Author: tlinnet
Date: Sat Jul 26 13:34:18 2014
New Revision: 24774
URL: http://svn.gna.org/viewcvs/relax?rev=24774&view=rev
Log:
Renamed the interpolating function for offset, and improved the epydoc
information.
sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho
analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
Modified:
branches/r1rho_plotting/specific_analyses/relax_disp/data.py
Modified: branches/r1rho_plotting/specific_analyses/relax_disp/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/specific_analyses/relax_disp/data.py?rev=24774&r1=24773&r2=24774&view=diff
==============================================================================
--- branches/r1rho_plotting/specific_analyses/relax_disp/data.py
(original)
+++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py Sat
Jul 26 13:34:18 2014
@@ -898,6 +898,78 @@
return interpolated_flag, back_calc, cpmg_frqs_new, spin_lock_nu1_new,
chemical_shifts, spin_lock_fields_inter, offsets, tilt_angles, Delta_omega,
w_eff
+def interpolate_offset(spin=None, spin_id=None, si=None, num_points=None,
extend=None):
+ """Interpolate function for 2D Grace plotting function for the
dispersion curves, interpolating through spin-lock offset in rad/s.
+
+ @keyword spin: The specific spin data container.
+ @type spin: SpinContainer instance.
+ @keyword spin_id: The spin ID string.
+ @type spin_id: str
+ @keyword si: The index of the given spin in the cluster.
+ @type si: int
+ @keyword num_points: The number of points to generate the
interpolated fitted curves with.
+ @type num_points: int
+ @keyword extend: How far to extend the interpolated fitted curves
to in offset ppm.
+ @type extend: float
+ @return: The interpolated_flag, list of back calculated
R2eff/R1rho values in rad/s {Ei, Si, Mi, Oi, Di}, list of interpolated
spin-lock offsets in ppm {Ei, Si, Mi, Oi}, chemical shifts in rad/s {Ei, Si,
Mi}, list of interpolated spin-lock field strength frequencies for
spin_lock_fields_inter in Hz {Ei, Si, Mi, Oi, Di}, interpolated spin-lock
offsets in rad/s {Ei, Si, Mi, Oi}, interpolated rotating frame tilt angles
{Ei, Si, Mi, Oi, Di}, interpolated average resonance offset in the rotating
frame in rad/s {Ei, Si, Mi, Oi, Di} and the interpolated effective field in
rotating frame in rad/s {Ei, Si, Mi, Oi, Di}.
+ @rtype: boolean, rank-4 list of numpy rank-1 float
arrays, rank-3 list of numpy rank-1 float arrays, rank-2 list of numpy rank-1
float arrays, rank-4 list of numpy rank-1 float arrays, rank-3 list of numpy
rank-1 float arrays, rank-4 list of numpy rank-1 float arrays, rank-4 list of
numpy rank-1 float arrays, rank-4 list of numpy rank-1 float arrays
+ """
+
+ # Set the flag.
+ interpolated_flag = True
+
+ # Initialise some structures.
+ spin_lock_offset_new = []
+
+ # Get the spin-lock field strengths.
+ spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
+
+ # Get the current minimum and maximum spin_lock_offset
+ if not hasattr(cdp, 'spin_lock_offset'):
+ min_offset = 0
+ max_offset = 0
+
+ else:
+ min_offset = min(cdp.spin_lock_offset_list)
+ max_offset = max(cdp.spin_lock_offset_list)
+
+ if spin_lock_nu1 != None and len(spin_lock_nu1[0][0][0]):
+ for ei in range(len(spin_lock_nu1)):
+ # Add a new dimension for ei.
+ spin_lock_offset_new.append([])
+
+ # Add a new dimension for si.
+ spin_lock_offset_new[ei].append([])
+
+ # Then loop over the spectrometer frequencies.
+ for mi in range(len(spin_lock_nu1[ei])):
+ # Add a new dimension for mi.
+ spin_lock_offset_new[ei][0].append([])
+
+ # Interpolate (adding the extended amount to the end).
+ for oi in range(num_points+1):
+ offset_point = oi * (max_offset+extend) / num_points
+ spin_lock_offset_new[ei][0][mi].append(offset_point)
+
+ # Convert to a numpy array.
+ spin_lock_offset_new[ei][0][mi] =
array(spin_lock_offset_new[ei][0][mi], float64)
+
+ # Number of spectrometer fields.
+ fields = [None]
+ field_count = 1
+ if hasattr(cdp, 'spectrometer_frq_count'):
+ fields = cdp.spectrometer_frq_list
+ field_count = cdp.spectrometer_frq_count
+
+ # The offset data.
+ chemical_shifts, spin_lock_fields_inter, offsets, tilt_angles,
Delta_omega, w_eff = return_offset_data(spins=[spin], spin_ids=[spin_id],
field_count=field_count, spin_lock_offset=spin_lock_offset_new,
fields=spin_lock_nu1)
+
+ # Back calculate R2eff data for the second sets of plots.
