Hi Nat, That gave me six and a bit: specifically sm.show() print f.second_moment(use_binning = False) 6.46063790107 The E^2 = I/<I> need to be computed in bins. After that (E^2)^2 should be fine. This got me confused - it must be in there somewhere Thanks, Graeme On 13 Dec 2012, at 16:01, Nathaniel Echols wrote:

On Thu, Dec 13, 2012 at 3:00 AM, wrote:

...

Trying to write some code to return the average E^4 across (some) bins for an mtz file, I got to ... but I have no idea how to actually extract the information I want from sm as this only has show() which gives ... Really I would like the value programatically or at least a way of getting back an array of the binned values so I can average them myself (which is obviously trivial)

Won't simply passing use_binning=False to second_moment() do what you want? It returns a float in this mode (which is common to most methods which have a use_binning parameter). If you want to obtain the value for a subset of bins you can use array.select() to pull out the bin(s) and then call second_moment(use_binning=False).

Or am I completely misunderstanding the question?

-Nat _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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Thanks Nat, that hit the spot. For reference the final code I got was def main(): import sys from iotbx import reflection_file_reader for argv in sys.argv[1:]: reflection_file = reflection_file_reader.any_reflection_file( file_name = argv) if reflection_file.file_type() is None: continue miller_arrays = reflection_file.as_miller_arrays() for ma in miller_arrays: print ma.info().label_string(), E4(ma) def E4(ma): f = ma.as_intensity_array() f = f.array(data=f.data()/f.epsilons().data().as_double()) f.set_observation_type_xray_intensity() f.setup_binner(auto_binning = True) sm = f.second_moment(use_binning = True) moments = [sm.data[j] for j in f.binner().range_used()] return sum(moments) / len(moments) if __name__ == '__main__': main() Best wishes, Graeme On 13 Dec 2012, at 16:29, Nathaniel Echols wrote:

On Thu, Dec 13, 2012 at 8:18 AM, wrote:

...

That gave me six and a bit: specifically

sm.show() print f.second_moment(use_binning = False)

6.46063790107

The E^2 = I/<I> need to be computed in bins. After that (E^2)^2 should be fine. This got me confused - it must be in there somewhere

Ah, I think I see - look at the "data" attribute:

sm = f.second_moment(use_binning=True) print sm. data [None, 2.3279309836355044, 2.8099112859261517, 2.1769967857271175, 2.200637763782145, 2.2919308734359407, 2.000356888782398, 1.7555453224108684, 1.4836662688931992, None]

(using a dataset from the PDB) I've never fully understood what the first and last elements are supposed to mean (at least one is for "unused" data) - but you can get the elements of interested this way:

for i_bin in f.binner().range_used() : # etc.

-Nat _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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