Author: tlinnet
Date: Fri Jul 25 13:59:22 2014
New Revision: 24744
URL: http://svn.gna.org/viewcvs/relax?rev=24744&view=rev
Log:
Split out the interpolating in
specific_analyses.relax_disp.data.plot_disp_curves() into separate function.
This is to prepare for a interpolating function for spin-lock offset rather
than spin-lock field strength for R1rho models.
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=24744&r1=24743&r2=24744&view=diff
==============================================================================
--- branches/r1rho_plotting/specific_analyses/relax_disp/data.py
(original)
+++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py Fri
Jul 25 13:59:22 2014
@@ -1580,8 +1580,11 @@
linetype = []
linestyle = []
- # The unique file name.
- file_name = "disp%s.agr" % spin_id.replace('#', '_').replace(':',
'_').replace('@', '_')
+ # Set up the interpolated curve data structures.
+ interpolated_flag = False
+ if not spin.model in [MODEL_R2EFF]:
+ # Interpolate through disp points.
+ file_name, interpolated_flag, back_calc, cpmg_frqs_new,
spin_lock_nu1_new = plot_disp_curves_interpolate_disp(spin, spin_id,
num_points, extend)
# Open the file for writing.
file_path = get_file_path(file_name, dir)
@@ -1591,117 +1594,6 @@
proton = None
if proton_mmq_flag:
proton = return_attached_protons(spin_id)[0]
-
- # Set up the interpolated curve data structures.
- interpolated_flag = False
- if not spin.model in [MODEL_R2EFF]:
- # 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)
-
- # 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)
# Loop over each experiment type.
graph_index = 0
@@ -1976,6 +1868,135 @@
else:
file_name = expanduser(file_name)
chmod(file_name, S_IRWXU|S_IRGRP|S_IROTH)
+
+
+def plot_disp_curves_interpolate_disp(spin, spin_id, num_points, extend):
+ """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 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
+ """
+
+ # The unique file name.
+ file_name = "disp%s.agr" % spin_id.replace('#', '_').replace(':',
'_').replace('@', '_')
+
+ # 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)
+
+ # 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 file_name, interpolated_flag, back_calc, cpmg_frqs_new,
spin_lock_nu1_new
def plot_exp_curves(file=None, dir=None, force=None, norm=None):
r24744 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py