Author: tlinnet
Date: Tue Jul 29 10:25:04 2014
New Revision: 24795
URL: http://svn.gna.org/viewcvs/relax?rev=24795&view=rev
Log:
Added keywords to be used to backend function of Ãplot_disp_curves.
The keyword 'y_axis', determine which y data to be plotted on this axis.
The keyword 'x_axis', determine which x data to be plotted on this axis.
extend_hz, determine how far to extend interpolated CPMG frequency or
spin-Ãlock field strenght.
extend_ppm, determine how far to extend interpolated spin-lock offsets.
interpolate, determine to interpolate dispersion points, or offset.
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
branches/r1rho_plotting/user_functions/relax_disp.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=24795&r1=24794&r2=24795&view=diff
==============================================================================
--- branches/r1rho_plotting/specific_analyses/relax_disp/data.py
(original)
+++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py Tue
Jul 29 10:25:04 2014
@@ -760,7 +760,7 @@
desel_spin(spin_id)
-def interpolate_disp(spin=None, spin_id=None, si=None, num_points=None,
extend=None):
+def interpolate_disp(spin=None, spin_id=None, si=None, num_points=None,
extend_hz=None):
"""Interpolate function for 2D Grace plotting function for the
dispersion curves.
@keyword spin: The specific spin data container.
@@ -771,8 +771,8 @@
@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
+ @keyword extend_hz: How far to extend the interpolated fitted curves
to (in Hz).
+ @type extend_hz: 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
"""
@@ -810,7 +810,7 @@
# 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
+ max_frq = max(cpmg_frqs[ei][mi][oi]) +
round(extend_hz / min_frq) * min_frq
num_points = int(round(max_frq / min_frq))
# Interpolate (adding the extended amount to the
end).
@@ -846,7 +846,7 @@
# 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
+ point = (di + 1) *
(max(cpmg_frqs[ei][mi][oi])+extend_hz) / num_points
cpmg_frqs_new[ei][mi][oi].append(point)
# Convert to a numpy array.
@@ -876,7 +876,7 @@
# 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
+ point = (di + 1) *
(max(spin_lock_nu1[ei][mi][oi])+extend_hz) / num_points
spin_lock_nu1_new[ei][mi][oi].append(point)
# Convert to a numpy array.
@@ -901,7 +901,7 @@
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):
+def interpolate_offset(spin=None, spin_id=None, si=None, num_points=None,
extend_ppm=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.
@@ -912,8 +912,8 @@
@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
+ @keyword extend_ppm: How far to extend the interpolated fitted curves
to in offset ppm.
+ @type extend_ppm: 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
"""
@@ -951,7 +951,7 @@
# Interpolate (adding the extended amount to the end).
for oi in range(num_points+1):
- offset_point = oi * (max_offset+extend) / num_points
+ offset_point = oi * (max_offset+extend_ppm) / num_points
spin_lock_offset_new[ei][0][mi].append(offset_point)
# Convert to a numpy array.
@@ -1750,7 +1750,7 @@
current_spin.r2eff_bc[key] = back_calc[ei][si][mi][oi][di]
-def plot_disp_curves(dir=None, num_points=1000, extend=500.0, force=False):
+def plot_disp_curves(dir=None, y_axis="r2eff", x_axis="disp",
num_points=1000, extend_hz=500.0, extend_ppm=500.0, interpolate="disp",
force=False):
"""Custom 2D Grace plotting function for the dispersion curves.
One file will be created per spin system.
@@ -1759,10 +1759,18 @@
@keyword dir: The optional directory to place the file into.
@type dir: str
+ @keyword y_axis: String flag to tell which data on Y axis to plot
for. Option can be either "r2eff" which plot 'r2eff' for CPMG experiments or
'r1rho' for R1rho experiments or option can be "r1rho_r2", which for R1rho
experiments plot R2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho -
R_1 * cos^2(theta) ) / sin^2(theta).
+ @type y_axis: str
+ @keyword x_axis: String flag to tell which data on X axis to plot
for. Option can be either "disp" which plot 'CPMG frequency (Hz)' for CPMG
experiments or 'Spin-lock field strength (Hz)' for R1rho experiments or
option can be either "w_eff" or "theta" for R1rho experiments, which plot
'Effective field in rotating frame (rad/s)' or 'Rotating frame tilt angle
theta (rad)'.
