API reference¶

The Python API client is primarily a GraphQL client that interacts with our GraphQL API endpoint. Install the cryoet-data-portal package to use the following classes with methods for searching and downloading datasets, tomograms, annotations and related files and metadata from the portal.

class cryoet_data_portal.Alignment¶

Tiltseries Alignment

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
annotation_files	List[AnnotationFile]	The annotation files of this alignment
per_section_alignments	List[PerSectionAlignmentParameters]	The per section alignment parameters of this alignment
deposition	Deposition	The deposition this alignment is a part of
deposition_id	int	None
tiltseries	TiltSeries	The tilt series this alignment is a part of
tiltseries_id	int	None
tomograms	List[Tomogram]	The tomograms of this alignment
run	Run	The run this alignment is a part of
run_id	int	None
alignment_type	str	Whether this a LOCAL or GLOBAL alignment
alignment_method	str	The method used to create this alignment
volume_x_dimension	float	X dimension of the reconstruction volume in angstrom
volume_y_dimension	float	Y dimension of the reconstruction volume in angstrom
volume_z_dimension	float	Z dimension of the reconstruction volume in angstrom
volume_x_offset	float	X shift of the reconstruction volume in angstrom
volume_y_offset	float	Y shift of the reconstruction volume in angstrom
volume_z_offset	float	Z shift of the reconstruction volume in angstrom
x_rotation_offset	float	Additional X rotation of the reconstruction volume in degrees
tilt_offset	float	Additional tilt offset in degrees
affine_transformation_matrix	str	A placeholder for the affine transformation matrix.
s3_alignment_metadata	str	S3 path to the metadata file for this alignment
https_alignment_metadata	str	HTTPS url to the metadata file for this alignment
is_portal_standard	bool	Whether this is the portal standard alignment

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> alignments = Alignment.find(client, query_filters=[Alignment.run.name == "TS_026"])

Get all results for this type:

>>> alignments = Alignment.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an Alignment by ID:

>>> alignment = Alignment.get_by_id(client, 1)
>>> print(alignment.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Annotation¶

Metadata for an annotation

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
run	Run	The run this annotation is a part of
run_id	int	None
annotation_shapes	List[AnnotationShape]	The annotation shapes of this annotation
method_links	List[AnnotationMethodLink]	The annotation method links of this annotation
authors	List[AnnotationAuthor]	The annotation authors of this annotation
deposition	Deposition	The deposition this annotation is a part of
deposition_id	int	None
s3_metadata_path	str	S3 path for the metadata json file for this annotation
https_metadata_path	str	HTTPS path for the metadata json file for this annotation
annotation_publication	str	DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs.
annotation_method	str	Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching)
ground_truth_status	bool	Whether an annotation is considered ground truth, as determined by the annotator.
object_id	str	Gene Ontology Cellular Component identifier or UniProtKB accession for the annotation object.
object_name	str	Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane)
object_description	str	A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state.
object_state	str	Molecule state annotated (e.g. open, closed)
object_count	int	Number of objects identified
confidence_precision	float	Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive
confidence_recall	float	Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly
ground_truth_used	str	Annotation filename used as ground truth for precision and recall
annotation_software	str	Software used for generating this annotation
is_curator_recommended	bool	Data curator’s subjective choice as the best annotation of the same annotation object ID
method_type	str	The method type for generating the annotation (e.g. manual, hybrid, automated)
deposition_date	date	Date when an annotation set is initially received by the Data Portal.
release_date	date	Date when annotation data is made public by the Data Portal.
last_modified_date	date	Date when an annotation was last modified in the Data Portal

download(dest_path=None, format=None, shape=None)¶

Download annotation files for a given format and/or shape

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

shape : Optional[str], optional¶

Choose a specific shape type to download (e.g.: OrientedPoint, SegmentationMask)

format : Optional[str], optional¶

Choose a specific file format to download (e.g.: mrc, ndjson)

download_metadata(dest_path=None)¶

Download annotation metadata

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> annotations = Annotation.find(client, query_filters=[Annotation.run.name == "TS_026"])

Get all results for this type:

>>> annotations = Annotation.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an Annotation by ID:

