sfftkrw¶

This module defines a user-friendly adapter API (compared to the one generated by generateDS). It is designed to fulfill several requirements:

allow multiple versions of generateDS APIs to exist for the same adapter;
implement more convenient ways of working with the classes of the API;
easily integrate new EMDB-SFF entities into the API;
decouple the file format from the data model: most classes in this adapter implement methods to handle conversion to non-XML formats (XML is the only format that generateDS writes to)

Here is an example of how the SFFSegmentation class is defined using these classes (details omitted for brevity):

from .base import SFFType, SFFAttribute

class SFFSegmentation(SFFType):
    """Adapter class to make using the output of ``generateDS`` easier to use"""
    gds_type = sff.segmentation
    gds_tag_name = "segmentation"
    repr_string = "SFFSegmentation(...)"

    # attributes
    name = SFFAttribute('name', required=True)
    version = SFFAttribute('version')
    software_list = SFFAttribute('software_list', sff_type=SFFSoftwareList)
    primary_descriptor = SFFAttribute('primary_descriptor')
    transform_list = SFFAttribute('transform_list', sff_type=SFFTransformList)
    bounding_box = SFFAttribute('bounding_box', sff_type=SFFBoundingBox)
    global_external_references = SFFAttribute('global_external_references', sff_type=SFFGlobalExternalReferences)
    segment_list = SFFAttribute('segment_list', sff_type=SFFSegmentList)
    lattice_list = SFFAttribute('lattice_list', sff_type=SFFLatticeList)
    details = SFFAttribute('details')

In the above example, the SFFSegmentation class inherits from SFFType; SFFType uses the first three attributes (gds_type, gds_tag_name and repr_string) to configure the user class SFFSegmentation. The API user can now exploit SFFSegmentation without any need to know the underlying implementation while benefiting from the aforementioned facilities:

from sfftkrw import SFFSegmentation

# to create a new empty EMDB-SFF segmentation object
# provide the only required attribute
seg = SFFSegmentation(name='my name')
seg.to_file('file.sff') # export

# to read an XML-, HDF5- or JSON-formatted file, respectively
seg = SFFSegmentation('file.sff')
seg = SFFSegmentation('file.hff')
seg = SFFSegmentation('file.json')

The attributes (name, version, etc.) are all instances of SFFAttribute, which takes the name (first positional argument) and an optional keyword argument sff_type denoting the class of the attribute. In the above example, the software_list attribute will be of type SFFSoftwareList.

To learn more about the core classes please refer to sfftkrw.schema.base.

`SFFSegmentation` class¶

class sfftkrw.SFFSegmentation(name=None, software_list=None, primary_descriptor=None, details=None, transform_list=None, bounding_box=None, segment_list=None, lattice_list=None)¶

Bases: sfftkrw.schema.base.SFFType

Adapter class to make using the output of generateDS easier to use

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

bounding_box¶: the bounding box in which the segmentation sits; a sfftkrw.schema.adapter.SFFBoundingBox object

clear_annotation(from_id)¶

Clear all annotations from the segment with ID specified

Parameters:	from_id – segment ID
Returns:

copy_annotation(from_id, to_id)¶

Copy annotation across segments

Parameters:	from_id (int/list) – segment ID to get notes from; use -1 for for global notes to_id (int/list) – segment ID to copy notes to; use -1 for global notes

details¶: any other details about this segmentation (free text)

export(fn, args=None, *_args, **_kwargs)¶

Export to a file on disc

Return int status:
Parameters:	fn (str or io.TextIOWrapper or io.RawIOBase or io.BufferedIOBase or file) – filename to export to; the output format is determined by the extension:
	exit code from `os` library

.sff - XML
.hff - HDF5
.json - JSON

classmethod from_file(fn, args=None)¶

Instantiate an SFFSegmentations object from a file name

The file suffix determines how the data is extracted.

Parameters:	fn (str) – name of a file hosting an EMDB-SFF-structured segmentation
Return seg:	the corresponding `SFFSegmentation` object
Rtype seg:	`SFFSegmentation`

classmethod from_gds_type(inst=None)¶

Create an SFFType subclass directly from a gds_type object

Notice that we ignore do not pass *args, **kwargs as we assume the inst is complete.

