ImageD11.transformer
index
/sware/exp/fable/standalone/redhate4-a64/lib/python2.5/site-packages/ImageD11/transformer.py

# ImageD11_v1.1 Software for beamline ID11
# Copyright (C) 2005 - 2008  Jon Wright
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 
Modules
       
ImageD11.columnfile
logging
math
numpy
ImageD11.transform
ImageD11.unitcell

 
Classes
       
transformer

 
class transformer
    Handles the algorithmic, fitting and state information for 
fitting parameters to give experimental calibrations
 
  Methods defined here:
__init__(self, parfile=None, fltfile=None)
Nothing is passed in
...will need to loadfileparameters and also peaks
addcellpeaks(self, limit=None)
Adds unit cell predicted peaks for fitting against
Optional arg limit gives highest angle to use
 
Depends on parameters:
    'cell__a','cell__b','cell__c', 'wavelength' # in angstrom
    'cell_alpha','cell_beta','cell_gamma' # in degrees
    'cell_lattice_[P,A,B,C,I,F,R]'
addcolumn(self, col, name)
Return the data
applyargs(self, args)
for use with simplex/gof function, alter parameters
compute_histo(self, colname)
Compute the histogram over twotheta for peaks previous read in
Filtering is moved to a separate function
compute_tth_eta(self)
Compute the twotheta and eta for peaks previous read in
compute_tth_histo(self)
Give hardwire access to tth
computegv(self)
Using tth, eta and omega angles, compute x,y,z of spot
in reciprocal space
filter_min(self, col, minval)
and filter peaks out falling in bins with less than min_prob
fit(self, tthmin=0, tthmax=180)
Apply simplex to improve fit of obs/calc tth
get_variable_list(self)
getaxis(self)
Compute the rotation axis
This handles omegasign in a more elegant way
getcols(self)
getcolumn(self, name)
Return the data
getvars(self)
decide what is refinable
gof(self, args)
Compute how good is the fit of obs/calc peak positions in tth
loadfileparameters(self, filename)
Read in beam center etc from file
loadfiltered(self, filename)
Read in 3D peaks from peaksearch
savegv(self, filename)
Save g-vectors into a file
Use crappy .ass format from previous for now (testing)
saveparameters(self, filename)
Save beam center etc to file
setvars(self, varlist)
set the things to refine
setxyomcols(self, xname, yname, omeganame)
tth_entropy(self)
Compute the entropy of the two theta values
... this may depend on the number of tth bins (perhaps?)
... to be used for cell parameter free line straightening
S = \sum -p log p
updateparameters(self)
write_colfile(self, filename)
Save out the column file (all info stored we hope)
write_graindex_gv(self, filename)

 
Data
        PARAMETERS = [<ImageD11.parameters.par instance at 0x2a9a2156c8>, <ImageD11.parameters.par instance at 0x2a9a215710>, <ImageD11.parameters.par instance at 0x2a9a215758>, <ImageD11.parameters.par instance at 0x2a9a2157a0>, <ImageD11.parameters.par instance at 0x2a9a2157e8>, <ImageD11.parameters.par instance at 0x2a9a215830>, <ImageD11.parameters.par instance at 0x2a9a215878>, <ImageD11.parameters.par instance at 0x2a9a2158c0>, <ImageD11.parameters.par instance at 0x2a9a215908>, <ImageD11.parameters.par instance at 0x2a9a215950>, <ImageD11.parameters.par instance at 0x2a9a215998>, <ImageD11.parameters.par instance at 0x2a9a2159e0>, <ImageD11.parameters.par instance at 0x2a9a215a28>, <ImageD11.parameters.par instance at 0x2a9a215a70>, <ImageD11.parameters.par instance at 0x2a9a215ab8>, <ImageD11.parameters.par instance at 0x2a9a215b00>, <ImageD11.parameters.par instance at 0x2a9a215b48>, <ImageD11.parameters.par instance at 0x2a9a215b90>, <ImageD11.parameters.par instance at 0x2a9a215bd8>, <ImageD11.parameters.par instance at 0x2a9a215c20>, ...]