dials.algorithms.integration

class dials.algorithms.integration.integrator.Executor

Bases: instance

__init__((object)arg1) → None :

C++ signature :

void __init__(_object*)

process((Executor)arg1, (object)arg2, (reflection_table)arg3) → None :

C++ signature :

void process(dials::algorithms::Executor {lvalue},int,dials::af::reflection_table)

process( (Executor)arg1, (object)arg2, (reflection_table)arg3) -> None :

C++ signature :

void process(dials::algorithms::boost_python::ExecutorWrapper {lvalue},int,dials::af::reflection_table)

class dials.algorithms.integration.integrator.Integrator(experiments, reflections, params)

Bases: object

The integrator class

__init__(experiments, reflections, params)

Initialize the integrator

Parameters:

• experiments – The experiment list

• reflections – The reflections to process

• params – The parameters to use

fit_profiles()

Do profile fitting if appropriate.

Sets self.profile_validation_report and self.profile_model_report.

Returns profile_fitter (may be none)

integrate()

Integrate the data

report()

Return the report of the processing

summary(block_size, block_size_units)

Print a summary of the integration stuff.

class dials.algorithms.integration.integrator.Integrator2D(experiments, reflections, params)

Bases: Integrator

Integrator for 2D algorithms

ProcessorClass

alias of Processor2D

static finalize_reflections(reflections, experiments, params)

A post-processing function for oscillation data.

static initialize_reflections(experiments, params, reflections)

A pre-processing class for oscillation data.

class dials.algorithms.integration.integrator.Integrator3D(experiments, reflections, params)

Bases: Integrator

Integrator for 3D algorithms

ProcessorClass

alias of Processor3D

static finalize_reflections(reflections, experiments, params)

A post-processing function for oscillation data.

static initialize_reflections(experiments, params, reflections)

A pre-processing class for oscillation data.

class dials.algorithms.integration.integrator.Integrator3DThreaded(experiments, reflections, params)

Bases: object

Integrator for 3D algorithms

__init__(experiments, reflections, params)

Initialize the integrator

Parameters:

• experiments – The experiment list

• reflections – The reflections to process

• params – The parameters to use

finalise()

Finalise the integrator

initialise()

Initialise the integrator

integrate()

Integrate the data

report()

Return the report of the processing

summary(block_size, block_size_units)

Print a summary of the integration stuff.

class dials.algorithms.integration.integrator.IntegratorExecutor(experiments, profile_fitter=None, valid_foreground_threshold=0.75)

Bases: Executor

The class to process the integration data

__init__(experiments, profile_fitter=None, valid_foreground_threshold=0.75)

Initialize the executor

Parameters:

experiments – The experiment list

data()

Return data

finalize()

Finalize the processing

initialize(frame0, frame1, reflections)

Initialize the processing for the job

Parameters:

• frame0 – The first frame to process

• frame1 – The last frame to process

• reflections – The reflections to process

process(frame, reflections)

Process the reflections on a frame

Parameters:

• frame – The frame to process

• reflections – The reflections to process

class dials.algorithms.integration.integrator.IntegratorFlat3D(experiments, reflections, params)

Bases: Integrator

Integrator for flattened 3D algorithms

ProcessorClass

alias of ProcessorFlat3D

static finalize_reflections(reflections, experiments, params)

A post-processing function for oscillation data.

static initialize_reflections(experiments, params, reflections)

A pre-processing class for oscillation data.

class dials.algorithms.integration.integrator.IntegratorSingle2D(experiments, reflections, params)

Bases: Integrator

Integrator for 2D algorithms on a single image

ProcessorClass

alias of ProcessorSingle2D

static finalize_reflections(reflections, experiments, params)

A post-processing function for oscillation data.

static initialize_reflections(experiments, params, reflections)

A pre-processing class for oscillation data.

class dials.algorithms.integration.integrator.IntegratorStills(experiments, reflections, params)

Bases: Integrator

Integrator for still algorithms

ProcessorClass

alias of ProcessorStills

static finalize_reflections(reflections, experiments, params)

A post-processing function for stills data.

static initialize_reflections(experiments, params, reflections)

A pre-processing class for stills data.

class dials.algorithms.integration.integrator.JobList

Bases: instance

__init__((object)arg1) → None :

C++ signature :

void __init__(_object*)

__init__( (object)arg1, (object)arg2, (tiny_int_2)arg3) -> None :

C++ signature :

void __init__(_object*,scitbx::af::tiny<int, 2ul>,scitbx::af::const_ref<scitbx::af::tiny<int, 2ul>, scitbx::af::trivial_accessor>)

add((JobList)arg1, (object)arg2, (object)arg3, (object)arg4, (object)arg5) → None :

C++ signature :

void add(dials::algorithms::JobList {lvalue},scitbx::af::tiny<int, 2ul>,scitbx::af::tiny<int, 2ul>,int,int)

shoebox_memory((JobList)arg1, (reflection_table)arg2, (object)arg3) → size_t :

C++ signature :

scitbx::af::shared<unsigned long> shoebox_memory(dials::algorithms::JobList,dials::af::reflection_table,bool)

split((JobList)arg1, (reflection_table)arg2) → None :

C++ signature :

void split(dials::algorithms::JobList,dials::af::reflection_table)

class dials.algorithms.integration.integrator.Parameters

Bases: object

A stack of classes to represent the integration parameters

class Filter

Bases: object

Filter parameters

__init__()

class Profile

Bases: object

Profile parameters

class Validation

Bases: object

__init__()

__init__()

__init__()

Initialize

static from_phil(params)

Convert the phil parameters

class dials.algorithms.integration.integrator.Processor2D(experiments, reflections, params)

Bases: _ProcessorRot

Top level processor for 2D processing.