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.segmentation

global_external_references¶: a list of external references that apply to the whole segmentation (global); a sfftkrw.schema.adapter.SFFGlobalexternal_references object

lattice_list¶: the list of lattices (if any) containing 3D volumes referred to; a sfftkrw.schema.adapter.SFFLatticeList object

merge_annotation(other_seg, include_colour=False)¶

Merge the annotation from another sff_seg to this one

Parameters:	other_seg (`sfftkrw.SFFSegmentation`) – segmentation to get annotations from include_colour (bool) – copy the colours from the source (useful if you want control over the colours)

name¶: the name of this segmentation

primary_descriptor¶: the main type of representation used for this segmentation; can be one of ‘mesh_list’, ‘shape_primitive_list’ or ‘threeDVolume’

segment_list¶: the list of annotated segments; a sfftkrw.schema.adapter.SFFSegmentList object

software_list¶: the list of software tools used to crate this segmentation a sfftkrw.schema.adapter.SFFSoftwareList object

to_file(*args, **kwargs)¶: Alias for export() method. Passes all args and kwargs onto SFFSegmentation.export()

transform_list¶: a list of transforms; a sfftkrw.schema.adapter.SFFTransformList object

version¶: EMDB-SFF version

`SFFSoftwareList` class¶

class sfftkrw.SFFSoftwareList¶

Bases: sfftkrw.schema.base.SFFListType

List of SFFSoftware objects

as_hff(parent_group, name='software_list', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='software_list', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

`SFFSoftware` class¶

class sfftkrw.SFFSoftware(name=None, version=None, processing_details=None)¶

Bases: sfftkrw.schema.base.SFFIndexType

Class definition for specifying software used to create this segmentation

name¶: The name of the software used

version¶: The version string

processing_details¶: Details of how the segmentation was produced

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

id¶: the software ID

name: the software/programmeu’s name

processing_details: a description of how the data was processed to produce the segmentation

version: the version used

`SFFTransformList` class¶

class sfftkrw.SFFTransformList¶

Bases: sfftkrw.schema.base.SFFListType

Container for transforms

as_hff(parent_group, name='transform_list', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='transform_list', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.transform_listType

`SFFTransformationMatrix` class¶

class sfftkrw.SFFTransformationMatrix(id=None, rows=None, cols=None, data=None)¶

Bases: sfftkrw.schema.base.SFFIndexType

Transformation matrix transform

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

cols¶: the number of columns in this matrix

data¶: a string sequence by row of the data in this matrix

classmethod from_array(ndarray, **kwargs)¶

Construct an SFFTransformationMatrix object from a numpy numpy.ndarray array

Parameters:	ndarray (`numpy.ndarray`) – a numpy array
Returns:	a `SFFTransformationMatrix` object

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.transformation_matrix_type

id¶: an ID for this transform

rows¶: the number of rows in this matrix

static stringify(array)¶: Convert a numpy.ndarray to a space-separated list of numbers

`SFFBoundingBox` class¶

class sfftkrw.SFFBoundingBox(xmin=0.0, xmax=None, ymin=0.0, ymax=None, zmin=0.0, zmax=None)¶

Bases: sfftkrw.schema.base.SFFType

Dimensions of bounding box

as_hff(parent_group, name='bounding_box', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='bounding_box', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

xmax¶: maximum x co-ordinate value

xmin¶: minimum x co-ordinate value

ymax¶: maximum y co-ordinate value

ymin¶: minimum y co-ordinate value

zmax¶: maximum z co-ordinate value

zmin¶: minimum z co-ordinate value

`SFFGlobalExternalReferenceList` class¶

class sfftkrw.SFFGlobalExternalReferenceList¶

Bases: sfftkrw.schema.base.SFFListType

Container for global external references

as_hff(parent_group, name='global_external_references', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='global_external_references', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

`SFFExternalReferenceList` class¶

class sfftkrw.SFFExternalReferenceList¶

Bases: sfftkrw.schema.base.SFFListType

Container for external references

as_hff(parent_group, name='external_references', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='external_references', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

`SFFExternalReference` class¶

class sfftkrw.SFFExternalReference(id=None, resource=None, url=None, accession=None, label=None, description=None)¶

