Changelog
Attention
The v3 Python API was deprecated on Wednesday, February 26, 2025. Please update your Python API client to continue accessing the cryoet-data-portal package.
v4 Python API
8 new classes were added to the API:
Class name |
Description |
|---|
Alignment
|
Tilt series alignment |
AnnotationMethodLink
|
A set of links to models, source code, documentation, etc referenced by annotation method |
AnnotationShape
|
Shapes associated with an annotation |
DepositionType
|
The type of data submitted as a part of a deposition (e.g. annotation, dataset, tomogram) |
Frame
|
Raw frames used for generating tilt series |
FrameAcquisitionFile
|
References to files containing more information about frame acquisition |
GainFile
|
Gain values for frames in this run |
PerSectionAlignmentParameters
|
Map alignment parameters to tilt series frames |
Changes to the Client
The v4 release of the Python API was paired with the v3 release of the Client. A summary of the changes between Client v2 and Client v3 is below.
Client V2 Field |
Client V3 Field |
|---|
Annotation.files
|
Annotation.annotation_shapes[*].annotation_files
|
Annotation.tomogram_voxel_spacing
|
Annotation.annotation_shapes[*].annotation_files[*].tomogram_voxel_spacing
|
AnnotationFile.annotation
|
AnnotationFile.annotation_shape.annotation
|
AnnotationFile.shape_type
|
AnnotationFile.annotation_shape.shape_type
|
AnnotationAuthor.primary_annotator_status
|
removed |
Dataset.dataset_citations
|
removed |
Dataset.organism_taxid
|
Converted from str -> int |
Dataset.related_database_links
|
Dataset.related_database_entries
|
TiltSeries.frames_count
|
TiltSeries.tiltseries_frames_count
|
TiltSeries.https_mrc_bin1
|
TiltSeries.https_mrc_file
|
TiltSeries.s3_mrc_bin1
|
TiltSeries.s3_mrc_file
|
TiltSeries.s3_alignment_file
|
TiltSeries.alignments[*].download_alignment_file(FORMAT)
|
TiltSeries.https_alignment_file
|
TiltSeries.alignments[*].download_alignment_file(FORMAT)
|
Tomogram.https_mrc_scale0
|
Tomogram.https_mrc_file
|
Tomogram.s3_mrc_scale0
|
Tomogram.s3_mrc_file
|
Tomogram.type
|
Replaced with Tomogram.is_canonical and Tomogram.is_standardized |
Tomogram.affine_transformation_matrix
|
Tomogram.alignment.affine_transformation_matrix
|
Deposition.dataset
|
Deposition.datasets
|
Deposition.deposition_types
|
Deposition.deposition_types[*].type
|
Deposition.https_prefix
|
removed |
TomogramVoxelSpacing.annotations
|
TomogramVoxelSpacing.annotation_files[*].annotation_shape.annotations
|
Tiltseries.download_collection_metadata()
|
removed |