Author: tlinnet
Date: Sat Jul 26 13:34:13 2014
New Revision: 24773
URL: http://svn.gna.org/viewcvs/relax?rev=24773&view=rev
Log:
Renamed and improved epydoc information for interpolating fucntion for
dispersion values.
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=24773&r1=24772&r2=24773&view=diff
==============================================================================
--- branches/r1rho_plotting/specific_analyses/relax_disp/data.py
(original)
+++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py Sat
Jul 26 13:34:13 2014
@@ -760,6 +760,144 @@
desel_spin(spin_id)
+def interpolate_disp(spin=None, spin_id=None, si=None, num_points=None,
extend=None):
+ """Interpolate function for 2D Grace plotting function for the
dispersion curves.
+
+ @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 Hz).
+ @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
frequencies for cpmg_frqs in Hz {Ei, Si, Mi, Oi, Di}, list of interpolated
spin-lock field strength frequencies for spin_lock_nu1_new in Hz {Ei, Si, Mi,
Oi, Di}, 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-4 list of numpy rank-1 float arrays, rank-4 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.
+ cpmg_frqs_new = None
+ spin_lock_nu1_new = None
+
+ # Interpolate the CPMG frequencies (numeric models).
+ if spin.model in MODEL_LIST_NUMERIC_CPMG or spin.model in [MODEL_B14,
MODEL_B14_FULL]:
+ cpmg_frqs = return_cpmg_frqs(ref_flag=False)
+ relax_times = return_relax_times()
+ if cpmg_frqs != None and len(cpmg_frqs[0][0]):
+ cpmg_frqs_new = []
+ for ei in range(len(cpmg_frqs)):
+ # Add a new dimension.
+ cpmg_frqs_new.append([])
+
+ # Then loop over the spectrometer frequencies.
+ for mi in range(len(cpmg_frqs[ei])):
+ # Add a new dimension.
+ cpmg_frqs_new[ei].append([])
+
+ # Finally the offsets.
+ for oi in range(len(cpmg_frqs[ei][mi])):
+ # Add a new dimension.
+ cpmg_frqs_new[ei][mi].append([])
+
+ # No data.
+ if not len(cpmg_frqs[ei][mi][oi]):
+ continue
+
+ # The minimum frequency unit.
+ min_frq = 1.0 / relax_times[ei][mi]
+ max_frq = max(cpmg_frqs[ei][mi][oi]) + round(extend
/ min_frq) * min_frq
+ num_points = int(round(max_frq / min_frq))
+
+ # Interpolate (adding the extended amount to the
end).
+ for di in range(num_points):
+ point = (di + 1) * min_frq
+ cpmg_frqs_new[ei][mi][oi].append(point)
+
+ # Convert to a numpy array.
+ cpmg_frqs_new[ei][mi][oi] =
array(cpmg_frqs_new[ei][mi][oi], float64)
+
+ # Interpolate the CPMG frequencies (analytic models).
+ else:
+ cpmg_frqs = return_cpmg_frqs(ref_flag=False)
+ if cpmg_frqs != None and len(cpmg_frqs[0][0]):
+ cpmg_frqs_new = []
+ for ei in range(len(cpmg_frqs)):
+ # Add a new dimension.
+ cpmg_frqs_new.append([])
+
+ # Then loop over the spectrometer frequencies.
+ for mi in range(len(cpmg_frqs[ei])):
+ # Add a new dimension.
+ cpmg_frqs_new[ei].append([])
+
+ # Finally the offsets.
+ for oi in range(len(cpmg_frqs[ei][mi])):
+ # Add a new dimension.
+ cpmg_frqs_new[ei][mi].append([])
+
+ # No data.
+ if not len(cpmg_frqs[ei][mi][oi]):
+ continue
+
+ # Interpolate (adding the extended amount to the
end).
+ for di in range(num_points):
+ point = (di + 1) *
(max(cpmg_frqs[ei][mi][oi])+extend) / num_points
+ cpmg_frqs_new[ei][mi][oi].append(point)
+
+ # Convert to a numpy array.
+ cpmg_frqs_new[ei][mi][oi] =
array(cpmg_frqs_new[ei][mi][oi], float64)
+
+ # Interpolate the spin-lock field strengths.
+ spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
+ if spin_lock_nu1 != None and len(spin_lock_nu1[0][0][0]):
+ spin_lock_nu1_new = []
+ for ei in range(len(spin_lock_nu1)):
+ # Add a new dimension.
+ spin_lock_nu1_new.append([])
+
+ # Then loop over the spectrometer frequencies.
+ for mi in range(len(spin_lock_nu1[ei])):
+ # Add a new dimension.
+ spin_lock_nu1_new[ei].append([])
+
+ # Finally the offsets.
+ for oi in range(len(spin_lock_nu1[ei][mi])):
+ # Add a new dimension.
+ spin_lock_nu1_new[ei][mi].append([])
+
+ # No data.
+ if not len(spin_lock_nu1[ei][mi][oi]):
+ continue
+
+ # Interpolate (adding the extended amount to the end).
+ for di in range(num_points):
+ point = (di + 1) *
(max(spin_lock_nu1[ei][mi][oi])+extend) / num_points
+ spin_lock_nu1_new[ei][mi][oi].append(point)
+
+ # Convert to a numpy array.
+ spin_lock_nu1_new[ei][mi][oi] =
array(spin_lock_nu1_new[ei][mi][oi], 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, fields=spin_lock_nu1_new)
+
+ # 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, cpmg_frqs=cpmg_frqs_new, spin_lock_nu1=spin_lock_nu1_new)
+
+ 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 is_cpmg_exp_type(id=None):
"""Determine if the given spectrum ID corresponds to a CPMG experiment
type.
@@ -1632,7 +1770,7 @@
interpolated_flag = False
if not spin.model in [MODEL_R2EFF]:
# Interpolate through disp points.
- interpolated_flag, back_calc, cpmg_frqs_new, spin_lock_nu1_new,
chemical_shifts, spin_lock_fields_inter, offsets_inter, tilt_angles_inter,
Delta_omega_inter, w_eff_inter = plot_disp_curves_interpolate_disp(spin=spin,
spin_id=spin_id, si=si, num_points=num_points, extend=extend)
+ interpolated_flag, back_calc, cpmg_frqs_new, spin_lock_nu1_new,
chemical_shifts, spin_lock_fields_inter, offsets_inter, tilt_angles_inter,
Delta_omega_inter, w_eff_inter = interpolate_disp(spin=spin, spin_id=spin_id,
si=si, num_points=num_points, extend=extend)
else:
back_calc = None
@@ -1751,7 +1889,7 @@
if not spin.model in [MODEL_R2EFF]:
# Interpolate through disp points.
- interpolated_flag, back_calc, cpmg_frqs_new, spin_lock_nu1_new,
chemical_shifts, spin_lock_fields_inter, offsets_inter, tilt_angles_inter,
Delta_omega_inter, w_eff_inter = plot_disp_curves_interpolate_disp(spin=spin,
spin_id=spin_id, si=si, num_points=num_points, extend=extend)
+ interpolated_flag, back_calc, cpmg_frqs_new, spin_lock_nu1_new,
chemical_shifts, spin_lock_fields_inter, offsets_inter, tilt_angles_inter,
Delta_omega_inter, w_eff_inter = interpolate_disp(spin=spin, spin_id=spin_id,
si=si, num_points=num_points, extend=extend)
else:
back_calc = None
@@ -1830,144 +1968,6 @@
# Add the file to the results file list.
add_result_file(type='grace', label='Grace', file=file_path)
-
-
-def plot_disp_curves_interpolate_disp(spin=None, spin_id=None, si=None,
num_points=None, extend=None):
- """Interpolate function for 2D Grace plotting function for the
dispersion curves.
-
- @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 Hz).
- @type extend: float
- @return: The file_name, 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: string, 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.
- cpmg_frqs_new = None
- spin_lock_nu1_new = None
-
- # Interpolate the CPMG frequencies (numeric models).
