dxtbx.model.experiment_list

class dxtbx.model.ExperimentList

Bases: Boost.Python.instance

__init__((object)arg1)None :
C++ signature :

void __init__(_object*)

__init__( (object)arg1, (object)arg2) -> object :

C++ signature :

void* __init__(boost::python::api::object,boost::python::api::object)

all_sequences()

Check if all the experiments are from sequences

all_stills()

Check if all the experiments are stills

append((ExperimentList)arg1, (Experiment)arg2)None :
C++ signature :

void append(dxtbx::model::ExperimentList {lvalue},dxtbx::model::Experiment)

as_file(filename, **kwargs)

Dump experiment list as file.

as_json(filename=None, compact=False, split=False)

Dump experiment list as json

beams()

Get a list of the unique beams (includes None).

change_basis(change_of_basis_ops, in_place=False)

Apply change of basis operators to an ExperimentList

Parameters
  • change_of_basis_ops – This can either be a single cctbx.sgtbx.change_of_basis_op to be applied to all experiments, or a list of operators, one per experiment.

  • in_place (bool) – Apply the change of basis operations in-place to the current ExperimentList. Default is to return a copy of the ExperimentList.

Returns

The reindexed ExperimentList

clear((ExperimentList)arg1)None :
C++ signature :

void clear(dxtbx::model::ExperimentList {lvalue})

crystals()

Get a list of the unique crystals (includes None).

detectors()

Get a list of the unique detectors (includes None).

empty((ExperimentList)arg1)bool :
C++ signature :

bool empty(dxtbx::model::ExperimentList {lvalue})

extend((ExperimentList)arg1, (ExperimentList)arg2)None :
C++ signature :

void extend(dxtbx::model::ExperimentList {lvalue},dxtbx::model::ExperimentList)

find((ExperimentList)arg1, (str)arg2)int :
C++ signature :

int find(dxtbx::model::ExperimentList {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

static from_file(filename: str, check_format: bool = True)dxtbx_model_ext.ExperimentList

Load an ExperimentList from a serialized file.

Parameters
  • filename – The filename to load an ExperimentList from

  • check_format – If True, will attempt to verify image data type

static from_templates(templates, **kwargs)

Import an experiment list from templates

goniometers()

Get a list of the unique goniometers (includes None).

identifiers((ExperimentList)arg1)std_string :
C++ signature :

scitbx::af::shared<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > identifiers(dxtbx::model::ExperimentList {lvalue})

imagesets()

Get a list of the unique imagesets.

indices((ExperimentList)arg1, (BeamBase)arg2)size_t :
C++ signature :

scitbx::af::shared<unsigned long> indices(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::BeamBase>)

indices( (ExperimentList)arg1, (Detector)arg2) -> size_t :

C++ signature :

scitbx::af::shared<unsigned long> indices(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::Detector>)

indices( (ExperimentList)arg1, (Goniometer)arg2) -> size_t :

C++ signature :

scitbx::af::shared<unsigned long> indices(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::Goniometer>)

indices( (ExperimentList)arg1, (Scan)arg2) -> size_t :

C++ signature :

scitbx::af::shared<unsigned long> indices(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::Scan>)

indices( (ExperimentList)arg1, (CrystalBase)arg2) -> size_t :

C++ signature :

scitbx::af::shared<unsigned long> indices(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::CrystalBase>)

indices( (ExperimentList)arg1, (object)arg2) -> size_t :

C++ signature :

scitbx::af::shared<unsigned long> indices(dxtbx::model::ExperimentList {lvalue},boost::python::api::object)

is_consistent((ExperimentList)arg1)bool :
C++ signature :

bool is_consistent(dxtbx::model::ExperimentList {lvalue})

nullify_all_single_file_reader_format_instances()

Parallel reading of HDF5 from the same handle is not allowed. Python multiprocessing is a bit messed up and used fork on linux so need to close and reopen file.

profiles()

Get a list of the unique profile models (includes None).

remove_on_experiment_identifiers((ExperimentList)arg1, (list)arg2)None :
C++ signature :

void remove_on_experiment_identifiers(dxtbx::model::ExperimentList {lvalue},boost::python::list)

replace((ExperimentList)arg1, (BeamBase)arg2, (BeamBase)arg3)None :
C++ signature :

void replace(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::BeamBase>,boost::shared_ptr<dxtbx::model::BeamBase>)

replace( (ExperimentList)arg1, (Detector)arg2, (Detector)arg3) -> None :

C++ signature :

void replace(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::Detector>,boost::shared_ptr<dxtbx::model::Detector>)

replace( (ExperimentList)arg1, (Goniometer)arg2, (Goniometer)arg3) -> None :

C++ signature :

void replace(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::Goniometer>,boost::shared_ptr<dxtbx::model::Goniometer>)

replace( (ExperimentList)arg1, (Scan)arg2, (Scan)arg3) -> None :

