dxtbx.imageset

class dxtbx.imageset.ExternalLookup

Bases: instance

__init__((object)arg1) → None :

C++ signature :

void __init__(_object*)

property dx

property dy

property gain

property mask

property pedestal

class dxtbx.imageset.ExternalLookupItemBool

Bases: instance

__init__((object)arg1) → None :

C++ signature :

void __init__(_object*)

property data

property filename

class dxtbx.imageset.ExternalLookupItemDouble

Bases: instance

__init__((object)arg1) → None :

C++ signature :

void __init__(_object*)

property data

property filename

class dxtbx.imageset.ImageGrid

Bases: ImageSet

__init__((object)arg1, (ImageSetData)data, (object)grid_size) → None :

C++ signature :

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

__init__( (object)arg1, (ImageSetData)data, (size_t)indices, (object)grid_size) -> None :

C++ signature :

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

static from_imageset((ImageSet)arg1, (object)arg2) → ImageGrid :

C++ signature :

dxtbx::ImageGrid from_imageset(dxtbx::ImageSet,scitbx::af::tiny<int, 2ul>)

get_grid_size((ImageGrid)arg1) → tuple :

C++ signature :

scitbx::af::tiny<int, 2ul> get_grid_size(dxtbx::ImageGrid {lvalue})

class dxtbx.imageset.ImageSequence

Bases: ImageSet

__init__((object)arg1, (ImageSetData)data, (BeamBase)beam, (Detector)detector, (Goniometer)goniometer, (Scan)scan) → None :

C++ signature :

void __init__(_object*,dxtbx::ImageSetData,std::shared_ptr<dxtbx::model::BeamBase>,std::shared_ptr<dxtbx::model::Detector>,std::shared_ptr<dxtbx::model::Goniometer>,std::shared_ptr<dxtbx::model::Scan>)

__init__( (object)arg1, (ImageSetData)data, (size_t)indices, (BeamBase)beam, (Detector)detector, (Goniometer)goniometer, (Scan)scan) -> None :

C++ signature :

void __init__(_object*,dxtbx::ImageSetData,scitbx::af::const_ref<unsigned long, scitbx::af::trivial_accessor>,std::shared_ptr<dxtbx::model::BeamBase>,std::shared_ptr<dxtbx::model::Detector>,std::shared_ptr<dxtbx::model::Goniometer>,std::shared_ptr<dxtbx::model::Scan>)

complete_set((ImageSequence)arg1) → ImageSequence :

C++ signature :

dxtbx::ImageSequence complete_set(dxtbx::ImageSequence {lvalue})

get_array_range((ImageSequence)arg1) → tuple :

C++ signature :

scitbx::af::tiny<int, 2ul> get_array_range(dxtbx::ImageSequence {lvalue})

get_beam((ImageSequence)arg1[, (object)arg2]) → BeamBase :

C++ signature :

std::shared_ptr<dxtbx::model::BeamBase> get_beam(dxtbx::ImageSequence {lvalue} [,unsigned long])

get_detector((ImageSequence)arg1[, (object)arg2]) → Detector :

C++ signature :

std::shared_ptr<dxtbx::model::Detector> get_detector(dxtbx::ImageSequence {lvalue} [,unsigned long])

get_goniometer((ImageSequence)arg1[, (object)arg2]) → Goniometer :

C++ signature :

std::shared_ptr<dxtbx::model::Goniometer> get_goniometer(dxtbx::ImageSequence {lvalue} [,unsigned long])

get_scan((ImageSequence)arg1[, (object)arg2]) → Scan :

C++ signature :

std::shared_ptr<dxtbx::model::Scan> get_scan(dxtbx::ImageSequence {lvalue} [,unsigned long])

get_template()

Return the template

partial_set((ImageSequence)arg1, (object)arg2, (object)arg3, (object)arg4) → ImageSequence :

C++ signature :

dxtbx::ImageSequence partial_set(dxtbx::ImageSequence {lvalue},boost::python::api::object,unsigned long,unsigned long)

set_beam((ImageSequence)arg1, (BeamBase)arg2[, (object)arg3]) → None :

C++ signature :

void set_beam(dxtbx::ImageSequence {lvalue},std::shared_ptr<dxtbx::model::BeamBase> [,unsigned long])

set_detector((ImageSequence)arg1, (Detector)arg2[, (object)arg3]) → None :

C++ signature :

void set_detector(dxtbx::ImageSequence {lvalue},std::shared_ptr<dxtbx::model::Detector> [,unsigned long])

set_goniometer((ImageSequence)arg1, (Goniometer)arg2[, (object)arg3]) → None :

C++ signature :

void set_goniometer(dxtbx::ImageSequence {lvalue},std::shared_ptr<dxtbx::model::Goniometer> [,unsigned long])

set_scan((ImageSequence)arg1, (Scan)arg2[, (object)arg3]) → None :