- if spin.model in MODEL_LIST_NUMERIC_CPMG or spin.model in [MODEL_B14,
MODEL_B14_FULL]:
- cpmg_frqs = return_cpmg_frqs(ref_flag=False)
- relax_times = return_relax_times()
- if cpmg_frqs != None and len(cpmg_frqs[0][0]):
- cpmg_frqs_new = []
- for ei in range(len(cpmg_frqs)):
- # Add a new dimension.
- cpmg_frqs_new.append([])
-
- # Then loop over the spectrometer frequencies.
- for mi in range(len(cpmg_frqs[ei])):
- # Add a new dimension.
- cpmg_frqs_new[ei].append([])
-
- # Finally the offsets.
- for oi in range(len(cpmg_frqs[ei][mi])):
- # Add a new dimension.
- cpmg_frqs_new[ei][mi].append([])
-
- # No data.
- if not len(cpmg_frqs[ei][mi][oi]):
- continue
-
- # The minimum frequency unit.
- min_frq = 1.0 / relax_times[ei][mi]
- max_frq = max(cpmg_frqs[ei][mi][oi]) + round(extend
/ min_frq) * min_frq
- num_points = int(round(max_frq / min_frq))
-
- # Interpolate (adding the extended amount to the
end).
- for di in range(num_points):
- point = (di + 1) * min_frq
- cpmg_frqs_new[ei][mi][oi].append(point)
-
- # Convert to a numpy array.
- cpmg_frqs_new[ei][mi][oi] =
array(cpmg_frqs_new[ei][mi][oi], float64)
-
- # Interpolate the CPMG frequencies (analytic models).
- else:
- cpmg_frqs = return_cpmg_frqs(ref_flag=False)
- if cpmg_frqs != None and len(cpmg_frqs[0][0]):
- cpmg_frqs_new = []
- for ei in range(len(cpmg_frqs)):
- # Add a new dimension.
- cpmg_frqs_new.append([])
-
- # Then loop over the spectrometer frequencies.
- for mi in range(len(cpmg_frqs[ei])):
- # Add a new dimension.
- cpmg_frqs_new[ei].append([])
-
- # Finally the offsets.
- for oi in range(len(cpmg_frqs[ei][mi])):
- # Add a new dimension.
- cpmg_frqs_new[ei][mi].append([])
-
- # No data.
- if not len(cpmg_frqs[ei][mi][oi]):
- continue
-
- # Interpolate (adding the extended amount to the
end).
- for di in range(num_points):
- point = (di + 1) *
(max(cpmg_frqs[ei][mi][oi])+extend) / num_points
- cpmg_frqs_new[ei][mi][oi].append(point)
-
- # Convert to a numpy array.
- cpmg_frqs_new[ei][mi][oi] =
array(cpmg_frqs_new[ei][mi][oi], float64)
-
- # Interpolate the spin-lock field strengths.
- spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False)
- if spin_lock_nu1 != None and len(spin_lock_nu1[0][0][0]):
- spin_lock_nu1_new = []
- for ei in range(len(spin_lock_nu1)):
- # Add a new dimension.
- spin_lock_nu1_new.append([])
-
- # Then loop over the spectrometer frequencies.
- for mi in range(len(spin_lock_nu1[ei])):
- # Add a new dimension.
- spin_lock_nu1_new[ei].append([])
-
- # Finally the offsets.
- for oi in range(len(spin_lock_nu1[ei][mi])):
- # Add a new dimension.
- spin_lock_nu1_new[ei][mi].append([])
-
- # No data.
- if not len(spin_lock_nu1[ei][mi][oi]):
- continue
-
- # Interpolate (adding the extended amount to the end).
- for di in range(num_points):
- point = (di + 1) *
(max(spin_lock_nu1[ei][mi][oi])+extend) / num_points
- spin_lock_nu1_new[ei][mi][oi].append(point)
-
- # Convert to a numpy array.
- spin_lock_nu1_new[ei][mi][oi] =
array(spin_lock_nu1_new[ei][mi][oi], 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, fields=spin_lock_nu1_new)
-
- # 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, cpmg_frqs=cpmg_frqs_new, spin_lock_nu1=spin_lock_nu1_new)
-
- 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 plot_disp_curves_interpolate_sl_offset(spin=None, spin_id=None, si=None,
num_points=None, extend=None):
r24773 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py