__init__(experiments, reflections, params)

Initialise the manager and the processor.

class dials.algorithms.integration.integrator.Processor3D(experiments, reflections, params)

Bases: _ProcessorRot

Top level processor for 3D processing.

__init__(experiments, reflections, params)

Initialise the manager and the processor.

class dials.algorithms.integration.integrator.ProcessorFlat3D(experiments, reflections, params)

Bases: _ProcessorRot

Top level processor for flat 3D processing.

__init__(experiments, reflections, params)

Initialise the manager and the processor.

class dials.algorithms.integration.integrator.ProcessorSingle2D(experiments, reflections, params)

Bases: _ProcessorRot

Top level processor for still image processing.

__init__(experiments, reflections, params)

Initialise the manager and the processor.

class dials.algorithms.integration.integrator.ProcessorStills(experiments, reflections, params)

Bases: _Processor

Top level processor for still image processing.

__init__(experiments, reflections, params)

Initialise the manager and the processor.

class dials.algorithms.integration.integrator.ProfileModellerExecutor(experiments, profile_fitter)

Bases: Executor

The class to do profile modelling calculations

__init__(experiments, profile_fitter)

Initialise the executor

Parameters:

experiments – The experiment list

data()

Returns:

the modeller

finalize()

Finalize the processing

initialize(frame0, frame1, reflections)

Initialise the processing for a job

Parameters:

• frame0 – The first frame in the job

• frame1 – The last frame in the job

• reflections – The reflections that will be processed

process(frame, reflections)

Process the data

Parameters:

• frame – The frame being processed

• reflections – The reflections to process

class dials.algorithms.integration.integrator.ProfileValidatorExecutor(experiments, profile_fitter)

Bases: Executor

The class to do profile validation calculations

__init__(experiments, profile_fitter)

Initialise the executor

Parameters:

experiments – The experiment list

data()

Returns:

the modeller

finalize()

Finalize the processing

initialize(frame0, frame1, reflections)

Initialise the processing for a job

Parameters:

• frame0 – The first frame in the job

• frame1 – The last frame in the job

• reflections – The reflections that will be processed

process(frame, reflections)

Process the data

Parameters:

• frame – The frame being processed

• reflections – The reflections to process

class dials.algorithms.integration.integrator.ReflectionManager

Bases: instance

__init__((object)arg1, (JobList)jobs, (reflection_table)data) → None :

C++ signature :

void __init__(_object*,dials::algorithms::JobList,dials::af::reflection_table)

accumulate((ReflectionManager)arg1, (object)arg2, (reflection_table)arg3) → None :

C++ signature :

void accumulate(dials::algorithms::ReflectionManager {lvalue},unsigned long,dials::af::reflection_table)

data((ReflectionManager)arg1) → reflection_table :

C++ signature :

dials::af::reflection_table data(dials::algorithms::ReflectionManager {lvalue})

finished((ReflectionManager)arg1) → bool :

C++ signature :

bool finished(dials::algorithms::ReflectionManager {lvalue})

job((ReflectionManager)arg1, (object)arg2) → Job :

C++ signature :

dials::algorithms::JobList::Job job(dials::algorithms::ReflectionManager {lvalue},unsigned long)

num_reflections((ReflectionManager)arg1, (object)arg2) → int :

C++ signature :

unsigned long num_reflections(dials::algorithms::ReflectionManager {lvalue},unsigned long)

split((ReflectionManager)arg1, (object)arg2) → reflection_table :

C++ signature :

dials::af::reflection_table split(dials::algorithms::ReflectionManager {lvalue},unsigned long)

dials.algorithms.integration.integrator.frame_hist(bbox, width=80, symbol='#', prefix='')

A utility function to print a histogram of reflections on frames.

Parameters:

• bbox – The bounding boxes

• width – The width of each line

• symbol – The histogram symbol

• prefix – A string to prefix to each line

Returns:

The histogram string

dials.algorithms.integration.integrator.generate_phil_scope()

Generate the integration phil scope.

Returns:

The phil scope

dials.algorithms.integration.integrator.hist(data, width=80, symbol='#', prefix='')

A utility function to print a histogram of reflections on frames.

Parameters:

• data – The data to histogram

• width – The number of characters in each line

• symbol – The plot symbol

• prefix – String to prefix to each line

Returns:

The histogram string

dials.algorithms.integration.integrator.nframes_hist(bbox, width=80, symbol='#', prefix='')

A utility function to print a histogram of number of frames.

Parameters:

• bbox – The bounding boxes

• width – The width of each line

• symbol – The histogram symbol

• prefix – A string to prefix to each line

Returns:

The histogram string