[cctbxbb] Computing E^4 from an mtz file

[Graeme.Winter at diamond.ac.uk]

Hi Folks,

Trying to write some code to return the average E^4 across (some) bins for an mtz file, I got to


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:
            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)
    sm.show()

if __name__ == '__main__':
    main()


but I have no idea how to actually extract the information I want from sm as this only has show() which gives

Graemes-MacBook-Pro:PlayPen graeme$ cctbx.python E4.py /Users/graeme/projects/sci-397/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled.mtz 

unused:         - 20.8668 [  0/7  ]
bin  1: 20.8668 -  5.8873 [221/235]  2.3863
bin  2:  5.8873 -  4.6904 [216/221]  1.9823
bin  3:  4.6904 -  4.1026 [221/222]  1.9925
<snip>
bin 47:  1.6553 -  1.6435 [153/209]  2.2051
bin 48:  1.6435 -  1.6320 [143/198]  2.2021
bin 49:  1.6320 -  1.6208 [141/204]  2.7085
unused:  1.6208 -         [  0/0  ]

unused:         - 20.8668 [  0/9  ]
bin  1: 20.8668 -  7.1654 [201/225]  2.2405
bin  2:  7.1654 -  5.7261 [202/213]  1.9109
bin  3:  5.7261 -  5.0137 [216/223]  2.0162
bin  4:  5.0137 -  4.5605 [207/212]  2.0043
<snip>
bin 87:  1.6456 -  1.6393 [126/192]  2.5521
bin 88:  1.6393 -  1.6330 [122/210]  2.0195
bin 89:  1.6330 -  1.6269 [131/224]  2.6251
bin 90:  1.6269 -  1.6208 [120/212]  3.0912
unused:  1.6208 -         [  0/0  ]

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)

Any suggestions?

Thanks,

Graeme

ps - most of this code is ripped from iotbx.reflection_statistics :o)
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