+ @type x_axis: 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
+ @keyword extend_hz: How far to extend the interpolated fitted curves
to, when interpolating over CPMG frequency or spin-lock field strength (in
Hz).
+ @type extend_hz: float
+ @keyword extend_ppm: How far to extend the interpolated fitted curves
to, when interpolating over spin-lock offset (in ppm).
+ @type extend_ppm: float
+ @keyword interpolate: How to interpolate the fitted curves. Either by
option "disp" which interpolate CPMG frequency or spin-lock field strength,
or by option "offset" which interpole over spin-lock offset.
+ @type interpolate: float
@param force: Boolean argument which if True causes the files
to be overwritten if it already exists.
@type force: bool
"""
@@ -1779,24 +1787,22 @@
# Plot dispersion curves, extending over number of dispersion points.
file_name_ini = "disp"
- plot_disp_curves_disp(file_name_ini=file_name_ini, dir=dir,
num_points=num_points, extend=extend, force=force,
proton_mmq_flag=proton_mmq_flag, colour_order=colour_order)
+ plot_disp_curves_disp(file_name_ini=file_name_ini, dir=dir,
num_points=num_points, extend_hz=extend_hz, force=force,
proton_mmq_flag=proton_mmq_flag, colour_order=colour_order)
# For R1rho models, interpolate through spin-lock field strength, and
plot R1rho R2 as function of effective field in rotating frame w_eff.
if cdp.exp_type_list == [EXP_TYPE_R1RHO]:
file_name_ini = "r2_r1rho_as_func_of_w_eff_inter_w1"
x_axis = "w_eff"
- interpolate = "disp"
-
plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=file_name_ini,
dir=dir, x_axis=x_axis, interpolate=interpolate, num_points=num_points,
extend=extend, force=force, proton_mmq_flag=proton_mmq_flag,
colour_order=colour_order)
+
plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=file_name_ini,
dir=dir, y_axis=y_axis, x_axis=x_axis, interpolate=interpolate,
num_points=num_points, extend_hz=extend_hz, extend_ppm=extend_ppm,
force=force, proton_mmq_flag=proton_mmq_flag, colour_order=colour_order)
file_name_ini = "r1rho_as_func_of_theta_inter_w1"
x_axis = "theta"
- interpolate = "disp"
-
plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=file_name_ini,
dir=dir, x_axis=x_axis, interpolate=interpolate, num_points=num_points,
extend=extend, force=force, proton_mmq_flag=proton_mmq_flag,
colour_order=colour_order)
+
plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=file_name_ini,
dir=dir, y_axis=y_axis, x_axis=x_axis, interpolate=interpolate,
num_points=num_points, extend_hz=extend_hz, extend_ppm=extend_ppm,
force=force, proton_mmq_flag=proton_mmq_flag, colour_order=colour_order)
file_name_ini = "r1rho_as_func_of_theta_inter_offset"
x_axis = "theta"
interpolate = "offset"
-
plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=file_name_ini,
dir=dir, x_axis=x_axis, interpolate=interpolate, num_points=num_points,
extend=extend, force=force, proton_mmq_flag=proton_mmq_flag,
colour_order=colour_order)
+
plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=file_name_ini,
dir=dir, y_axis=y_axis, x_axis=x_axis, interpolate=interpolate,
num_points=num_points, extend_hz=extend_hz, extend_ppm=extend_ppm,
force=force, proton_mmq_flag=proton_mmq_flag, colour_order=colour_order)
# Write a python "grace to PNG/EPS/SVG..." conversion script.
# Open the file for writing.
@@ -1816,7 +1822,7 @@
chmod(file_name, S_IRWXU|S_IRGRP|S_IROTH)
-def plot_disp_curves_disp(file_name_ini=None, dir=None, num_points=None,
extend=None, force=None, proton_mmq_flag=None, colour_order=None):
+def plot_disp_curves_disp(file_name_ini=None, dir=None, num_points=None,
extend_hz=None, force=None, proton_mmq_flag=None, colour_order=None):
"""Custom 2D Grace plotting function for the dispersion curves, looping
over dispersion points.
One file will be created per spin system.
@@ -1827,8 +1833,8 @@
@type dir: 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
+ @keyword extend_hz: How far to extend the interpolated fitted
curves to (in Hz).
+ @type extend_hz: float
@param force: Boolean argument which if True causes the
files to be overwritten if it already exists.
