Author: bugman
Date: Wed Dec 4 19:40:07 2013
New Revision: 21787
URL: http://svn.gna.org/viewcvs/relax?rev=21787&view=rev
Log:
The relax_disp.r2eff_read_spin user function now can handle offset data in
the file.
If the new offset_col argument is set and disp_point_col is not, then the
file being read can
contain the spin-lock offset information rather than the spin-lock field
strength values. This is
only for R1rho-type data.
Modified:
trunk/specific_analyses/relax_disp/disp_data.py
trunk/user_functions/relax_disp.py
Modified: trunk/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21787&r1=21786&r2=21787&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/disp_data.py (original)
+++ trunk/specific_analyses/relax_disp/disp_data.py Wed Dec 4 19:40:07 2013
@@ -44,7 +44,7 @@
from lib.errors import RelaxError, RelaxNoSpectraError, RelaxNoSpinError,
RelaxSpinTypeError
from lib.float import isNaN
from lib.io import extract_data, get_file_path, open_write_file,
read_spin_data, strip, write_data, write_spin_data
-from lib.nmr import frequency_to_rad_per_s
+from lib.nmr import frequency_to_ppm, frequency_to_rad_per_s
from lib.physical_constants import g1H, return_gyromagnetic_ratio
from lib.software.grace import write_xy_data, write_xy_header,
script_grace2images
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
@@ -1734,7 +1734,7 @@
spin_lock_field(spectrum_id=id, field=disp_frq)
-def r2eff_read_spin(id=None, spin_id=None, file=None, dir=None,
disp_point_col=None, data_col=None, error_col=None, sep=None):
+def r2eff_read_spin(id=None, spin_id=None, file=None, dir=None,
disp_point_col=None, offset_col=None, data_col=None, error_col=None,
sep=None):
"""Read R2eff/R1rho values from file whereby each row is a different
dispersion point.
@keyword id: The experiment ID string to associate the
data with. This will be modified to include the dispersion point data as
"%s_%s" % (id, disp_point).
@@ -1747,6 +1747,8 @@
@type dir: str or None
@keyword disp_point_col: The column containing the dispersion point
information. For CPMG-type data, this is the frequency of the CPMG pulse
train. For R1rho-type data, this is the spin-lock field strength (nu1). The
units must be Hertz.
@type disp_point_col: int
+ @keyword offset_col: This is for R1rho data - the dispersion
point column can be substituted for the offset values in Hertz.
+ @type offset_col: None or int
@keyword data_col: The column containing the R2eff/R1rho data
in Hz.
@type data_col: int
@keyword error_col: The column containing the R2eff/R1rho errors.
@@ -1784,15 +1786,21 @@
continue
# Unpack.
- disp_point = line[disp_point_col-1]
+ if disp_point_col != None:
+ ref_data = line[disp_point_col-1]
+ if offset_col != None:
+ ref_data = line[offset_col-1]
value = line[data_col-1]
error = line[error_col-1]
- # Convert and check the dispersion point.
+ # Convert and check the dispersion point or offset.
try:
- disp_point = float(disp_point)
+ ref_data = float(ref_data)
except ValueError:
- warn(RelaxWarning("The dispersion point data of the line %s is
invalid." % line))
+ if disp_point_col != None:
+ warn(RelaxWarning("The dispersion point data of the line %s
is invalid." % line))
+ if offset_col != None:
+ warn(RelaxWarning("The offset data of the line %s is
invalid." % line))
continue
# Convert and check the value.
@@ -1828,17 +1836,29 @@
# Find a close enough dispersion point (to one decimal place to
allow for user truncation).