>>> annotation = Annotation.get_by_id(client, 1)
>>> print(annotation.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.AnnotationAuthor¶

Metadata for an annotation’s authors

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
annotation	Annotation	The annotation this annotation author is a part of
annotation_id	int	None
author_list_order	int	The order in which the author appears in the publication
orcid	str	A unique, persistent identifier for researchers, provided by ORCID.
name	str	Full name of an annotation author (e.g. Jane Doe).
email	str	Email address for this author
affiliation_name	str	Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations.
affiliation_address	str	Address of the institution an annotator is affiliated with.
affiliation_identifier	str	A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR).
corresponding_author_status	bool	Indicates whether an annotator is the corresponding author
primary_author_status	bool	Indicates whether an author is the main person executing the annotation, especially on manual annotation

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> annotation_authors = AnnotationAuthor.find(client, query_filters=[AnnotationAuthor.annotation.run.name._in(['TS_026', 'TS_027']), AnnotationAuthor.annotation.object_name.ilike('%membrane%')])

Get all results for this type:

>>> annotation_authors = AnnotationAuthor.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an AnnotationAuthor by ID:

>>> annotation_author = AnnotationAuthor.get_by_id(client, 1)
>>> print(annotation_author.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.AnnotationFile¶

Metadata for files associated with an annotation

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
alignment	Alignment	The alignment this annotation file is a part of
alignment_id	int	None
annotation_shape	AnnotationShape	The annotation shape this annotation file is a part of
annotation_shape_id	int	None
tomogram_voxel_spacing	TomogramVoxelSpacing	The tomogram voxel spacing this annotation file is a part of
tomogram_voxel_spacing_id	int	None
format	str	File format for this file
s3_path	str	s3 path of the annotation file
https_path	str	HTTPS path for this annotation file
is_visualization_default	bool	Data curator’s subjective choice of default annotation to display in visualization for an object
source	str	The source type for the annotation file (dataset_author, community, or portal_standard)

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Get all results for this type:

>>> annotation_files = AnnotationFile.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an AnnotationFile by ID:

>>> annotation_file = AnnotationFile.get_by_id(client, 1)
>>> print(annotation_file.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.AnnotationMethodLink¶

A set of links to models, source code, documentation, etc referenced by annotation method

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
annotation	Annotation	The annotation this annotation method link is a part of
annotation_id	int	None
link_type	str	Type of link (e.g. model, source code, documentation)
name	str	user readable name of the resource
link	str	URL to the resource

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> annotation_method_links = AnnotationMethodLink.find(client, query_filters=[AnnotationMethodLink.annotation.run.name._in(['TS_026', 'TS_027']), AnnotationMethodLink.annotation.object_name.ilike('%membrane%')])

Get all results for this type:

>>> annotation_method_links = AnnotationMethodLink.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an AnnotationMethodLink by ID:

>>> annotation_method_link = AnnotationMethodLink.get_by_id(client, 1)
>>> print(annotation_method_link.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.AnnotationShape¶

Shapes associated with an annotation

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
annotation	Annotation	The annotation this annotation shape is a part of
annotation_id	int	None
annotation_files	List[AnnotationFile]	The annotation files of this annotation shape
shape_type	str	The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh)

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> annotation_shapes = AnnotationShape.find(client, query_filters=[AnnotationShape.annotation.run.name._in(['TS_026', 'TS_027']), AnnotationShape.annotation.object_name.ilike('%membrane%')])

Get all results for this type:

>>> annotation_shapes = AnnotationShape.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an AnnotationShape by ID:

>>> annotation_shape = AnnotationShape.get_by_id(client, 1)
>>> print(annotation_shape.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Client¶

A GraphQL Client library that can traverse all the metadata in the CryoET Data Portal

Parameters:

url : Optional[str]

The API URL to connect to, defaults to the latest portal endpoint.