C++ signature :

void set_scan(dxtbx::ImageSequence {lvalue},std::shared_ptr<dxtbx::model::Scan> [,unsigned long])

update_detector_px_mm_data((ImageSequence)arg1) → None :

C++ signature :

void update_detector_px_mm_data(dxtbx::ImageSequence {lvalue})

class dxtbx.imageset.ImageSet

Bases: instance

A class to inject additional methods into the imageset class

__init__((object)arg1, (ImageSetData)data[, (object)indices=None]) → object :

C++ signature :

void* __init__(boost::python::api::object,dxtbx::ImageSetData [,boost::python::api::object=None])

as_imageset((ImageSet)arg1) → ImageSet :

C++ signature :

dxtbx::ImageSet as_imageset(dxtbx::ImageSet {lvalue})

clear_cache((ImageSet)arg1) → None :

C++ signature :

void clear_cache(dxtbx::ImageSet {lvalue})

complete_set((ImageSet)arg1) → ImageSet :

C++ signature :

dxtbx::ImageSet complete_set(dxtbx::ImageSet {lvalue})

data((ImageSet)arg1) → ImageSetData :

C++ signature :

dxtbx::ImageSetData data(dxtbx::ImageSet {lvalue})

property external_lookup

get_beam((ImageSet)arg1[, (object)index=0]) → BeamBase :

C++ signature :

std::shared_ptr<dxtbx::model::BeamBase> get_beam(dxtbx::ImageSet {lvalue} [,unsigned long=0])

get_corrected_data((ImageSet)arg1, (object)arg2) → tuple :

C++ signature :

boost::python::tuple get_corrected_data(dxtbx::ImageSet {lvalue},unsigned long)

get_detector((ImageSet)arg1[, (object)index=0]) → Detector :

C++ signature :

std::shared_ptr<dxtbx::model::Detector> get_detector(dxtbx::ImageSet {lvalue} [,unsigned long=0])

get_detectorbase(index)

A function to be injected into the imageset to get the detectorbase instance

get_format_class()

Get format class name

get_gain((ImageSet)arg1, (object)arg2) → tuple :

C++ signature :

boost::python::tuple get_gain(dxtbx::ImageSet {lvalue},unsigned long)

get_goniometer((ImageSet)arg1[, (object)index=0]) → Goniometer :

C++ signature :

std::shared_ptr<dxtbx::model::Goniometer> get_goniometer(dxtbx::ImageSet {lvalue} [,unsigned long=0])

get_image_identifier((ImageSet)arg1, (object)arg2) → str :

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > get_image_identifier(dxtbx::ImageSet {lvalue},unsigned long)

get_mask((ImageSet)arg1, (object)arg2) → tuple :

C++ signature :

boost::python::tuple get_mask(dxtbx::ImageSet {lvalue},unsigned long)

get_path((ImageSet)arg1, (object)arg2) → str :

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > get_path(dxtbx::ImageSet {lvalue},unsigned long)

get_pedestal((ImageSet)arg1, (object)arg2) → tuple :

C++ signature :

boost::python::tuple get_pedestal(dxtbx::ImageSet {lvalue},unsigned long)

get_raw_data((ImageSet)arg1, (object)arg2) → tuple :

C++ signature :

boost::python::tuple get_raw_data(dxtbx::ImageSet {lvalue},unsigned long)

get_scan((ImageSet)arg1[, (object)index=0]) → Scan :

C++ signature :

std::shared_ptr<dxtbx::model::Scan> get_scan(dxtbx::ImageSet {lvalue} [,unsigned long=0])

get_spectrum(index)

Get the spectrum if available

get_vendortype(index)

Get the vendor information.

has_dynamic_mask((ImageSet)arg1) → bool :

C++ signature :

bool has_dynamic_mask(dxtbx::ImageSet {lvalue})

indices((ImageSet)arg1) → size_t :

C++ signature :

scitbx::af::shared<unsigned long> indices(dxtbx::ImageSet {lvalue})

is_marked_for_rejection((ImageSet)arg1, (object)arg2) → bool :

C++ signature :

bool is_marked_for_rejection(dxtbx::ImageSet {lvalue},unsigned long)

mark_for_rejection((ImageSet)arg1, (object)arg2, (object)arg3) → None :

C++ signature :

void mark_for_rejection(dxtbx::ImageSet {lvalue},unsigned long,bool)

masker()

Return the masker

params()

Get the parameters

partial_set((ImageSet)arg1, (object)arg2, (object)arg3, (object)arg4) → ImageSet :

C++ signature :

dxtbx::ImageSet partial_set(dxtbx::ImageSet {lvalue},boost::python::api::object,unsigned long,unsigned long)

paths()

Return the list of paths

reader()

Return the reader

set_beam((ImageSet)arg1, (BeamBase)arg2[, (object)index=0]) → None :