Bases: sfftkrw.schema.base.SFFIndexType

accession¶: the accession for this external reference

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

description¶: a long description of this external reference

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

id¶: this external reference’s ID

label¶: a short description of this external reference

resource¶: the ontology/archive name

url¶: a URL/IRI where data for this external reference may be obtained

`SFFSegmentList` class¶

class sfftkrw.SFFSegmentList¶

Bases: sfftkrw.schema.base.SFFListType

Container for segments

as_hff(parent_group, name='segment_list', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='segment_list', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

`SFFSegment` class¶

class sfftkrw.SFFSegment(id=None, biological_annotation=None, colour=None, mesh_list=None, three_d_volume=None, shape_primitive_list=None)¶

Bases: sfftkrw.schema.base.SFFIndexType

Class that encapsulates segment data

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶: Format this segment as JSON

biological_annotation¶: the biological annotation for this segment; described using a sfftkrw.schema.adapter.SFFBiologicalAnnotation object

colour¶: this segments colour; described using a sfftkrw.schema.adapter.SFFRGBA object

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.segment_type

id¶: the ID for this segment; segment IDs begin at 1 with the value of 0 implying the segmentation i.e. all segments are children of the root segment (the segmentation)

mesh_list¶: the list of mesh_list (if any) that describe this segment; a sfftkrw.schema.adapter.SFFMeshList object

parent_id¶: the ID for the segment that contains this segment; defaults to 0 (the whole segmentation)

shape_primitive_list¶: the list of shape primitives that describe this segment; a sfftkrw.schema.adapter.SFFShapePrimitiveList object

three_d_volume¶: the 3D volume (if any) that describes this segment; a sfftkrw.schema.adapter.SFFThreeDVolume object

`SFFBiologicalAnnotation` class¶

class sfftkrw.SFFBiologicalAnnotation(name=None, description=None, external_references=None)¶

Bases: sfftkrw.schema.base.SFFType

Biological annotation

as_hff(parent_group, name='biological_annotation', args=None)¶: Return the data of this object as an HDF5 group in the given parent group

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

description¶: a brief description for this segment

external_references¶: the set of external references

classmethod from_hff(parent_group, name='biological_annotation', args=None)¶: Return an SFFType object given an HDF5 object

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

name¶: the name of this segment

number_of_instances¶: the number of instances of this segment

`SFFRGBA` class¶

class sfftkrw.SFFRGBA(red=None, green=None, blue=None, alpha=1.0, random_colour=False)¶

Bases: sfftkrw.schema.base.SFFType

Colours

alpha¶: alpha (opacity) channel

as_hff(parent_group, name='colour', args=None)¶: Return the data of this object as an HDF5 group in the given parent group

as_json(args=None)¶: Export as JSON

blue¶: blue channel

classmethod from_hff(parent_group, name='colour', args=None)¶: Return an SFFType object given an HDF5 object

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

green¶: green channel

red¶: red channel

`SFFEncodedSequence` class¶

class sfftkrw.SFFEncodedSequence(*args, **kwargs)¶

Bases: sfftkrw.schema.base.SFFType

Abstract base class for SFFVertices, SFFNormals and SFFTriangles

static _decode(bin64, mode=None, endianness=None, **kwargs)¶

Decode a base64-encoded byte sequence to a numpy array

Parameters:	bin64 (bytes or unicode) – the base64-encoded byte sequence mode (str) – the data type endianness (str) – the byte orientation
Returns:	a `numpy.ndarray` object
Return type:	`numpy.ndarray`

static _encode(array, mode=None, endianness=None, **kwargs)¶

Encode a numpy.ndarray as a base64-encoded byte sequence

Parameters:	array (`numpy.ndarray`) – a `numpy.ndarray` array mode (str) – the data type endianness (str) – the byte orientation
Return str:	the corresponding encoded sequence

classmethod from_array(data, mode=None, endianness=None)¶

Create a SFFVertices object from a numpy array inferring size and assuming certain defaults

Parameters:	data (`numpy.ndarray`) – the data as a `numpy.ndarray` object mode (bytes or str or unicode) – the size of each voxel; valid values are: int8, uint8, int16, uint16, int32, uint32, int64, uint64``float32, float64 endianness (bytes or str or unicode) – byte ordering: `little` (default) or `big`
Returns:	a `SFFVertices` object
Return type:	`SFFVertices`

classmethod from_bytes(byte_seq, num_items, mode=None, endianness=None)¶

Create a SFFVertices object using a bytes object

Parameters:	byte_seq (bytes or unicode) – the data as a base64-encoded sequence; can be bytes or unicode num_vertices (int) – the number of vertices contained (for validation) mode (bytes or str or unicode) – the size of each voxel; valid values are: int8, uint8, int16, uint16, int32, uint32, int64, uint64``float32, float64 endianness (bytes or str or unicode) – byte ordering: `little` (default) or `big`
Returns:	a `SFFVertices` object
Return type:	`SFFVertices`

