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.X Python API¶

2 classes (Frame and GainFile) were modified and 1 class (PerSectionParameter) was added to the API. The changes are detailed below:

Frame Class Modifications¶

Name	Status	Nullable	Data Type	Description
accumulatedDose	New	False	float	Dose (in e⁻/Å²) that was applied to the region of interest before this frame stack was acquired
exposureDose	New	False	float	Dose (in e⁻/Å²) that was applied during acquisition of this frame stack
dose	Remove	True	float	This is removed in favour of adding fields with more standardized naming.
rawAngle	Remove	True	float	This is moved to the perSectionParameter.rawAngle

Summary of new class PerSectionParameter¶

Name	Status	Data Type	Is Nullable	Description
astigmaticAngle	New	float	True	Angle (in degrees) from reciprocal space X axis to the major axis of defocus.
frameId	New	int	False	ID of the frame this entry is associated with.
frame	New	Frame	False	The frame this entry is associated with.
id	New	int	False	ID for the per section parameter record
majorDefocus	New	float	True	Defocus (major axis) estimated for this tilt image in Å (underfocus has positive sign).
minorDefocus	New	float	True	Defocus (minor axis) estimated for this tilt image in Å (underfocus has positive sign).
phaseShift	New	float	True
maxResolution	New	float	True
rawAngle	New	float	False	Nominal tilt angle for this tilt image reported by the microscope.
runId	New	int	False	ID of the Run this entry is associated with.
run	New	Run	False	The run this entry is associated with.
tiltseriesId	New	int	False	ID of the tiltseries this entry is associated with.
tiltseries	New	Tiltseries	False	The tiltseries this entry is associated with.
zIndex	New	int	False	Index (0-based) of this tilt image in the tilt series stack.

Changes to the Client¶

The python client’s data model was also updated to include new data models and update existing data models.

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