Returns:

A GraphQL API Client library

Examples

Generate a client that connects to the default GraphQL API:

>>> client = cryoet_data_portal.Client()

class cryoet_data_portal.Dataset¶

A collection of imaging experiments on the same organism

Attributes:

Name	Type	Description
id	int	An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree
deposition	Deposition	The deposition this dataset is a part of
deposition_id	int	None
funding_sources	List[DatasetFunding]	The dataset fundings of this dataset
authors	List[DatasetAuthor]	The dataset authors of this dataset
runs	List[Run]	The runs of this dataset
title	str	Title of a CryoET dataset
description	str	A short description of a CryoET dataset, similar to an abstract for a journal article or dataset.
organism_name	str	Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens
organism_taxid	int	NCBI taxonomy identifier for the organism, e.g. 9606
tissue_name	str	Name of the tissue from which a biological sample used in a CryoET study is derived from.
tissue_id	str	UBERON identifier for the tissue
cell_name	str	Name of the cell from which a biological sample used in a CryoET study is derived from.
cell_type_id	str	Cell Ontology identifier for the cell type
cell_strain_name	str	Cell line or strain for the sample.
cell_strain_id	str	Link to more information about the cell strain
sample_type	str	Type of samples used in a CryoET study. (cell, tissue, organism, intact organelle, in-vitro mixture, in-silico synthetic data, other)
sample_preparation	str	Describe how the sample was prepared.
grid_preparation	str	Describe Cryo-ET grid preparation.
other_setup	str	Describe other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication
key_photo_url	str	URL for the dataset preview image.
key_photo_thumbnail_url	str	URL for the thumbnail of preview image.
cell_component_name	str	Name of the cellular component
cell_component_id	str	If the dataset focuses on a specific part of a cell, the subset is included here
deposition_date	date	Date when a dataset is initially received by the Data Portal.
release_date	date	Date when a dataset is made available on the Data Portal.
last_modified_date	date	Date when a released dataset is last modified.
dataset_publications	str	Comma-separated list of DOIs for publications associated with the dataset.
related_database_entries	str	If a CryoET dataset is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers.
s3_prefix	str	The S3 public bucket path where this dataset is contained
https_prefix	str	The https directory path where this dataset is contained

download_everything(dest_path=None)¶

Download all of the data for this dataset.

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Get all results for this type:

>>> datasets = Dataset.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an Dataset by ID:

>>> dataset = Dataset.get_by_id(client, 1)
>>> print(dataset.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.DatasetAuthor¶

An author of a dataset

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
dataset	Dataset	The dataset this dataset author is a part of
dataset_id	int	None
author_list_order	int	The order in which the author appears in the publication
orcid	str	A unique, persistent identifier for researchers, provided by ORCID.
name	str	Full name of an author (e.g. Jane Doe).
email	str	Email address for this author
affiliation_name	str	Name of the institutions an author is affiliated with. Comma separated
affiliation_address	str	Address of the institution an author is affiliated with.
affiliation_identifier	str	A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR).
corresponding_author_status	bool	Indicates whether an author is the corresponding author
primary_author_status	bool	Indicates whether an author is the main person associated with the corresponding dataset

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter dataset authors by attributes, including attributes in related models:

>>> dataset_authors = DatasetAuthor.find(client, query_filters=[DatasetAuthor.name == "TS_026", DatasetAuthor.dataset.id == 10000])

Get all results for this type:

>>> dataset_authors = DatasetAuthor.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an DatasetAuthor by ID:

>>> dataset_author = DatasetAuthor.get_by_id(client, 1)
>>> print(dataset_author.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.DatasetFunding¶

Metadata for a dataset’s funding sources

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
dataset	Dataset	The dataset this dataset funding is a part of
dataset_id	int	None
funding_agency_name	str	Name of the funding agency.
grant_id	str	Grant identifier provided by the funding agency.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter dataset fundings by attributes, including attributes in related models:

>>> dataset_fundings = DatasetFunding.find(client, query_filters=[DatasetFunding.dataset.id == 10000])

Get all results for this type:

>>> dataset_fundings = DatasetFunding.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an DatasetFunding by ID:

>>> dataset_funding = DatasetFunding.get_by_id(client, 1)
>>> print(dataset_funding.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Deposition¶

