xfel.cxi package¶

Subpackages¶

Submodules¶

xfel.cxi.average_spots module¶

xfel.cxi.average_spots.ImageFactory(path)¶

xfel.cxi.average_spots.img_add(path, img_sum, dist_sum, nrg_sum, nmemb)¶

xfel.cxi.average_spots.main(argv=None)¶

xfel.cxi.average_spots.spot_add(path, spot_sum, dist_sum, nrg_sum, nmemb)¶

xfel.cxi.completeness_plot module¶

xfel.cxi.correction_vector_plot module¶

class xfel.cxi.correction_vector_plot.lines(params)¶

Bases: correction_vector_store

literals()¶

vectors()¶

class xfel.cxi.correction_vector_plot.manage_sql(params)¶

Bases: object

get_cursor()¶

get_frame_dictionary()¶

initialize_tables_and_insert_command()¶

insert(run, itile, tokens)¶

send_insert_command()¶

xfel.cxi.correction_vector_plot.run_correction_vector_plot(working_phil)¶

xfel.cxi.cxi_cc module¶

xfel.cxi.cxi_cc.binned_correlation(self, other, include_negatives=False)¶

xfel.cxi.cxi_cc.correlation(self, other, include_negatives=False)¶

xfel.cxi.cxi_cc.load_cc_data(params, reindexing_op, output)¶

xfel.cxi.cxi_cc.r1_factor(self, other, scale_factor=None, assume_index_matching=False, use_binning=False)¶

Get the R1 factor according to this formula

\[R1 = \dfrac{\sum{||F| - k|F'||}}{\sum{|F|}}\]

where F is self.data() and F’ is other.data() and k is the factor to put F’ on the same scale as F

xfel.cxi.cxi_cc.r_split(self, other, assume_index_matching=False, use_binning=False)¶

xfel.cxi.cxi_cc.run_cc(params, reindexing_op, output)¶

xfel.cxi.cxi_cc.scale_factor(self, other, weights=None, cutoff_factor=None, use_binning=False)¶

The analytical expression for the least squares scale factor.

K = sum(w * yo * yc) / sum(w * yc^2)

If the optional cutoff_factor argument is provided, only the reflections whose magnitudes are greater than cutoff_factor * max(yo) will be included in the calculation.

xfel.cxi.cxi_cc.split_sigma_test(self, other, scale, use_binning=False, show_plot=False)¶

Calculates the split sigma ratio test by Peter Zwart: ssr = sum( (Iah-Ibh)^2 ) / sum( sigma_ah^2 + sigma_bh^2)

where Iah and Ibh are merged intensities for a given hkl from two halves of a dataset (a and b). Likewise for sigma_ah and sigma_bh.

ssr (split sigma ratio) should approximately equal 1 if the errors are correctly estimated.

xfel.cxi.display_powder_arcs module¶

xfel.cxi.display_powder_arcs.apply_gaussian_noise(image, params)¶

xfel.cxi.display_powder_arcs.get_mmtbx_icalc(code, d_min, anomalous_flag=False)¶

xfel.cxi.display_powder_arcs.is_pinwheel_region(dx, dy)¶

xfel.cxi.display_powder_arcs.superimpose_powder_arcs(image, params)¶

xfel.cxi.display_spots module¶

xfel.cxi.display_spots.ImageFactory(filename)¶

class xfel.cxi.display_spots.empty¶: Bases: object

xfel.cxi.display_spots.run_one(path, *command_line, **kwargs)¶

xfel.cxi.display_spots.run_one_index(path, *arguments, **kwargs)¶

xfel.cxi.display_spots.run_one_index_core(horizons_phil)¶

xfel.cxi.display_spots.view_raw_image(path, *command_line, **kwargs)¶

class xfel.cxi.display_spots.wrapper_of_callback(info=None)¶

Bases: object

display(path)¶

display_with_callback(path)¶

user_callback(dc, wxpanel, wx)¶

for spot in self.spotfinder.images[self.frames[0]][“spots_total”]:

for pxl in spot.bodypixels:

x,y = wxpanel._img.image_coords_as_screen_coords(: pxl.y, pxl.x)

dc.SetPen(wx.Pen(‘red’)) dc.SetBrush(wx.RED_BRUSH) dc.DrawCircle(x,y,1)

x,y = wxpanel._img.image_coords_as_screen_coords(

spot.ctr_mass_y(), spot.ctr_mass_x())

dc.SetPen(wx.Pen(‘green’)) dc.SetBrush(wx.GREEN_BRUSH) dc.DrawCircle(x,y,1)

xfel.cxi.integrate_image_api module¶

xfel.cxi.integrate_image_api.integrate_one_image(data, **kwargs)¶

xfel.cxi.merging_database module¶

xfel.cxi.merging_database_fs module¶

xfel.cxi.merging_database_sqlite3 module¶

xfel.cxi.strong_zulu module¶

xfel.cxi.strong_zulu.integrate_one_image(data)¶

xfel.cxi.util module¶

xfel.cxi.util.is_odd_numbered(file_name, use_hash=False)¶