ wiz_filesel_style = FD_SAVE
+)
+uf.add_keyarg(
+ name = "dir",
+ default = "grace",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory name.",
+ 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 file to be
overwritten."
+)
+uf.add_keyarg(
+ name = "norm",
+ default = False,
+ py_type = "bool",
+ desc_short = "normalisation flag",
+ desc = "A flag which, if set to True, will cause all graphs to be
normalised to a starting value of 1. This is for the normalisation of series
type data."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This is used to created 2D Grace plots of the
individual exponential curves used to find the R2eff values. This
supplements the grace.write user function which is not capable of generating
these curves in a reasonable format.")
+uf.backend = relax_disp_obj._plot_exp_curves
+uf.menu_text = "&plot_exp_curves"
+uf.gui_icon = "oxygen.actions.document-save"
+uf.wizard_size = (800, 600)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'grace.png'
+
+
# The relax_disp.relax_time user function.
uf = uf_info.add_uf('relax_disp.relax_time')
uf.title = "Set the relaxation delay time associated with each spectrum."
r19492 - in /branches/relax_disp: specific_analyses/relax_disp.py user_functions/relax_disp.py