C++ signature :

void set_beam(dxtbx::ImageSet {lvalue},std::shared_ptr<dxtbx::model::BeamBase> [,unsigned long=0])

set_detector((ImageSet)arg1, (Detector)arg2[, (object)index=0]) → None :

C++ signature :

void set_detector(dxtbx::ImageSet {lvalue},std::shared_ptr<dxtbx::model::Detector> [,unsigned long=0])

set_goniometer((ImageSet)arg1, (Goniometer)arg2[, (object)index=0]) → None :

C++ signature :

void set_goniometer(dxtbx::ImageSet {lvalue},std::shared_ptr<dxtbx::model::Goniometer> [,unsigned long=0])

set_scan((ImageSet)arg1, (Scan)arg2[, (object)index=0]) → None :

C++ signature :

void set_scan(dxtbx::ImageSet {lvalue},std::shared_ptr<dxtbx::model::Scan> [,unsigned long=0])

size((ImageSet)arg1) → int :

C++ signature :

unsigned long size(dxtbx::ImageSet {lvalue})

update_detector_px_mm_data((ImageSet)arg1) → None :

C++ signature :

void update_detector_px_mm_data(dxtbx::ImageSet {lvalue})

class dxtbx.imageset.ImageSetData

Bases: instance

__init__((object)arg1, (object)reader, (object)masker) → object :

C++ signature :

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

__init__( (object)arg1, (object)reader, (object)masker [, (str)template=’’ [, (str)vendor=’’ [, (dict)params=None [, (object)format=None]]]]) -> object :

C++ signature :

void* __init__(boost::python::api::object,boost::python::api::object,boost::python::api::object [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,boost::python::dict=None [,boost::python::api::object=None]]]])

property external_lookup

get_beam((ImageSetData)arg1, (object)arg2) → BeamBase :

C++ signature :

std::shared_ptr<dxtbx::model::BeamBase> get_beam(dxtbx::ImageSetData {lvalue},unsigned long)

get_data((ImageSetData)arg1, (object)arg2) → ImageBuffer :

C++ signature :

dxtbx::format::ImageBuffer get_data(dxtbx::ImageSetData {lvalue},unsigned long)

get_detector((ImageSetData)arg1, (object)arg2) → Detector :

C++ signature :

std::shared_ptr<dxtbx::model::Detector> get_detector(dxtbx::ImageSetData {lvalue},unsigned long)

get_format_class((ImageSetData)arg1) → object :

C++ signature :

boost::python::api::object get_format_class(dxtbx::ImageSetData {lvalue})

get_goniometer((ImageSetData)arg1, (object)arg2) → Goniometer :

C++ signature :

std::shared_ptr<dxtbx::model::Goniometer> get_goniometer(dxtbx::ImageSetData {lvalue},unsigned long)

get_image_identifier((ImageSetData)arg1, (object)arg2) → str :

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > get_image_identifier(dxtbx::ImageSetData {lvalue},unsigned long)

get_master_path((ImageSetData)arg1) → str :

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > get_master_path(dxtbx::ImageSetData {lvalue})

get_params((ImageSetData)arg1) → object :

C++ signature :

boost::python::api::object get_params(dxtbx::ImageSetData {lvalue})

get_path((ImageSetData)arg1, (object)arg2) → str :

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > get_path(dxtbx::ImageSetData {lvalue},unsigned long)

get_scan((ImageSetData)arg1, (object)arg2) → Scan :

C++ signature :

std::shared_ptr<dxtbx::model::Scan> get_scan(dxtbx::ImageSetData {lvalue},unsigned long)

get_template((ImageSetData)arg1) → str :

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > get_template(dxtbx::ImageSetData {lvalue})

get_vendor((ImageSetData)arg1) → str :

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > get_vendor(dxtbx::ImageSetData {lvalue})

has_single_file_reader((ImageSetData)arg1) → bool :

C++ signature :

bool has_single_file_reader(dxtbx::ImageSetData {lvalue})

is_marked_for_rejection((ImageSetData)arg1, (object)arg2) → bool :

C++ signature :

bool is_marked_for_rejection(dxtbx::ImageSetData {lvalue},unsigned long)

mark_for_rejection((ImageSetData)arg1, (object)arg2, (object)arg3) → None :

C++ signature :

void mark_for_rejection(dxtbx::ImageSetData {lvalue},unsigned long,bool)

masker((ImageSetData)arg1) → GoniometerShadowMasker :

C++ signature :

std::shared_ptr<dxtbx::masking::GoniometerShadowMasker> masker(dxtbx::ImageSetData {lvalue})

partial_data((ImageSetData)arg1, (object)arg2, (object)arg3, (object)arg4) → ImageSetData :