Deposition metadata

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
authors	List[DepositionAuthor]	The deposition authors of this deposition
alignments	List[Alignment]	The alignments of this deposition
annotations	List[Annotation]	The annotations of this deposition
datasets	List[Dataset]	The datasets of this deposition
frames	List[Frame]	The frames of this deposition
tiltseries	List[TiltSeries]	The tilt series of this deposition
tomograms	List[Tomogram]	The tomograms of this deposition
title	str	Title for the deposition
description	str	Description for the deposition
deposition_types	List[DepositionType]	The deposition types of this deposition
deposition_publications	str	The publications related to this deposition
related_database_entries	str	The related database entries to this deposition
deposition_date	date	The date the deposition was deposited
release_date	date	The date the deposition was released
last_modified_date	date	The date the deposition was last modified
key_photo_url	str	URL for the deposition preview image.
key_photo_thumbnail_url	str	URL for the deposition thumbnail image.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Get all results for this type:

>>> depositions = Deposition.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an Deposition by ID:

>>> deposition = Deposition.get_by_id(client, 1)
>>> print(deposition.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.DepositionAuthor¶

Authors for a deposition

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
deposition	Deposition	The deposition this deposition author is a part of
deposition_id	int	None
author_list_order	int	The order in which the author appears in the publication
orcid	str	A unique, persistent identifier for researchers, provided by ORCID.
name	str	Full name of a deposition author (e.g. Jane Doe).
email	str	Email address for this author
affiliation_name	str	Name of the institutions an author is affiliated with. Comma separated
affiliation_address	str	Address of the institution an author is affiliated with.
affiliation_identifier	str	A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR).
corresponding_author_status	bool	Indicates whether an author is the corresponding author
primary_author_status	bool	Indicates whether an author is the main person creating the deposition

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Get all results for this type:

>>> deposition_authors = DepositionAuthor.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an DepositionAuthor by ID:

>>> deposition_author = DepositionAuthor.get_by_id(client, 1)
>>> print(deposition_author.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.DepositionType¶

None

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
deposition	Deposition	The deposition this deposition type is a part of
deposition_id	int	None
type	str	The type of data submitted as a part of this deposition (annotation, dataset, tomogram)

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Get all results for this type:

>>> deposition_types = DepositionType.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an DepositionType by ID:

>>> deposition_type = DepositionType.get_by_id(client, 1)
>>> print(deposition_type.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Frame¶

None

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
deposition	Deposition	The deposition this frame is a part of
deposition_id	int	None
run	Run	The run this frame is a part of
run_id	int	None
raw_angle	float	Camera angle for a frame
acquisition_order	int	Frame’s acquistion order within a tilt experiment
dose	float	The raw camera angle for a frame
is_gain_corrected	bool	Whether this frame has been gain corrected
s3_frame_path	str	S3 path to the frame file
https_frame_path	str	HTTPS path to the frame file

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> frames = Frame.find(client, query_filters=[Frame.run.name == "TS_026"])

Get all results for this type:

>>> frames = Frame.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an Frame by ID:

>>> frame = Frame.get_by_id(client, 1)
>>> print(frame.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.FrameAcquisitionFile¶

References to files containing more information about frame acquisition

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
run	Run	The run this frame acquisition file is a part of
run_id	int	None
s3_mdoc_path	str	Path to the frame acquisition mdoc file in s3
https_mdoc_path	str	Path to the frame acquisition mdoc file as an https url

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> frame_acquisition_files = FrameAcquisitionFile.find(client, query_filters=[FrameAcquisitionFile.run.name == "TS_026"])

Get all results for this type:

>>> frame_acquisition_files = FrameAcquisitionFile.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an FrameAcquisitionFile by ID:

>>> frame_acquisition_file = FrameAcquisitionFile.get_by_id(client, 1)
>>> print(frame_acquisition_file.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.GainFile¶

Gain values for frames in this run

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
run	Run	The run this gain file is a part of
run_id	int	None
s3_file_path	str	Path to the file in s3
https_file_path	str	Path to the file as an https url

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> gain_files = GainFile.find(client, query_filters=[GainFile.run.name == "TS_026"])

Get all results for this type:

>>> gain_files = GainFile.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an GainFile by ID:

>>> gain_file = GainFile.get_by_id(client, 1)
>>> print(gain_file.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.PerSectionAlignmentParameters¶

