Author: bugman
Date: Tue Oct 29 17:52:13 2013
New Revision: 21328
URL: http://svn.gna.org/viewcvs/relax?rev=21328&view=rev
Log:
Implemented the relax_disp.r2eff_read_spin user function.
This allows R2eff/R1rho files for each spin to be read.
Modified:
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=21328&r1=21327&r2=21328&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Tue Oct 29
17:52:13 2013
@@ -40,8 +40,8 @@
from warnings import warn
# relax module imports.
-from lib.errors import RelaxError, RelaxNoSpectraError, RelaxSpinTypeError
-from lib.io import get_file_path, open_write_file, read_spin_data,
write_spin_data
+from lib.errors import RelaxError, RelaxNoSpectraError, RelaxNoSpinError,
RelaxSpinTypeError
+from lib.io import extract_data, get_file_path, open_write_file,
read_spin_data, write_data, write_spin_data
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 RelaxNoSpinWarning
@@ -49,7 +49,7 @@
from pipe_control.mol_res_spin import check_mol_res_spin_data,
exists_mol_res_spin_data, generate_spin_id_unique, return_spin, spin_loop
from pipe_control.result_files import add_result_file
from pipe_control.selection import desel_spin
-from pipe_control.spectrum import add_spectrum_id, check_spectrum_id
+from pipe_control.spectrum import add_spectrum_id, check_spectrum_id, get_ids
from pipe_control.spectrometer import set_frequency
from specific_analyses.relax_disp.checks import check_exp_type,
check_mixed_curve_types
from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG,
EXP_TYPE_DESC_CPMG, EXP_TYPE_DESC_DQ_CPMG, EXP_TYPE_DESC_R1RHO,
EXP_TYPE_DESC_MQ_CPMG, EXP_TYPE_DESC_MQ_R1RHO, EXP_TYPE_DESC_ZQ_CPMG,
EXP_TYPE_DQ_CPMG, EXP_TYPE_LIST, EXP_TYPE_LIST_CPMG, EXP_TYPE_LIST_R1RHO,
EXP_TYPE_MQ_CPMG, EXP_TYPE_MQ_R1RHO, EXP_TYPE_R1RHO, EXP_TYPE_ZQ_CPMG
@@ -1182,6 +1182,146 @@
spin_lock_field(spectrum_id=spectrum_id, field=disp_frq)
+def r2eff_read_spin(spin_id=None, file=None, dir=None, exp_type=None,
frq=None, disp_point_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 spin_id: The spin ID string.
+ @type spin_id: str
+ @keyword file: The name of the file to open.
+ @type file: str
+ @keyword dir: The directory containing the file (defaults
to the current directory if None).
+ @type dir: str or None
+ @keyword exp_type: The relaxation dispersion experiment type.
+ @type exp_type: str
+ @keyword frq: The spectrometer frequency in Hertz.
+ @type frq: float
+ @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 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.
+ @type error_col: int
+ @keyword sep: The column separator which, if None,
defaults to whitespace.
+ @type sep: str or None
+ """
+
+ # Data checks.
+ pipes.test()
+ check_mol_res_spin_data()
+
+ # Get the spin.
+ spin = return_spin(spin_id)
+ if spin == None:
+ raise RelaxNoSpinError(spin_id)
+
+ # Extract the data from the file, removing comments and blank lines.
+ file_data = extract_data(file, dir, sep=sep)
+
+ # Loop over the data.
+ data = []
+ for line in file_data:
+ # Invalid columns.
+ if disp_point_col > len(line):
+ warn(RelaxWarning("The data %s is invalid, no dispersion point
column can be found." % line))
+ continue
+ if data_col > len(line):
+ warn(RelaxWarning("The R2eff/R1rho data %s is invalid, no data
column can be found." % line))
+ continue
+ if error_col > len(line):
+ warn(RelaxWarning("The R2eff/R1rho data %s is invalid, no error
column can be found." % line))
+ continue
+
+ # Unpack.
