How to use the binner in cctbx.miller?
Hi, as documentation is lacking on this: How can I use the binner from cctbx.miller to bin reflections into different groups according to their d-value and would it be possible afterwards to get integral intesities of each binned group easily? Thanks, Jan
Does this do what you want?
miller_array.setup_binner(reflections_per_bin=100)
miller_array.mean(use_binning=True)
Cheers,
Richard
2012/1/2 Jan Marten Simons
Hi,
as documentation is lacking on this: How can I use the binner from cctbx.miller to bin reflections into different groups according to their d-value and would it be possible afterwards to get integral intesities of each binned group easily?
Thanks, Jan _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
Am Montag 02 Januar 2012 20:14:03 schrieb Richard Gildea:
Does this do what you want?
miller_array.setup_binner(reflections_per_bin=100) miller_array.mean(use_binning=True)
Thanks, this pushed me into the right direction. But now I think I've found a bug: f_calc = struct.structure_factors(d_min=1.5).f_calc() I_calc = f_calc.intensities() I_calc.setup_binner_d_star_sq_step(d_star_sq_step=0.01) I_calc.mean(use_binning=True).show() # works I_calc.sum(use_binning=True).show() # gives error (see below) ... I_calc.sum(use_binning=True).show() File "/home/marten/cctbx/cctbx- dev/sources/cctbx_project/cctbx/miller/__init__.py", line 2633, in sum mean.data[i] *= counts[i] TypeError: unsupported operand type(s) for *=: 'NoneType' and 'int'
From looking at the code this seems to be caused by empty bins, which fail during the multiplication step. Also I think it's strange that the sum (and sum_sq) functions use the mean values instead of just using the sum function of the miller/flex array. Doesn't this induce some overhead?
With regards, Dipl. Phys. Jan M. Simons Institute of Crystallography RWTH Aachen University
Hi Jan,
I've fixed the bug. Thanks for pointing out the problem.
The implementation could be streamlined but I doubt it is worth the effort.
Ralf
2012/1/3 Jan Marten Simons
Am Montag 02 Januar 2012 20:14:03 schrieb Richard Gildea:
Does this do what you want?
miller_array.setup_binner(reflections_per_bin=100) miller_array.mean(use_binning=True)
Thanks, this pushed me into the right direction. But now I think I've found a bug:
f_calc = struct.structure_factors(d_min=1.5).f_calc() I_calc = f_calc.intensities() I_calc.setup_binner_d_star_sq_step(d_star_sq_step=0.01) I_calc.mean(use_binning=True).show() # works I_calc.sum(use_binning=True).show() # gives error (see below)
... I_calc.sum(use_binning=True).show() File "/home/marten/cctbx/cctbx- dev/sources/cctbx_project/cctbx/miller/__init__.py", line 2633, in sum mean.data[i] *= counts[i] TypeError: unsupported operand type(s) for *=: 'NoneType' and 'int'
From looking at the code this seems to be caused by empty bins, which fail during the multiplication step. Also I think it's strange that the sum (and sum_sq) functions use the mean values instead of just using the sum function of the miller/flex array. Doesn't this induce some overhead?
With regards,
Dipl. Phys. Jan M. Simons
Institute of Crystallography RWTH Aachen University _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
participants (3)
-
Jan Marten Simons -
Ralf Grosse-Kunstleve -
Richard Gildea