Author: bugman
Date: Fri Feb 21 16:59:37 2014
New Revision: 22241
URL: http://svn.gna.org/viewcvs/relax?rev=22241&view=rev
Log:
Expanded the capabilities of the spectrum.read_intensities user function.
Now multiple files can be loaded simultaneously.
Modified:
trunk/pipe_control/spectrum.py
Modified: trunk/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/spectrum.py?rev=22241&r1=22240&r2=22241&view=diff
==============================================================================
--- trunk/pipe_control/spectrum.py (original)
+++ trunk/pipe_control/spectrum.py Fri Feb 21 16:59:37 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2013 Edward d'Auvergne
#
+# Copyright (C) 2004-2014 Edward d'Auvergne
#
# Copyright (C) 2008 Sebastien Morin
#
# Copyright (C) 2013 Troels E. Linnet
#
#
#
@@ -465,8 +465,8 @@
def read(file=None, dir=None, spectrum_id=None, dim=1, int_col=None,
int_method=None, spin_id_col=None, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None,
spin_id=None, ncproc=None, verbose=True):
"""Read the peak intensity data.
- @keyword file: The name of the file containing the peak
intensities.
- @type file: str
+ @keyword file: The name of the file(s) containing the peak
intensities.
+ @type file: str or list of str
@keyword dir: The directory where the file is located.
@type dir: str
@keyword spectrum_id: The spectrum identification string.
@@ -511,13 +511,48 @@
if hasattr(cdp, 'int_method') and cdp.int_method != int_method:
raise RelaxError("The '%s' measure of peak intensities does not
match '%s' of the previously loaded spectra." % (int_method, cdp.int_method))
+ # Multiple ID flags.
+ flag_multi = False
+ flag_multi_file = False
+ flag_multi_col = False
+ if isinstance(spectrum_id, list) or spectrum_id == 'auto':
+ flag_multi = True
+ if isinstance(file, list):
+ flag_multi_file = True
+ if isinstance(int_col, list) or spectrum_id == 'auto':
+ flag_multi_col = True
+
+ # List argument checks.
+ if flag_multi:
+ # Too many lists.
+ if flag_multi_file and flag_multi_col:
+ raise RelaxError("If a list of spectrum IDs is supplied, the
file names and intensity column arguments cannot both be lists.")
+
+ # Not enough lists.
+ if not flag_multi_file and not flag_multi_col:
+ raise RelaxError("If a list of spectrum IDs is supplied, either
the file name or intensity column arguments must be a list of equal length.")
+
+ # List lengths for multiple files.
+ if flag_multi_file and len(spectrum_id) != len(file):
+ raise RelaxError("The file list %s and spectrum ID list %s
do not have the same number of elements." % (file, spectrum_id))
+
+ # List lengths for multiple intensity columns.
+ if flag_multi_col and spectrum_id != 'auto' and len(spectrum_id) !=
len(int_col):
+ raise RelaxError("The spectrum ID list %s and intensity column
list %s do not have the same number of elements." % (spectrum_id, int_col))
+
+ # More list argument checks (when only one spectrum ID is supplied).
+ else:
+ # Multiple files.
+ if flag_multi_file:
+ raise RelaxError("If multiple files are supplied, then multiple
spectrum IDs must also be supplied.")
+
+ # Multiple intensity columns.
+ if flag_multi_col:
+ raise RelaxError("If multiple intensity columns are supplied,
then multiple spectrum IDs must also be supplied.")
+
# Intensity column checks.
- if isinstance(spectrum_id, list) and not isinstance(int_col, list):
- raise RelaxError("If a list of spectrum IDs is supplied, the
intensity column argument must also be a list of equal length.")
- if spectrum_id != 'auto' and not isinstance(spectrum_id, list) and
isinstance(int_col, list):
+ if spectrum_id != 'auto' and not flag_multi and flag_multi_col:
raise RelaxError("If a list of intensity columns is supplied, the
spectrum ID argument must also be a list of equal length.")
- if isinstance(spectrum_id, list) and len(spectrum_id) != len(int_col):
- raise RelaxError("The spectrum ID list %s has a different number of
elements to the intensity column list %s." % (spectrum_id, int_col))
# Check the intensity measure.
if not int_method in ['height', 'point sum', 'other']:
@@ -526,87 +561,94 @@
# Set the peak intensity measure.
cdp.int_method = int_method
- # Read the peak list data.
- peak_list = read_peak_list(file=file, dir=dir, int_col=int_col,
spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, sep=sep, spin_id=spin_id)
-
- # Automatic spectrum IDs.
- if spectrum_id == 'auto':
- spectrum_id = peak_list[0].intensity_name
-
- # Loop over the assignments.
- data = []
- data_flag = False
- for assign in peak_list:
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=assign.res_nums[dim-1],
spin_name=assign.spin_names[dim-1])
-
- # Convert the intensity data and spectrum IDs to lists if needed.
- intensity = assign.intensity
- if not isinstance(intensity, list):
- intensity = [intensity]
- if not isinstance(spectrum_id, list):
- spectrum_id = [spectrum_id]
-
- # Checks for matching length of spectrum IDs and intensities columns.