+ disp_point = line[disp_point_col-1]
+ value = line[data_col-1]
+ error = line[error_col-1]
+
+ # Convert and check the dispersion point.
+ try:
+ disp_point = float(disp_point)
+ except ValueError:
+ warn(RelaxWarning("The dispersion point data of the line %s is
invalid." % line))
+ continue
+
+ # Convert and check the value.
+ if value == 'None':
+ value = None
+ if value != None:
+ try:
+ value = float(value)
+ except ValueError:
+ warn(RelaxWarning("The R2eff/R1rho value of the line %s is
invalid." % line))
+ continue
+
+ # Convert and check the error.
+ if error == 'None':
+ error = None
+ if error != None:
+ try:
+ error = float(error)
+ except ValueError:
+ warn(RelaxWarning("The R2eff/R1rho error of the line %s is
invalid." % line))
+ continue
+
+ # Test the error value (cannot be 0.0).
+ if error == 0.0:
+ raise RelaxError("An invalid error value of zero has been
encountered.")
+
+ # Create a key for the global data (the pseudo-spectrum ID).
+ spectrum_id = "%s_%s" % (frq, disp_point)
+
+ # The dispersion point key.
+ point_key = return_param_key_from_data(frq=frq, point=disp_point)
+
+ # Store the R2eff data.
+ if data_col:
+ # Initialise if necessary.
+ if not hasattr(spin, 'r2eff'):
+ spin.r2eff = {}
+
+ # Store.
+ spin.r2eff[point_key] = value
+
+ # Store the R2eff error.
+ if error_col:
+ # Initialise if necessary.
+ if not hasattr(spin, 'r2eff_err'):
+ spin.r2eff_err = {}
+
+ # Store.
+ spin.r2eff_err[point_key] = error
+
+ # Update the global structures.
+ if not spectrum_id in get_ids():
+ # Store the spectrum ID.
+ add_spectrum_id(spectrum_id)
+
+ # Set the spectrometer frequency information.
+ set_frequency(id=spectrum_id, frq=frq)
+
+ # Set the experiment type.
+ set_exp_type(spectrum_id=spectrum_id, exp_type=exp_type)
+
+ # Set the dispersion point frequency.
+ if exp_type in EXP_TYPE_LIST_CPMG:
+ cpmg_frq(spectrum_id=spectrum_id, cpmg_frq=disp_point)
+ else:
+ spin_lock_field(spectrum_id=spectrum_id, field=disp_point)
+
+ # Append the data for printout.
+ data.append(["%20.15f" % disp_point, "%20.15f" % value, "%20.15f" %
error])
+ # Data added.
+ data_flag = True
+
+ # No data, so fail hard!
+ if not len(data):
+ raise RelaxError("No R2eff/R1rho data could be extracted.")
+
+ # Print out.
+ print("The following R2eff/R1rho data has been loaded into the relax
data store:\n")
+ write_data(out=sys.stdout, headings=["Disp_point", "R2eff",
"R2eff_error"], data=data)
+
+
def randomise_R1(spin=None, ri_id=None, N=None):
"""Randomise the R1 data for the given spin for use in the Monte Carlo
simulations.
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=21328&r1=21327&r2=21328&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Tue Oct 29 17:52:13 2013
@@ -38,7 +38,7 @@
from pipe_control.mol_res_spin import get_spin_ids
from specific_analyses.relax_disp.catia import catia_execute, catia_input
from specific_analyses.relax_disp.cpmgfit import cpmgfit_execute,
cpmgfit_input
-from specific_analyses.relax_disp.disp_data import cpmg_frq, insignificance,
plot_disp_curves, plot_exp_curves, r2eff_read, relax_time, set_exp_type,
spin_lock_field, spin_lock_offset
+from specific_analyses.relax_disp.disp_data import cpmg_frq, insignificance,
plot_disp_curves, plot_exp_curves, r2eff_read, r2eff_read_spin, relax_time,
set_exp_type, spin_lock_field, spin_lock_offset
from specific_analyses.relax_disp.nessy import nessy_input
from specific_analyses.relax_disp.parameters import copy
from specific_analyses.relax_disp.sherekhan import sherekhan_input
@@ -651,6 +651,103 @@
uf.desc[-1].add_paragraph("This will read R2eff/R1rho data directly from a
file. The format of this text file must be that each row corresponds to a
unique spin system and that there is one file per dispersion point (i.e. per
CPMG frequency nu_CPMG or per spin-lock field strength n1). The file must be
in columnar format and information to identify the spin must be in columns of
the file.")