Map alignment parameters to tilt series frames

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
alignment	Alignment	The alignment this per section alignment parameters is a part of
alignment_id	int	None
z_index	int	z-index of the frame in the tiltseries
x_offset	float	In-plane X-shift of the projection in angstrom
y_offset	float	In-plane Y-shift of the projection in angstrom
volume_x_rotation	float	X-axis rotation in degrees
in_plane_rotation	List[List[float]]	In-plane rotation of the projection in degrees
tilt_angle	float	Tilt angle of the projection in degrees

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Get all results for this type:

>>> per_section_alignment_parameters = PerSectionAlignmentParameters.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an PerSectionAlignmentParameters by ID:

>>> per_section_alignment_parameters = PerSectionAlignmentParameters.get_by_id(client, 1)
>>> print(per_section_alignment_parameters.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Run¶

None

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
alignments	List[Alignment]	The alignments of this run
annotations	List[Annotation]	The annotations of this run
dataset	Dataset	The dataset this run is a part of
dataset_id	int	None
frames	List[Frame]	The frames of this run
gain_files	List[GainFile]	The gain files of this run
frame_acquisition_files	List[FrameAcquisitionFile]	The frame acquisition files of this run
tiltseries	List[TiltSeries]	The tilt series of this run
tomogram_voxel_spacings	List[TomogramVoxelSpacing]	The tomogram voxel spacings of this run
tomograms	List[Tomogram]	The tomograms of this run
name	str	Short name for this experiment run
s3_prefix	str	The S3 public bucket path where this run is contained
https_prefix	str	The HTTPS directory path where this run is contained url

download_everything(dest_path=None)¶

Download all of the data for this run.

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an Run by ID:

>>> run = Run.get_by_id(client, 1)
>>> print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.TiltSeries¶

None

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
alignments	List[Alignment]	The alignments of this tilt series
run	Run	The run this tilt series is a part of
run_id	int	None
deposition	Deposition	The deposition this tilt series is a part of
deposition_id	int	None
s3_omezarr_dir	str	S3 path to this tiltseries in multiscale OME-Zarr format
s3_mrc_file	str	S3 path to this tiltseries in MRC format (no scaling)
https_omezarr_dir	str	HTTPS path to this tiltseries in multiscale OME-Zarr format
https_mrc_file	str	HTTPS path to this tiltseries in MRC format (no scaling)
s3_angle_list	str	S3 path to the angle list file for this tiltseries
https_angle_list	str	HTTPS path to the angle list file for this tiltseries
acceleration_voltage	int	Electron Microscope Accelerator voltage in volts
spherical_aberration_constant	float	Spherical Aberration Constant of the objective lens in millimeters
microscope_manufacturer	str	Name of the microscope manufacturer (FEI, TFS, JEOL)
microscope_model	str	Microscope model name
microscope_energy_filter	str	Energy filter setup used
microscope_phase_plate	str	Phase plate configuration
microscope_image_corrector	str	Image corrector setup
microscope_additional_info	str	Other microscope optical setup information, in addition to energy filter, phase plate and image corrector
camera_manufacturer	str	Name of the camera manufacturer
camera_model	str	Camera model name
tilt_min	float	Minimal tilt angle in degrees
tilt_max	float	Maximal tilt angle in degrees
tilt_range	float	Total tilt range in degrees
tilt_step	float	Tilt step in degrees
tilting_scheme	str	The order of stage tilting during acquisition of the data
tilt_axis	float	Rotation angle in degrees
total_flux	float	Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series
data_acquisition_software	str	Software used to collect data
related_empiar_entry	str	If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier
binning_from_frames	float	Describes the binning factor from frames to tilt series file
tilt_series_quality	int	Author assessment of tilt series quality within the dataset (1-5, 5 is best)
is_aligned	bool	Whether this tilt series is aligned
pixel_spacing	float	Pixel spacing equal in both axes in angstroms
aligned_tiltseries_binning	int	Binning factor of the aligned tilt series
size_x	int	Number of pixels in the 3D data fast axis
size_y	int	Number of pixels in the 3D data medium axis
size_z	int	Number of pixels in the 3D data slow axis

download_alignment_file(dest_path=None)¶

Download the alignment file for this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_angle_list(dest_path=None)¶

Download the angle list for this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_mrcfile(dest_path=None)¶

Download an MRC file for this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_omezarr(dest_path=None)¶

Download the omezarr version of this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> tilt_series = TiltSeries.find(client, query_filters=[TiltSeries.run.name == "TS_026"])

Get all results for this type:

>>> tilt_series = TiltSeries.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an TiltSeries by ID:

>>> tilt_series = TiltSeries.get_by_id(client, 1)
>>> print(tilt_series.id)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Tomogram¶

Metadata describing a tomogram.

