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dxtbx.serialize

dxtbx.serialize.dump.compact_simple_list(match)

Callback function. Given a simple list match, compact it and ensure that it wraps around by 80 characters.

Params:

match The regular expression match

Returns:The string to replace the expression with

dxtbx.serialize.dump.compact_simple_lists(string)

Find simple lists in the string and compact.

Params:

string The input JSON string

Returns:The output JSON string

dxtbx.serialize.dump.datablock(obj, outfile, **kwargs)

Dump the given object to file.

dxtbx.serialize.dump.experiment_list(obj, outfile)

Dump an experiment list.

dxtbx.serialize.dump.imageset(obj, outfile, compact=False)

Dump the given object to file.

Params:

obj The imageset to dump outfile The output file name or file object compact Write in compact representation

dxtbx.serialize.dump.imageset_to_string(obj, compact=False)

Dump the given object to string.

Params:

obj The imageset compact Write in compact representation

Returns:The JSON string

dxtbx.serialize.imageset.basic_imageset_from_dict(d, directory=None)

Construct an ImageSet class from the dictionary.

dxtbx.serialize.imageset.basic_imageset_to_dict(imageset)

Convert an imageset to a dictionary

Params:

imageset The imageset

Returns:A dictionary of the parameters

dxtbx.serialize.imageset.filename_or_none(filename)

dxtbx.serialize.imageset.filename_to_absolute(filename)

Convert filenames to absolute form.

dxtbx.serialize.imageset.imagesequence_from_dict(d, check_format=True, directory=None)

Construct and image sequence from the dictionary.

dxtbx.serialize.imageset.imagesequence_to_dict(sequence)

Convert a sequence to a dictionary

Params:

sequence The sequence

Returns:A dictionary of the parameters

dxtbx.serialize.imageset.imageset_from_dict(d, check_format=True, directory=None)

Convert the dictionary to a sequence

Params:

d The dictionary of parameters

Returns:The sequence

dxtbx.serialize.imageset.imageset_to_dict(imageset)

Convert the imageset to a dictionary

Params:

imageset The imageset

Returns:A dictionary of the parameters

dxtbx.serialize.load.crystal(infile)

Load the given JSON file.

Params:

infile The input filename or file object

Returns:The models

dxtbx.serialize.load.datablock(filename, check_format=True)

Load a given JSON or pickle file.

Params:

filename The input filename

Returns:The datablock

dxtbx.serialize.load.experiment_list(infile, check_format=True)

Load an experiment list from a serialzied format.

dxtbx.serialize.load.imageset(filename)

Load the given JSON file.

Params:

infile The input filename

Returns:The models

dxtbx.serialize.load.imageset_from_string(string, directory=None)

Load the string and return the models.

Params:

string The JSON string to load

Returns:The models

dxtbx.serialize.xds.to_crystal(filename)

Get the crystal model from the xparm file

Params:

filename The xparm/or integrate filename

Returns:The crystal model

dxtbx.serialize.xds.to_imageset(input_filename, extra_filename=None)

Get an image set from the xds input filename plus an extra filename

Params:

input_filename The XDS.INP file extra_filename A (G)XPARM.XDS, INTGRATE.HKL or XDS_ASCII.HKL file

Returns:The imageset

class dxtbx.serialize.xds.to_xds(sequence)

Bases: object

A class to export contents of a Sequence as XDS.INP or XPARM.XDS.

XDS_INP(space_group_number=None, real_space_a=None, real_space_b=None, real_space_c=None, job_card='XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT', as_str=None)

get_beam()

get_detector()

get_goniometer()

get_scan()

get_template()

xparm_xds(real_space_a, real_space_b, real_space_c, space_group)

dxtbx.serialize.xds.xds_detector_name(dxtbx_name)

Translate from a xia2 name from the detector library to an XDS detector name.