if hasattr(cdp, 'cpmg_frqs') and spectrum_id in cdp.cpmg_frqs:
- if abs(disp_point - cdp.cpmg_frqs[spectrum_id]) < 0.1:
+ if abs(ref_data - cdp.cpmg_frqs[spectrum_id]) < 0.1:
new_id = spectrum_id
break
- if hasattr(cdp, 'spin_lock_nu1') and spectrum_id in
cdp.spin_lock_nu1:
- if abs(disp_point - cdp.spin_lock_nu1[spectrum_id]) < 0.1:
+ if disp_point_col != None and hasattr(cdp, 'spin_lock_nu1') and
spectrum_id in cdp.spin_lock_nu1:
+ if abs(ref_data - cdp.spin_lock_nu1[spectrum_id]) < 0.1:
new_id = spectrum_id
break
+ if offset_col != None and hasattr(cdp, 'spin_lock_offset') and
spectrum_id in cdp.spin_lock_offset:
+ # Convert the data.
+ if offset_col != None:
+ data_new = frequency_to_ppm(frq=ref_data,
B0=cdp.spectrometer_frq[spectrum_id], isotope=spin.isotope)
+
+ # Store the ID.
+ if abs(data_new - cdp.spin_lock_offset[spectrum_id]) < 0.1:
+ new_id = spectrum_id
+ break
# No match.
if new_id == None:
- raise RelaxError("The experiment ID corresponding to the base ID
'%s' and the dispersion point '%s' could not be found." % (id, disp_point))
+ if disp_point_col != None:
+ raise RelaxError("The experiment ID corresponding to the
base ID '%s' and the dispersion point '%s' could not be found." % (id,
ref_data))
+ if offset_col != None:
+ raise RelaxError("The experiment ID corresponding to the
base ID '%s' and the offset '%s' could not be found." % (id, ref_data))
# Add the ID to the list.
new_ids.append(new_id)
@@ -1855,6 +1875,10 @@
exp_type = get_exp_type(id=new_id)
# The dispersion point key.
+ if disp_point_col != None:
+ disp_point = ref_data
+ if offset_col != None:
+ disp_point = cdp.spin_lock_nu1[new_id]
point_key = return_param_key_from_data(exp_type=exp_type, frq=frq,
point=disp_point)
# Store the R2eff data.
Modified: trunk/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/relax_disp.py?rev=21787&r1=21786&r2=21787&view=diff
==============================================================================
--- trunk/user_functions/relax_disp.py (original)
+++ trunk/user_functions/relax_disp.py Wed Dec 4 19:40:07 2013
@@ -702,11 +702,21 @@
)
uf.add_keyarg(
name = "disp_point_col",
- default = 1,
+ default = None,
min = 1,
py_type = "int",
desc_short = "dispersion point column",
- desc = "The column containing the CPMG frequency or spin-lock field
strength (Hz)."
+ desc = "The column containing the CPMG frequency or spin-lock field
strength (Hz).",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "offset_col",
+ default = None,
+ min = 1,
+ py_type = "int",
+ desc_short = "offset column",
+ desc = "The column containing the offset information for R1rho-type
data.",
+ can_be_none = True
)
uf.add_keyarg(
name = "data_col",
@@ -736,7 +746,7 @@
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This will read R2eff/R1rho data for a single spin
directly from a file. The data will be associated with an experiment ID
string. This ID can be used for setting the type of dispersion experiment
the data is from, spectrometer proton frequency of the data, and the time of
the relaxation period.")
-uf.desc[-1].add_paragraph("The format of this text file must be that each
row corresponds to a dispersion point (i.e. per CPMG frequency nu_CPMG or
per spin-lock field strength nu1) and that there is one file per unique spin
system. The file must be in columnar format.")
+uf.desc[-1].add_paragraph("The format of this text file must be that each
row corresponds to a dispersion point (i.e. per CPMG frequency nu_CPMG or per
spin-lock field strength nu1) and that there is one file per unique spin
system. The file must be in columnar format. For R1rho data, the dispersion
point column can be substituted for the offset values in Hertz.")
uf.backend = r2eff_read_spin
uf.menu_text = "&r2eff_read_spin"
uf.gui_icon = "oxygen.actions.document-open"
r21787 - in /trunk: specific_analyses/relax_disp/disp_data.py user_functions/relax_disp.py