Author: bugman
Date: Tue Dec 14 17:52:06 2010
New Revision: 11816
URL: http://svn.gna.org/viewcvs/relax?rev=11816&view=rev
Log:
Peak intensity data is now stored as a dictionary with the spectrum_id arg as
keys.
Modified:
branches/peak_list_handling/generic_fns/spectrum.py
Modified: branches/peak_list_handling/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_list_handling/generic_fns/spectrum.py?rev=11816&r1=11815&r2=11816&view=diff
==============================================================================
--- branches/peak_list_handling/generic_fns/spectrum.py (original)
+++ branches/peak_list_handling/generic_fns/spectrum.py Tue Dec 14 17:52:06
2010
@@ -116,8 +116,7 @@
def __errors_repl(verbosity=0):
"""Calculate the errors for peak intensities from replicated spectra.
- @keyword verbosity: The amount of information to print. The higher the
value, the greater the
- verbosity.
+ @keyword verbosity: The amount of information to print. The higher the
value, the greater the verbosity.
@type verbosity: int
"""
@@ -134,7 +133,6 @@
else:
print("All spectra replicated: No.")
-
# Test if the standard deviation has already been calculated.
if hasattr(cdp, 'sigma_I'):
raise RelaxError("The peak intensity standard deviation of all
spectra has already been calculated.")
@@ -183,16 +181,24 @@
spin.select = False
continue
+ # Missing data.
+ missing = False
+ for j in xrange(num_spectra):
+ if not spin.intensities.has_key(spectra[j]):
+ missing = True
+ if missing:
+ continue
+
# Average intensity.
ave_intensity = 0.0
for j in xrange(num_spectra):
- ave_intensity = ave_intensity + spin.intensities[indices[j]]
+ ave_intensity = ave_intensity + spin.intensities[spectra[j]]
ave_intensity = ave_intensity / num_spectra
# Sum of squared errors.
SSE = 0.0
for j in xrange(num_spectra):
- SSE = SSE + (spin.intensities[indices[j]] - ave_intensity)
** 2
+ SSE = SSE + (spin.intensities[spectra[j]] - ave_intensity)
** 2
# Variance.
#
@@ -757,39 +763,29 @@
@type dir: str
@keyword spectrum_id: The spectrum identification string.
@type spectrum_id: str
- @keyword heteronuc: The name of the heteronucleus as specified in
the peak intensity
- file.
+ @keyword heteronuc: The name of the heteronucleus as specified in
the peak intensity file.
@type heteronuc: str
@keyword proton: The name of the proton as specified in the peak
intensity file.
@type proton: str
- @keyword int_col: The column containing the peak intensity data
(used by the generic
- intensity file format).
+ @keyword int_col: The column containing the peak intensity data
(used by the generic intensity file format).
@type int_col: int
@keyword int_method: The integration method, one of 'height', 'point
sum' or 'other'.
@type int_method: str
- @keyword spin_id_col: The column containing the spin ID strings (used
by the generic intensity
- file format). If supplied, the mol_name_col,
res_name_col, res_num_col,
- spin_name_col, and spin_num_col arguments must
be none.
+ @keyword spin_id_col: The column containing the spin ID strings (used
by the generic intensity file format). If supplied, the mol_name_col,
res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be
none.
@type spin_id_col: int or None
- @keyword mol_name_col: The column containing the molecule name
information (used by the generic
- intensity file format). If supplied,
spin_id_col must be None.
+ @keyword mol_name_col: The column containing the molecule name
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
@type mol_name_col: int or None
- @keyword res_name_col: The column containing the residue name
information (used by the generic
- intensity file format). If supplied,
spin_id_col must be None.
+ @keyword res_name_col: The column containing the residue name
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
@type res_name_col: int or None
- @keyword res_num_col: The column containing the residue number
information (used by the
- generic intensity file format). If supplied,
spin_id_col must be None.
+ @keyword res_num_col: The column containing the residue number
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
@type res_num_col: int or None
- @keyword spin_name_col: The column containing the spin name information
(used by the generic
- intensity file format). If supplied,
spin_id_col must be None.
+ @keyword spin_name_col: The column containing the spin name information
(used by the generic intensity file format). If supplied, spin_id_col must
be None.
@type spin_name_col: int or None
- @keyword spin_num_col: The column containing the spin number
information (used by the generic
- intensity file format). If supplied,
spin_id_col must be None.
+ @keyword spin_num_col: The column containing the spin number
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
@type spin_num_col: int or None
@keyword sep: The column separator which, if None, defaults to
whitespace.
@type sep: str or None
- @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all
- spins.
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all spins.
@type spin_id: None or str
@keyword ncproc: The Bruker ncproc binary intensity scaling
factor.
@type ncproc: int or None
@@ -894,14 +890,14 @@
# Initialise.
if not hasattr(spin, 'intensities'):
- spin.intensities = []
+ spin.intensities = {}
# Intensity scaling.
if ncproc != None:
intensity = intensity / float(2**ncproc)
# Add the data.
- spin.intensities.append(intensity)
+ spin.intensities[spectrum_id] = intensity
def replicated(spectrum_ids=None):
r11816 - /branches/peak_list_handling/generic_fns/spectrum.py