@type force: bool
@keyword proton_mmq_flag: The flag specifying if proton SQ or MQ CPMG
data exists for the spin.
@@ -1864,7 +1870,7 @@
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 = 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_hz=extend_hz)
else:
back_calc = None
@@ -1937,7 +1943,7 @@
add_result_file(type='grace', label='Grace', file=file_path)
-def plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=None,
dir=None, x_axis=None, interpolate=None, num_points=None, extend=None,
force=None, proton_mmq_flag=None, colour_order=None):
+def plot_disp_curves_r1rho_r2_as_func_of_rot_param(file_name_ini=None,
dir=None, y_axis=None, x_axis=None, interpolate=None, num_points=None,
extend_hz=None, extend_ppm=None, force=None, proton_mmq_flag=None,
colour_order=None):
"""Custom 2D Grace plotting function for the dispersion curves,
interpolating theta through spin-lock offset rather than spin-lock field
strength.
One file will be created per spin system.
@@ -1946,14 +1952,18 @@
@type file_name_ini: str
@keyword dir: The optional directory to place the file
into.
@type dir: str
- @keyword x_axis: String flag to tell which X axis to plot
for. Can be either "w_eff" or "theta".
+ @keyword y_axis: String flag to tell which data on Y axis to
plot for. Option can be either "r2eff" which plot 'r2eff' for CPMG
experiments or 'r1rho' for R1rho experiments or option can be "r1rho_r2",
which for R1rho experiments plot R2 = R1rho / sin^2(theta) - R_1 /
tan^2(theta) = (R1rho - R_1 * cos^2(theta) ) / sin^2(theta).
+ @type y_axis: str
+ @keyword x_axis: String flag to tell which data on X axis to
plot for. Option can be either "disp" which plot 'CPMG frequency (Hz)' for
CPMG experiments or 'Spin-lock field strength (Hz)' for R1rho experiments or
option can be either "w_eff" or "theta" for R1rho experiments, which plot
'Effective field in rotating frame (rad/s)' or 'Rotating frame tilt angle
theta (rad)'.
@type x_axis: str
@keyword interpolate: String flag to tell which data type to
interpolate for. Can be either "disp" or "offset".
@type interpolate: 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
+ @keyword extend_hz: How far to extend the interpolated fitted
curves to, when interpolating over CPMG frequency or spin-lock field strength
(in Hz).
+ @type extend_hz: float
+ @keyword extend_ppm: How far to extend the interpolated fitted
curves to, when interpolating over spin-lock offset (in ppm).
+ @type extend_ppm: float
@param force: Boolean argument which if True causes the
files to be overwritten if it already exists.
@type force: bool
@keyword proton_mmq_flag: The flag specifying if proton SQ or MQ CPMG
data exists for the spin.
@@ -1990,11 +2000,11 @@
if interpolate == "disp":
# 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 = 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_hz=extend_hz)
elif interpolate == "offset":
# Interpolate through disp points.
- interpolated_flag, back_calc, spin_lock_offset_new,
chemical_shifts, spin_lock_fields_inter, offsets_inter, tilt_angles_inter,
Delta_omega_inter, w_eff_inter = interpolate_offset(spin=spin,
spin_id=spin_id, si=si, num_points=num_points, extend=extend)
+ interpolated_flag, back_calc, spin_lock_offset_new,
chemical_shifts, spin_lock_fields_inter, offsets_inter, tilt_angles_inter,
Delta_omega_inter, w_eff_inter = interpolate_offset(spin=spin,
spin_id=spin_id, si=si, num_points=num_points, extend_ppm=extend_ppm)
# The spin_lock field interpolated through each offset.
spin_lock_nu1_new = spin_lock_fields_inter
Modified: branches/r1rho_plotting/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/user_functions/relax_disp.py?rev=24795&r1=24794&r2=24795&view=diff
==============================================================================
--- branches/r1rho_plotting/user_functions/relax_disp.py (original)
+++ branches/r1rho_plotting/user_functions/relax_disp.py Tue Jul 29
10:25:04 2014
@@ -482,7 +482,7 @@
can_be_none = False
)
uf.add_keyarg(
- name = "extend",
+ name = "extend_hz",
py_type = "num",
default = 500.0,
desc_short = "interpolated dispersion curve extension (in Hz)",
r24795 - in /branches/r1rho_plotting: specific_analyses/relax_disp/data.py user_functions/relax_disp.py