Author: tlinnet
Date: Sun Dec 7 12:27:32 2014
New Revision: 26983
URL: http://svn.gna.org/viewcvs/relax?rev=26983&view=rev
Log:
Added function in pipe_control.spectrum.sn_ratio_deselection(), a function to
deselect spins according to the Signal to Noise ration.
The function is flexible, since it possible to use different comparison
operators.
And the function can be switched, so a selection is made instead.
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=26983&r1=26982&r2=26983&view=diff
==============================================================================
--- trunk/pipe_control/spectrum.py (original)
+++ trunk/pipe_control/spectrum.py Sun Dec 7 12:27:32 2014
@@ -27,18 +27,21 @@
# Python module imports.
from math import sqrt
+from numpy import asarray
+import operator
import sys
from warnings import warn
# relax module imports.
from lib.errors import RelaxError, RelaxImplementError, RelaxNoSpectraError
from lib.io import sort_filenames, write_data
-from lib.text.sectioning import section
+from lib.text.sectioning import section, subsection
from lib.spectrum.peak_list import read_peak_list
from lib.statistics import std
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
from pipe_control.mol_res_spin import check_mol_res_spin_data, create_spin,
generate_spin_id_unique, return_spin, spin_loop
from pipe_control.pipes import check_pipe
+from pipe_control.selection import desel_spin, sel_spin
def __errors_height_no_repl():
@@ -935,3 +938,143 @@
if verbose:
section(file=sys.stdout, text="Signal to noise ratio for spin ID
'%s'"%spin_id, prespace=1)
write_data(out=sys.stdout, headings=["Spectrum ID", "Signal",
"Noise", "S/N"], data=data_i)
+
+
+def sn_ratio_deselection(ratio=1.0, operation='<', all_sn=False,
select=False, verbose=True):
+ """Use user function deselect.spin on spins with signal to noise ratio
higher or lower than ratio. The operation determines the selection operation.
+
+ @keyword ratio: The ratio to compare to.
+ @type ratio: float
+ @keyword operation: The comparison operation by which to select the
spins. Of the operation(sn_ratio, ratio), where operation can either be:
'<', '<=', '>', '>=', '==', '!='.
+ @type operation: str
+ @keyword all_sn: A flag specifying if all the signal to noise
ratios per spin should match the comparison operator, of if just a single
comparison match is enough.
+ @type all_sn: bool
+ @keyword select: A flag specifying if the user function
select.spin should be used instead.
+ @type select: bool
+ @keyword verbose: A flag which if True will print additional
information out.
+ @type verbose: bool
+ """
+
+ # Tests.
+ check_pipe()
+ check_mol_res_spin_data()
+
+ # Test if spectra have been loaded.
+ if not hasattr(cdp, 'spectrum_ids'):
+ raise RelaxError("No spectra have been loaded.")
+
+ # Assign the comparison operator.
+ # "'<' : strictly less than"
+ if operation == '<':
+ op = operator.lt
+
+ # "'<=' : less than or equal"
+ elif operation == '<=':
+ op = operator.le
+
+ # "'>' : strictly greater than"
+ elif operation == '>':
+ op = operator.gt
+
+ # "'>=' : greater than or equal"
+ elif operation == '>=':
+ op = operator.ge
+
+ # "'==' : equal"
+ elif operation == '==':
+ op = operator.eq
+
+ # "'!=' : not equal",
+ elif operation == '!=':
+ op = operator.ne
+
+ # If not assigned, raise error.
+ else:
+ raise RelaxError("The compare operation does not belong to the
allowed list of methods: ['<', '<=', '>', '>=', '==', '!=']")
+
+ # Assign text for print out.
+ if all_sn:
+ text_all_sn = "all"
+ else:
+ text_all_sn = "any"
+
+ if select:
+ text_sel = "selected"
+ sel_func = sel_spin
+ else:
+ text_sel = "deselected"
+ sel_func = desel_spin
+
+ # Print
+ section(file=sys.stdout, text="Signal to noise ratio comparison
selection", prespace=1, postspace=0)
+ print("For the comparion test: S/N %s %1.1f"%(operation, ratio))
+
+ # Loop over the spins.
+ spin_ids = []
+ for spin, spin_id in spin_loop(return_id=True):
+ # Skip spins missing sn_ratio.
+ if not hasattr(spin, 'sn_ratio'):
+ # Skip warning for deselected spins.
+ if spin.select:
+ warn(RelaxWarning("Spin '%s' does not contain Signal to
Noise calculations. Perform the user function 'spectrum.sn_ratio'. This spin
is skipped." % spin_id))
+ continue
+
+ # Loop over the ID, collect and sort.
+ ids = []
+ for id in spin.peak_intensity:
+ # Append the ID to the list.
+ ids.append(id)
+
+ # Sort the ids alphanumeric.
+ ids = sort_filenames(filenames=ids, rev=False)
+
+ # Loop over the sorted ids.
+ sn_val = []
+ for id in ids:
+ # Append the Signal to Noise in the list.
+ sn_val.append(spin.sn_ratio[id])
+
+ # Convert the list to array.
+ sn_val = asarray(sn_val)
+
+ # Make the comparison for the whole array.
+ test_arr = op(sn_val, ratio)
+
+ # Determine how the test should evaluate.
+ if all_sn:
+ test = test_arr.all()
+ else:
+ test = test_arr.any()
+
+ # Make an numpy array for the ids, an extract id which failed the
test.
+ ids_arr = asarray(ids)
+ ids_test_arr = ids_arr[test_arr]
+
+ # Make inversion of bool
+ test_arr_inv = test_arr == False
+ ids_test_arr_inv = ids_arr[test_arr_inv]
+
+ # print
+ if verbose:
+ subsection(file=sys.stdout, text="Signal to noise ratio
comparison for spin ID '%s'"%spin_id, prespace=1, postspace=0)
+ print("Following spectra ID evaluated to True: %s"%ids_test_arr)
+ print("Following spectra ID evaluated to False:
%s"%ids_test_arr_inv)
+ print("'%s' comparisons have been used for evaluation, which
evaluated to: %s"%(text_all_sn, test))
+ if test:
+ print("The spin ID '%s' is %s"%(spin_id, text_sel))
+ else:
+ print("The spin ID '%s' is skipped"%spin_id)
+
+ # If the test evaluates to True, then do selection action.
+ if test:
+ # Select/Deselect the spin.
+ sel_func(spin_id=spin_id)
+
+ # Assign spin_id to list, for printing.
+ spin_ids.append(spin_id)
+
+ # Make summary
+ if verbose:
+ if len(spin_ids) > 0:
+ subsection(file=sys.stdout, text="For all of the S/N comparion
test, the following spin ID's was %s"%text_sel, prespace=1, postspace=0)
+ print(spin_ids)
r26983 - /trunk/pipe_control/spectrum.py