C++ signature :

void replace(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::Scan>,boost::shared_ptr<dxtbx::model::Scan>)

replace( (ExperimentList)arg1, (CrystalBase)arg2, (CrystalBase)arg3) -> None :

C++ signature :

void replace(dxtbx::model::ExperimentList {lvalue},boost::shared_ptr<dxtbx::model::CrystalBase>,boost::shared_ptr<dxtbx::model::CrystalBase>)

replace( (ExperimentList)arg1, (object)arg2, (object)arg3) -> None :

C++ signature :

void replace(dxtbx::model::ExperimentList {lvalue},boost::python::api::object,boost::python::api::object)

scaling_models()

Get a list of the unique scaling models (includes None).

scans()

Get a list of the unique scans (includes None).

select_on_experiment_identifiers((ExperimentList)arg1, (list)arg2)None :
C++ signature :

void select_on_experiment_identifiers(dxtbx::model::ExperimentList {lvalue},boost::python::list)

to_datablocks()

Return the experiment list as a datablock list. This assumes that the experiment contains 1 datablock.

to_dict()

Serialize the experiment list to dictionary.

where((ExperimentList)arg1[, (BeamBase)beam=None[, (Detector)detector=None[, (Goniometer)goniometer=None[, (Scan)scan=None[, (CrystalBase)crystal=None[, (object)profile=None[, (object)imageset=None[, (object)scaling_model=None]]]]]]]])size_t :
C++ signature :

scitbx::af::shared<unsigned long> where(dxtbx::model::ExperimentList {lvalue} [,boost::shared_ptr<dxtbx::model::BeamBase>=None [,boost::shared_ptr<dxtbx::model::Detector>=None [,boost::shared_ptr<dxtbx::model::Goniometer>=None [,boost::shared_ptr<dxtbx::model::Scan>=None [,boost::shared_ptr<dxtbx::model::CrystalBase>=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None]]]]]]]])

class dxtbx.model.experiment_list.BeamComparison(wavelength_tolerance=1e-06, direction_tolerance=1e-06, polarization_normal_tolerance=1e-06, polarization_fraction_tolerance=1e-06)[source]

Bases: object

A class to provide simple beam comparison

__init__(wavelength_tolerance=1e-06, direction_tolerance=1e-06, polarization_normal_tolerance=1e-06, polarization_fraction_tolerance=1e-06)[source]

Initialize self. See help(type(self)) for accurate signature.

class dxtbx.model.experiment_list.DetectorComparison(fast_axis_tolerance=1e-06, slow_axis_tolerance=1e-06, origin_tolerance=1e-06)[source]

Bases: object

A class to provide simple detector comparison

__init__(fast_axis_tolerance=1e-06, slow_axis_tolerance=1e-06, origin_tolerance=1e-06)[source]

Initialize self. See help(type(self)) for accurate signature.

class dxtbx.model.experiment_list.ExperimentListFactory[source]

Bases: object

A class to help instantiate experiment lists.

static from_args(args, unhandled=None)[source]

Try to load serialised experiments from any recognised format.

static from_datablock_and_crystal(datablock, crystal, load_models=True)[source]

Load an experiment list from a datablock.

static from_dict(obj, check_format=True, directory=None)[source]

Load an experiment list from a dictionary.

Parameters
  • obj (dict) – Dictionary containing either ExperimentList or DataBlock structure.

  • check_format (bool) – If True, the file will be read to verify metadata.

  • directory (str) –

Returns

The dictionary converted

Return type

ExperimentList

static from_filenames(filenames, unhandled=None, compare_beam=None, compare_detector=None, compare_goniometer=None, scan_tolerance=None, format_kwargs=None, load_models=True)[source]

Create a list of data blocks from a list of directory or file names.

static from_imageset_and_crystal(imageset, crystal, load_models=True)[source]

Load an experiment list from an imageset and crystal.

static from_json(text, check_format=True, directory=None)[source]

Load an experiment list from JSON.

static from_json_file(filename, check_format=True)[source]

Load an experiment list from a json file.

static from_pickle_file(filename)[source]

Decode an experiment list from a pickle file.

static from_sequence_and_crystal(imageset, crystal, load_models=True)[source]

Create an experiment list from sequence and crystal.

static from_serialized_format(filename, check_format=True)[source]

Try to load the experiment list from a serialized format.

static from_stills_and_crystal(imageset, crystal, load_models=True)[source]

Create an experiment list from stills and crystal.

static from_templates(templates, **kwargs)[source]

Import an experiment list from templates

static from_xds(xds_inp, xds_other)[source]

Generate an experiment list from XDS files.

class dxtbx.model.experiment_list.GoniometerComparison(rotation_axis_tolerance=1e-06, fixed_rotation_tolerance=1e-06, setting_rotation_tolerance=1e-06)[source]

Bases: object

A class to provide simple goniometer comparison

__init__(rotation_axis_tolerance=1e-06, fixed_rotation_tolerance=1e-06, setting_rotation_tolerance=1e-06)[source]

Initialize self. See help(type(self)) for accurate signature.