+ back_calc =
specific_analyses.relax_disp.optimisation.back_calc_r2eff(spin=spin,
spin_id=spin_id, spin_lock_offset=spin_lock_offset_new,
spin_lock_nu1=spin_lock_fields_inter)
+
+ return interpolated_flag, back_calc, spin_lock_offset_new,
chemical_shifts, spin_lock_fields_inter, offsets, tilt_angles, Delta_omega,
w_eff
+
+
def is_cpmg_exp_type(id=None):
"""Determine if the given spectrum ID corresponds to a CPMG experiment
type.
@@ -1968,78 +2040,6 @@
# Add the file to the results file list.
add_result_file(type='grace', label='Grace', file=file_path)
-
-
-def plot_disp_curves_interpolate_sl_offset(spin=None, spin_id=None, si=None,
num_points=None, extend=None):
- """Interpolate function for 2D Grace plotting function for the
dispersion curves, interpolating theta through spin-lock offset in rad/s.
-
- @keyword spin: The specific spin data container.
- @type spin: SpinContainer instance.
- @keyword spin_id: The spin ID string.
- @type spin_id: str
- @keyword si: The index of the given spin in the cluster.
- @type si: int
- @keyword num_points: The number of points to generate the
interpolated fitted curves with.
- @type num_points: int
- @keyword extend: How far to extend the interpolated fitted curves
to (in ppm).
- @type extend: float
- @return: The interpolated_flag, list of R2eff values for
back_calc, list of frequencies in Hz for interpolated cpmg_frqs_new and
spin_lock_nu1_new.
- @rtype: boolean, numpy rank-1 float64 array, numpy
rank-1 float64 array, numpy rank-1 float64 array
- """
-
- # Set the flag.
- interpolated_flag = True
-
- # Initialise some structures.
- spin_lock_offset_new = []
-
- # Get the spin-lock field strengths.
- spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
-
- # Get the current minimum and maximum spin_lock_offset
- if not hasattr(cdp, 'spin_lock_offset'):
- min_offset = 0
- max_offset = 0
-
- else:
- min_offset = min(cdp.spin_lock_offset_list)
- max_offset = max(cdp.spin_lock_offset_list)
-
- if spin_lock_nu1 != None and len(spin_lock_nu1[0][0][0]):
- for ei in range(len(spin_lock_nu1)):
- # Add a new dimension for ei.
- spin_lock_offset_new.append([])
-
- # Add a new dimension for si.
- spin_lock_offset_new[ei].append([])
-
- # Then loop over the spectrometer frequencies.
- for mi in range(len(spin_lock_nu1[ei])):
- # Add a new dimension for mi.
- spin_lock_offset_new[ei][0].append([])
-
- # Interpolate (adding the extended amount to the end).
- for oi in range(num_points+1):
- offset_point = oi * (max_offset+extend) / num_points
- spin_lock_offset_new[ei][0][mi].append(offset_point)
-
- # Convert to a numpy array.
- spin_lock_offset_new[ei][0][mi] =
array(spin_lock_offset_new[ei][0][mi], float64)
-
- # Number of spectrometer fields.
- fields = [None]
- field_count = 1
- if hasattr(cdp, 'spectrometer_frq_count'):
- fields = cdp.spectrometer_frq_list
- field_count = cdp.spectrometer_frq_count
-
- # The offset data.
- chemical_shifts, spin_lock_fields_inter, offsets, tilt_angles,
Delta_omega, w_eff = return_offset_data(spins=[spin], spin_ids=[spin_id],
field_count=field_count, spin_lock_offset=spin_lock_offset_new,
fields=spin_lock_nu1)
-
- # Back calculate R2eff data for the second sets of plots.
- back_calc =
specific_analyses.relax_disp.optimisation.back_calc_r2eff(spin=spin,
spin_id=spin_id, spin_lock_offset=spin_lock_offset_new,
spin_lock_nu1=spin_lock_fields_inter)
-
- return interpolated_flag, back_calc, spin_lock_offset_new,
chemical_shifts, spin_lock_fields_inter, offsets, tilt_angles, Delta_omega,
w_eff
def plot_disp_curves_loop_frq(exp_type=None, ei=None, current_spin=None,
spin_id=None, si=None, back_calc=None, spin_lock_nu1_new=None,
chemical_shifts=None, spin_lock_fields_inter=None, offsets_inter=None,
tilt_angles_inter=None, Delta_omega_inter=None, w_eff_inter=None,
interpolated_flag=None, graph_index=None, colour_order=None, data=None,
set_labels=None, set_colours=None, x_axis_type_zero=None, symbols=None,
symbol_sizes=None, linetype=None, linestyle=None, axis_labels=None):
r24774 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py