Attributes:

Name	Type	Description
id	int	Numeric identifier (May change!)
alignment	Alignment	The alignment this tomogram is a part of
alignment_id	int	None
authors	List[TomogramAuthor]	The tomogram authors of this tomogram
deposition	Deposition	The deposition this tomogram is a part of
deposition_id	int	None
run	Run	The run this tomogram is a part of
run_id	int	None
tomogram_voxel_spacing	TomogramVoxelSpacing	The tomogram voxel spacing this tomogram is a part of
tomogram_voxel_spacing_id	int	None
name	str	Short name for this tomogram
size_x	int	Number of pixels in the 3D data fast axis
size_y	int	Number of pixels in the 3D data medium axis
size_z	int	Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt
voxel_spacing	float	Voxel spacing equal in all three axes in angstroms
fiducial_alignment_status	str	Fiducial Alignment status: True = aligned with fiducial False = aligned without fiducial
reconstruction_method	str	Describe reconstruction method (WBP, SART, SIRT)
processing	str	Describe additional processing used to derive the tomogram
tomogram_version	float	Version of tomogram
processing_software	str	Processing software used to derive the tomogram
reconstruction_software	str	Name of software used for reconstruction
is_portal_standard	bool	whether this tomogram adheres to portal standards
is_author_submitted	bool	Whether this tomogram was submitted by the author of the dataset it belongs to.
is_visualization_default	bool	Data curator’s subjective choice of default tomogram to display in visualization for a run
s3_omezarr_dir	str	S3 path to this tomogram in multiscale OME-Zarr format
https_omezarr_dir	str	HTTPS path to this tomogram in multiscale OME-Zarr format
s3_mrc_file	str	S3 path to this tomogram in MRC format (no scaling)
https_mrc_file	str	HTTPS path to this tomogram in MRC format (no scaling)
scale_0_dimensions	str	comma separated x,y,z dimensions of the unscaled tomogram
scale_1_dimensions	str	comma separated x,y,z dimensions of the scale1 tomogram
scale_2_dimensions	str	comma separated x,y,z dimensions of the scale2 tomogram
ctf_corrected	bool	Whether this tomogram is CTF corrected
offset_x	int	x offset data relative to the canonical tomogram in pixels
offset_y	int	y offset data relative to the canonical tomogram in pixels
offset_z	int	z offset data relative to the canonical tomogram in pixels
key_photo_url	str	URL for the key photo
key_photo_thumbnail_url	str	URL for the thumbnail of key photo
neuroglancer_config	str	the compact json of neuroglancer config
publications	str	Comma-separated list of DOIs for publications associated with the tomogram.
related_database_entries	str	If a CryoET tomogram is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers.
deposition_date	date	The date a data item was received by the cryoET data portal.
release_date	date	The date a data item was received by the cryoET data portal.
last_modified_date	date	The date a piece of data was last modified on the cryoET data portal.

download_all_annotations(dest_path=None, format=None, shape=None)¶

Download all annotation files for this tomogram

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

shape : Optional[str], optional¶

Choose a specific shape type to download (e.g.: OrientedPoint, SegmentationMask)

format : Optional[str], optional¶

Choose a specific file format to download (e.g.: mrc, ndjson)

download_mrcfile(dest_path=None)¶

Download an MRC file of this tomogram

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_omezarr(dest_path=None)¶

Download the OME-Zarr version of this tomogram

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as: ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

>>> tomograms = Tomogram.find(client, query_filters=[Tomogram.run.name == "TS_026"])

Get all results for this type:

>>> tomograms = Tomogram.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get an Tomogram by ID:

>>> tomogram = Tomogram.get_by_id(client, 1)
>>> print(tomogram.name)

to_dict()¶

Return a dictionary representation of this object’s attributes