`SFFVertices` class¶

class sfftkrw.SFFVertices(num_vertices=None, mode="float32", endianness="little", data=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFEncodedSequence

Vertices: neither a list nor an index type but is encoded

Suggests the need for an SFFCodedType which has encoded data with _encode and _decode services/methods.

as_hff(parent_group, name='vertices', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

data¶: base64-encoded packed binary data

endianness¶: binary packing endianness [default: ‘little’]

classmethod from_hff(parent_group, name='vertices', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.vertices_type

mode¶: data type; valid values are: int8, uint8, int16, uint16, int32, uint32, int64, uint64, float32, float64 [default: ‘float32’]

num_vertices¶: the number of vertices contained

`SFFNormals` class¶

class sfftkrw.SFFNormals(num_normals=None, mode="float32", endianness="little", data=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFEncodedSequence

Normals

as_hff(parent_group, name='normals', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

data¶: base64-encoded packed binary data

endianness¶: binary packing endianness [default: ‘little’]

classmethod from_hff(parent_group, name='normals', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.normals_type

mode¶: data type; valid values are: int8, uint8, int16, uint16, int32, uint32, int64, uint64, float32, float64 [default: ‘float32’]

num_normals¶: the number of normals contained

`SFFTriangles` class¶

class sfftkrw.SFFTriangles(num_triangles=None, mode="uint32", endianness="little", data=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFEncodedSequence

Triangles

as_hff(parent_group, name='triangles', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

data¶: base64-encoded packed binary data

endianness¶: binary packing endianness [default: ‘little’]

classmethod from_hff(parent_group, name='triangles', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.triangles_type

mode¶: data type; valid values are: int8, uint8, int16, uint16, int32, uint32, int64, uint64, float32, float64 [default: ‘float32’]

num_triangles¶: the number of triangles contained

`SFFMeshList` class¶

class sfftkrw.SFFMeshList¶

Bases: sfftkrw.schema.base.SFFListType

Mesh list representation

as_hff(parent_group, name='mesh_list', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='mesh_list', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

`SFFMesh` class¶

class sfftkrw.SFFMesh(id=None, vertices=None, normals=None, triangles=None, transform_id=None)¶

Bases: sfftkrw.schema.base.SFFIndexType

Single mesh

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

id¶: the mesh ID

normals¶: a list of normals which correspond to vertices

transform_id¶: a transform applied to the mesh

triangles¶: a list of triangles; each triangle is represented by a trio of vertex indices

vertices¶: a list of vertices

`SFFThreeDVolume` class¶

class sfftkrw.SFFThreeDVolume(lattice_id=None, value=None, transform_id=None)¶

Bases: sfftkrw.schema.base.SFFType

Class representing segments described using a 3D volume

as_hff(parent_group, name='three_d_volume', args=None)¶: Return an SFFType object given an HDF5 object

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='three_d_volume', args=None)¶: Return an SFFType object given an HDF5 object

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

lattice_id¶: the ID of the lattice that has the data for this 3D volume

transform_id¶: a transform applied to this 3D volume [optional]

value¶: the voxel values associated with this 3D volume

`SFFLatticeList` class¶

class sfftkrw.SFFLatticeList¶

Bases: sfftkrw.schema.base.SFFListType

A container for lattice objects

as_hff(parent_group, name='lattice_list', args=None)¶: Return the data of this object as an HDF5 group in the given parent group

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='lattice_list', args=None)¶: Return an SFFType object given an HDF5 object

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

`SFFLattice` class¶

class sfftkrw.SFFLattice(id=None, mode=None, endianness=None, size=None, start=None, data=None)¶