C++ signature :

dxtbx::ImageSetData partial_data(dxtbx::ImageSetData {lvalue},boost::python::api::object,unsigned long,unsigned long)

reader((ImageSetData)arg1) → object :

C++ signature :

boost::python::api::object reader(dxtbx::ImageSetData {lvalue})

set_beam((ImageSetData)arg1, (BeamBase)arg2, (object)arg3) → None :

C++ signature :

void set_beam(dxtbx::ImageSetData {lvalue},std::shared_ptr<dxtbx::model::BeamBase>,unsigned long)

set_detector((ImageSetData)arg1, (Detector)arg2, (object)arg3) → None :

C++ signature :

void set_detector(dxtbx::ImageSetData {lvalue},std::shared_ptr<dxtbx::model::Detector>,unsigned long)

set_format_class((ImageSetData)arg1, (dict)arg2) → None :

C++ signature :

void set_format_class(dxtbx::ImageSetData {lvalue},boost::python::dict)

set_goniometer((ImageSetData)arg1, (Goniometer)arg2, (object)arg3) → None :

C++ signature :

void set_goniometer(dxtbx::ImageSetData {lvalue},std::shared_ptr<dxtbx::model::Goniometer>,unsigned long)

set_params((ImageSetData)arg1, (dict)arg2) → None :

C++ signature :

void set_params(dxtbx::ImageSetData {lvalue},boost::python::dict)

set_scan((ImageSetData)arg1, (Scan)arg2, (object)arg3) → None :

C++ signature :

void set_scan(dxtbx::ImageSetData {lvalue},std::shared_ptr<dxtbx::model::Scan>,unsigned long)

set_template((ImageSetData)arg1, (str)arg2) → None :

C++ signature :

void set_template(dxtbx::ImageSetData {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

set_vendor((ImageSetData)arg1, (str)arg2) → None :

C++ signature :

void set_vendor(dxtbx::ImageSetData {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class dxtbx.imageset.ImageSetFactory

Bases: object

Factory to create imagesets and sequences.

static from_template(template, image_range=None, check_headers=False, check_format=True, beam=None, detector=None, goniometer=None, scan=None)

Create a new sequence from a template.

Params:

template The template argument image_range The image range check_headers Check the headers to ensure all images are valid

Returns:

A list of sequences

static imageset_from_anyset(imageset)

Create a new ImageSet object from an imageset object. Converts ImageSequence to ImageSet.

static make_imageset(filenames, format_class=None, check_format=True, single_file_indices=None, format_kwargs=None)

Create an image set

static make_sequence(template, indices, format_class=None, beam=None, detector=None, goniometer=None, scan=None, check_format=True, format_kwargs=None)

Create a sequence

static new(filenames, check_headers=False, ignore_unknown=False)

Create an imageset or sequence

Params:

filenames A list of filenames check_headers Check the headers to ensure all images are valid ignore_unknown Ignore unknown formats

Returns:

A list of imagesets

class dxtbx.imageset.ImageSetLazy

Bases: ImageSet

Lazy ImageSet class that doesn’t necessitate setting the models ahead of time. Only when a particular model (like detector or beam) for an image is requested, it sets the model using the format class and then returns the model

get_beam((ImageSet)arg1[, (object)index=0]) → BeamBase :

C++ signature :

std::shared_ptr<dxtbx::model::BeamBase> get_beam(dxtbx::ImageSet {lvalue} [,unsigned long=0])

get_corrected_data((ImageSet)arg1, (object)arg2) → tuple :

C++ signature :

boost::python::tuple get_corrected_data(dxtbx::ImageSet {lvalue},unsigned long)

get_detector((ImageSet)arg1[, (object)index=0]) → Detector :

C++ signature :

std::shared_ptr<dxtbx::model::Detector> get_detector(dxtbx::ImageSet {lvalue} [,unsigned long=0])

get_gain((ImageSet)arg1, (object)arg2) → tuple :

C++ signature :

boost::python::tuple get_gain(dxtbx::ImageSet {lvalue},unsigned long)

get_goniometer((ImageSet)arg1[, (object)index=0]) → Goniometer :

C++ signature :

std::shared_ptr<dxtbx::model::Goniometer> get_goniometer(dxtbx::ImageSet {lvalue} [,unsigned long=0])

get_mask(index=None)

ImageSet::get_mask internally dereferences a pointer to the _detector member of ImageSetData, so we ensure the detector gets populated first.

get_scan((ImageSet)arg1[, (object)index=0]) → Scan :

C++ signature :

std::shared_ptr<dxtbx::model::Scan> get_scan(dxtbx::ImageSet {lvalue} [,unsigned long=0])

class dxtbx.imageset.MemReader(images)

Bases: object

A reader for data already loaded in memory

__init__(images)

copy(paths)

Experimental implementation where a copy of the reader also copies all the data

identifiers()

static is_single_file_reader()

static master_path()

paths()

read(index)