uf.backend = r2eff_read
uf.menu_text = "&r2eff_read"
+uf.gui_icon = "oxygen.actions.document-open"
+uf.wizard_size = (900, 600)
+uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
+
+
+# The relax_disp.r2eff_read_spin user function.
+uf = uf_info.add_uf('relax_disp.r2eff_read_spin')
+uf.title = "Read R2eff/R1rho values and errors for a single spin from a
file."
+uf.title_short = "Spin R2eff/R1rho value reading."
+uf.add_keyarg(
+ name = "spin_id",
+ py_type = "str",
+ arg_type = "spin ID",
+ desc_short = "spin ID string",
+ desc = "The spin identification string.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "file",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "file name",
+ desc = "The name of the file.",
+ wiz_filesel_style = FD_SAVE
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory name.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "exp_type",
+ default = "CPMG",
+ py_type = "str",
+ desc_short = "experiment type",
+ desc = "The type of relaxation dispersion experiment performed.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = [
+ "Single quantum (SQ) CPMG-type data",
+ "Zero quantum (ZQ) CPMG-type data",
+ "Double quantum (DQ) CPMG-type data",
+ "Multiple quantum (MQ) CPMG-type data",
+ "%s-type data" % r1rho
+ ],
+ wiz_combo_data = [
+ EXP_TYPE_CPMG,
+ EXP_TYPE_ZQ_CPMG,
+ EXP_TYPE_DQ_CPMG,
+ EXP_TYPE_MQ_CPMG,
+ EXP_TYPE_R1RHO
+ ],
+ wiz_read_only = True
+)
+uf.add_keyarg(
+ name = "frq",
+ py_type = "num",
+ desc_short = "spectrometer frequency",
+ desc = "The spectrometer frequency in Hertz. See the 'sfrq' parameter
in the Varian procpar file or the 'SFO1' parameter in the Bruker acqus file."
+)
+uf.add_keyarg(
+ name = "disp_point_col",
+ default = 1,
+ py_type = "int",
+ desc_short = "dispersion point column",
+ desc = "The column containing the CPMG frequency or spin-lock field
strength (Hz)."
+)
+uf.add_keyarg(
+ name = "data_col",
+ default = 2,
+ py_type = "int",
+ desc_short = "R2eff/R1rho data column",
+ desc = "The column containing the R2eff or R1rho data."
+)
+uf.add_keyarg(
+ name = "error_col",
+ default = 3,
+ py_type = "int",
+ desc_short = "R2eff/R1rho error column",
+ desc = "The column containing the R2eff or R1rho error."
+)
+uf.add_keyarg(
+ name = "sep",
+ py_type = "str",
+ desc_short = "column separator",
+ desc = "The column separator (the default is white space).",
+ wiz_element_type = "combo",
+ wiz_combo_choices = [",", ";", "\\t"],
+ can_be_none = True
+)
+# 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 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 n1) and that there is one file per unique spin
system. The file must be in columnar format.")
+uf.backend = r2eff_read_spin
+uf.menu_text = "&r2eff_read_spin"
uf.gui_icon = "oxygen.actions.document-open"
uf.wizard_size = (900, 600)
uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
r21328 - in /branches/relax_disp: specific_analyses/relax_disp/disp_data.py user_functions/relax_disp.py