- if len(spectrum_id) != len(intensity):
- raise RelaxError("The spectrum ID list %s has a different number
of elements to the intensity column list %s." % (spectrum_id, len(intensity)))
-
- # Loop over the intensity data.
- for i in range(len(intensity)):
- # Sanity check.
- if intensity[i] == 0.0:
- warn(RelaxWarning("A peak intensity of zero has been
encountered for the spin '%s' - this could be fatal later on." % spin_id))
-
- # Get the spin container.
- spin = return_spin(spin_id)
- if not spin:
- warn(RelaxNoSpinWarning(spin_id))
- continue
-
- # Skip deselected spins.
- if not spin.select:
- continue
-
- # Initialise.
- if not hasattr(spin, 'intensities'):
- spin.intensities = {}
-
- # Intensity scaling.
+ # Convert the file argument to a list if necessary.
+ if not isinstance(file, list):
+ file = [file]
+
+ # Loop over all files.
+ for file_index in range(len(file)):
+ # Read the peak list data.
+ peak_list = read_peak_list(file=file[file_index], dir=dir,
int_col=int_col, spin_id_col=spin_id_col, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id)
+
+ # Automatic spectrum IDs.
+ if spectrum_id == 'auto':
+ spectrum_id = peak_list[0].intensity_name
+
+ # Loop over the assignments.
+ data = []
+ data_flag = False
+ for assign in peak_list:
+ # Generate the spin_id.
+ spin_id =
generate_spin_id_unique(res_num=assign.res_nums[dim-1],
spin_name=assign.spin_names[dim-1])
+
+ # Convert the intensity data to a list if needed.
+ intensity = assign.intensity
+ if not isinstance(intensity, list):
+ intensity = [intensity]
+
+ # Loop over the intensity data.
+ for int_index in range(len(intensity)):
+ # Sanity check.
+ if intensity[int_index] == 0.0:
+ warn(RelaxWarning("A peak intensity of zero has been
encountered for the spin '%s' - this could be fatal later on." % spin_id))
+
+ # Get the spin container.
+ spin = return_spin(spin_id)
+ if not spin:
+ warn(RelaxNoSpinWarning(spin_id))
+ continue
+
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # Initialise.
+ if not hasattr(spin, 'intensities'):
+ spin.intensities = {}
+
+ # Intensity scaling.
+ if ncproc != None:
+ intensity[int_index] = intensity[int_index] /
float(2**ncproc)
+
+ # Add the data.
+ if flag_multi_file:
+ id = spectrum_id[file_index]
+ elif flag_multi_col:
+ id = spectrum_id[int_index]
+ else:
+ id = spectrum_id
+ spin.intensities[id] = intensity[int_index]
+
+ # Switch the flag.
+ data_flag = True
+
+ # Append the data for printing out.
+ data.append([spin_id, repr(intensity[int_index])])
+
+ # Add the spectrum id (and ncproc) to the relax data store.
+ spectrum_ids = spectrum_id
+ if isinstance(spectrum_id, str):
+ spectrum_ids = [spectrum_id]
+ if ncproc != None and not hasattr(cdp, 'ncproc'):
+ cdp.ncproc = {}
+ for i in range(len(spectrum_ids)):
+ add_spectrum_id(spectrum_ids[i])
if ncproc != None:
- intensity[i] = intensity[i] / float(2**ncproc)
-
- # Add the data.
- spin.intensities[spectrum_id[i]] = intensity[i]
-
- # Switch the flag.
- data_flag = True
-
- # Append the data for printing out.
- data.append([spin_id, repr(intensity[i])])
-
- # Add the spectrum id (and ncproc) to the relax data store.
- spectrum_ids = spectrum_id
- if isinstance(spectrum_id, str):
- spectrum_ids = [spectrum_id]
- if ncproc != None and not hasattr(cdp, 'ncproc'):
- cdp.ncproc = {}
- for i in range(len(spectrum_ids)):
- add_spectrum_id(spectrum_ids[i])
- if ncproc != None:
- cdp.ncproc[spectrum_ids[i]] = ncproc
-
- # No data.
- if not data_flag:
- # Delete all the data.
- delete(spectrum_id)
-
- # Raise the error.
- raise RelaxError("No data could be loaded from the peak list")
-
- # Print out.
- if verbose:
- print("\nThe following intensities have been loaded into the relax
data store:\n")
- write_data(out=sys.stdout, headings=["Spin_ID", "Intensity"],
data=data)
+ cdp.ncproc[spectrum_ids[i]] = ncproc
+
+ # No data.
+ if not data_flag:
+ # Delete all the data.
+ delete(spectrum_id)
+
+ # Raise the error.
+ raise RelaxError("No data could be loaded from the peak list")
+
+ # Printout.
+ if verbose:
+ print("\nThe following intensities have been loaded into the
relax data store:\n")
+ write_data(out=sys.stdout, headings=["Spin_ID", "Intensity"],
data=data)
+ print('')
def read_spins(file=None, dir=None, dim=1, spin_id_col=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, sep=None, spin_id=None, verbose=True):
r22241 - /trunk/pipe_control/spectrum.py