Bases: sfftkrw.schema.base.SFFIndexType

Class representing 3D

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

data¶: data provided by a numpy.ndarray, byte-sequence or unicode string; the dimensions should correspond with those specified in the ‘size’ attribute

data_array¶: The data as a numpy.ndarray

endianness¶: endianness; either ‘little’ (default) or ‘big’

classmethod from_array(data, size=None, mode='uint32', endianness='little', start=SFFVolumeIndex(rows=0, cols=0, sections=0))¶

Create a SFFLattice object from a numpy array inferring size and assuming certain defaults

Parameters:	data (`numpy.ndarray`) – the data as a `numpy.ndarray` object size (`SFFVolumeStructure`) – the size of the lattice as a `SFFVolumeStructure` object start (`SFFVolumeIndex`) – the values of the corner voxel mode (bytes or str or unicode) – the size of each voxel; valid values are: int8, uint8, int16, uint16, int32, uint32, int64, uint64``float32, float64 endianness (bytes or str or unicode) – byte ordering: `little` (default) or `big`
Returns:	a `SFFLattice` object
Return type:	`SFFLattice`

classmethod from_bytes(byte_seq, size, mode='uint32', endianness='little', start=SFFVolumeIndex(rows=0, cols=0, sections=0))¶

Create a SFFLattice object using a bytes object

Parameters:	byte_seq (bytes or unicode) – the data as a base64-encoded, zipped sequence; can be bytes or unicode size (`SFFVolumeStructure`) – the size of the lattice as a `SFFVolumeStructure` object start (`SFFVolumeIndex`) – the values of the corner voxel mode (bytes or str or unicode) – the size of each voxel; valid values are: int8, uint8, int16, uint16, int32, uint32, int64, uint64``float32, float64 endianness (bytes or str or unicode) – byte ordering: `little` (default) or `big`
Returns:	a `SFFLattice` object
Return type:	`SFFLattice`

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

id¶: the ID for this lattice (referenced by 3D volumes)

mode¶: type of data for each voxel; valid values are: int8, uint8, int16, uint16, int32, uint32, int64, uint64, float32, float64

size¶: size of the lattice described using a sfftkrw.schema.adapter.SFFVolumeStructure object

start¶: starting index of the lattices described using a:py:class:sfftkrw.schema.adapter.SFFVolumeIndex object

`SFFVolumeStructure` class¶

class sfftkrw.SFFVolumeStructure(rows=None, cols=None, sections=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFVolume

as_hff(parent_group, name='size', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

classmethod from_hff(parent_group, name='size', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

voxel_count¶: The number of voxels in this volume

`SFFVolumeIndex` class¶

class sfftkrw.SFFVolumeIndex(rows=None, cols=None, sections=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFVolume

Class representing volume indices

as_hff(parent_group, name='start', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

classmethod from_hff(parent_group, name='start', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

`SFFShapePrimitiveList` class¶

class sfftkrw.SFFShapePrimitiveList¶

Bases: sfftkrw.schema.base.SFFListType

Container for shapes

as_hff(parent_group, name='shape_primitive_list', args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name='shape_primitive_list', args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

num_cones¶: The number of cones in this container

num_cuboids¶: The number of cuboids in this container

num_cylinders¶: The number of cylinders in this container

num_ellipsoids¶: The number of ellipsoids in this container

`SFFShape` class¶

class sfftkrw.SFFShape(id=None, transform_id=None, attribute=None)¶

Bases: sfftkrw.schema.base.SFFIndexType

Base shape class

attribute¶: extra attribute information e.g. ‘FOM’

id¶: the ID of this shape

transform_id¶: the transform applied to this shape to position it in the space

classmethod update_counter(value)¶

Update the index for all subclasses sequentially for sibling classes

This method works alongside the index_in_super class attribute.

The superclass must specify this method to ensure correct sequencing of shared indices.

`SFFCone` class¶

class sfftkrw.SFFCone(id=None, height=None, bottom_radius=None, transform_id=None, attribute=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFShape

Cone shape class

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

bottom_radius¶: cone bottom radius

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

height¶: cone height

`SFFCuboid` class¶

class sfftkrw.SFFCuboid(id=None, x=None, y=None, z=None, transform_id=None, attribute=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFShape

Cuboid shape class

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.cuboid

x¶: length in x

y¶: length in y

z¶: length in z

`SFFCylinder` class¶

class sfftkrw.SFFCylinder(id=None, height=None, diameter=None, transform_id=None, attribute=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFShape

Cylinder shape class

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

diameter¶: cylinder diameter

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

height¶: cylinder height

`SFFEllipsoid` class¶

class sfftkrw.SFFEllipsoid(id=None, x=None, y=None, z=None, transform_id=None, attribute=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFShape

Ellipsoid shape class

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

gds_type¶: alias of sfftkrw.schema.v0_8_0_dev1.ellipsoid

x¶: length in x

y¶: length in y

z¶: length in z

`SFFSubtomogramAverage` class¶

class sfftkrw.SFFSubtomogramAverage(id=None, lattice_id, value=None, transform_id=None)¶

Bases: sfftkrw.schema.adapter_v0_8_0_dev1.SFFShape

Subtomogram average class

as_hff(parent_group, name=None, args=None)¶

Returns the current object as a group in an HDF5 file with the given name

For instances which are subclasses of base.SFFIndexType name will be a string version of the index (id). If id is None then we will generate a unique one so as to write the object to file. Therefore, the process of writing to HDF5 could end up looking slightly different from the original if the original had missing indexes for some objects.

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the populated parent group
Return type:	`Group`

as_json(args=None)¶

For all contained classes this method returns a dictionary which will be serialised into JSON. Only at the top level (SFFSegmentation) will the final serialisation be done.

Parameters:	args (`argparse.Namespace`) – command line arguments
Returns:	a set of nested dictionaries
Return type:	dict

classmethod from_hff(parent_group, name=None, args=None)¶

Convert HDF5 objects into EMDB-SFF objects It should either return a valid object or raise an SFFValueError due to failed validation

Parameters:	parent_group (`Group`) – an HDF5 Group that will contain the objects in this object args (`argparse.Namespace`) – command line arguments name (str or None) – the name to be given to this object in the object hierarchy (default: None)
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

classmethod from_json(data, args=None)¶

Deserialise the given json object into an EMDB-SFF object

Parameters:	data (dict) – the data to be converted into SFF* objects args (`argparse.Namespace`) – command line arguments
Returns:	the corresponding SFF* object
Return type:	`base.SFFType` subclass

lattice_id¶: the ID of the lattice holding the subtomogram average

transform_id¶: the transform applied to this shape to position it in the space

value¶: the value at which the contour is defined

sfftkrw¶

SFFSegmentation class¶

SFFSoftwareList class¶

SFFSoftware class¶

SFFTransformList class¶

SFFTransformationMatrix class¶

SFFBoundingBox class¶

SFFGlobalExternalReferenceList class¶

SFFExternalReferenceList class¶

SFFExternalReference class¶

SFFSegmentList class¶

SFFSegment class¶

SFFBiologicalAnnotation class¶

SFFRGBA class¶

SFFEncodedSequence class¶

SFFVertices class¶

SFFNormals class¶

SFFTriangles class¶

SFFMeshList class¶

SFFMesh class¶

SFFThreeDVolume class¶

SFFLatticeList class¶

SFFLattice class¶

SFFVolumeStructure class¶

SFFVolumeIndex class¶

SFFShapePrimitiveList class¶

SFFShape class¶

SFFCone class¶

SFFCuboid class¶

SFFCylinder class¶

SFFEllipsoid class¶

SFFSubtomogramAverage class¶

`SFFSegmentation` class¶

`SFFSoftwareList` class¶

`SFFSoftware` class¶

`SFFTransformList` class¶

`SFFTransformationMatrix` class¶

`SFFBoundingBox` class¶

`SFFGlobalExternalReferenceList` class¶

`SFFExternalReferenceList` class¶

`SFFExternalReference` class¶

`SFFSegmentList` class¶

`SFFSegment` class¶

`SFFBiologicalAnnotation` class¶

`SFFRGBA` class¶

`SFFEncodedSequence` class¶

`SFFVertices` class¶

`SFFNormals` class¶

`SFFTriangles` class¶

`SFFMeshList` class¶

`SFFMesh` class¶

`SFFThreeDVolume` class¶

`SFFLatticeList` class¶

`SFFLattice` class¶

`SFFVolumeStructure` class¶

`SFFVolumeIndex` class¶

`SFFShapePrimitiveList` class¶

`SFFShape` class¶

`SFFCone` class¶

`SFFCuboid` class¶

`SFFCylinder` class¶

`SFFEllipsoid` class¶

`SFFSubtomogramAverage` class¶