API
Project object
- class relion.Project(path, database='ISPyB', run_options=None, message_constructors=None)[source]
Reads information from a Relion project directory and makes it available in a structured, object-oriented, and pythonic fashion.
- property class2D
access the 2D classification stage of the project. Returns a dictionary-like object with job names as keys, and lists of Class2DParticleClass namedtuples as values.
- property class3D
access the 3D classification stage of the project. Returns a dictionary-like object with job names as keys, and lists of Class3DParticleClass namedtuples as values.
- property ctffind
access the CTFFind stage of the project. Returns a dictionary-like object with job names as keys, and lists of CTFMicrograph namedtuples as values.
- property motioncorrection
access the motion correction stage of the project. Returns a dictionary-like object with job names as keys, and lists of MCMicrograph namedtuples as values.
The individual stage accessors .ctffind
, .class2D
, etc. return a dictionary-like object that allows you to access individual Relion jobs within that particular stage.
The dictionary key names are the relion job names (usually jobXXX
), the dictionary value is a list of stage-specific named tuples, listed below.
Stage-specific information
- class relion._parser.ctffind.CTFMicrograph(micrograph_name, astigmatism, defocus_u, defocus_v, defocus_angle, max_resolution, fig_of_merit, amp_contrast, diagnostic_plot_path)
Contrast Transfer Function stage.
- property amp_contrast
Amplitude contrast.
- property astigmatism
Estimated astigmatism. Units angstrom (A).
- property defocus_angle
Estimated angle of astigmatism.
- property defocus_u
Averaged with Defocus V to give estimated defocus. Units angstrom (A).
- property defocus_v
Averaged with Defocus U to give estimated defocus. Units angstrom (A).
- property diagnostic_plot_path
Path to the CTF diagnostic (fit/data comparison) plot (jpeg).
- property fig_of_merit
Figure of merit/CC/correlation value. Confidence of the defocus estimation.
- property max_resolution
Maximum resolution that the software can detect. Units angstrom (A).
- property micrograph_name
Micrograph name. Useful for reference.
- class relion._parser.motioncorrection.MCMicrograph(micrograph_name, micrograph_snapshot_full_path, micrograph_number, total_motion, early_motion, late_motion, micrograph_timestamp, drift_data)
Motion Correction stage.
- property drift_data
Alias for field number 7
- property early_motion
Early motion.
- property late_motion
Late motion.
- property micrograph_name
Micrograph name. Useful for reference.
- property micrograph_number
Micrograph number: sequential in time.
- property micrograph_snapshot_full_path
Path to jpeg of the motion corrected micrograph.
- property micrograph_timestamp
Time stamp at which the micrograph was created.
- property total_motion
Total motion. The amount the sample moved during exposure. Units angstrom (A).
- class relion._parser.class2D.Class2DParticleClass(particle_sum, reference_image, class_distribution, accuracy_rotations, accuracy_translations_angst, estimated_resolution, overall_fourier_completeness, job)
2D Classification stage.
- property accuracy_rotations
Accuracy rotations.
- property accuracy_translations_angst
Accuracy translations angst.
- property class_distribution
Class Distribution. Proportional to the number of particles per class.
- property estimated_resolution
Estimated resolution.
- property job
Job number of the Class2D job.
- property overall_fourier_completeness
Overall Fourier completeness.
- property particle_sum
Sum of all particles in the class. Gives a tuple with the class number first, then the particle sum.
- property reference_image
Reference image.
- class relion._parser.class3D.Class3DParticleClass(particle_sum, reference_image, class_distribution, accuracy_rotations, accuracy_translations_angst, estimated_resolution, overall_fourier_completeness, initial_model_num_particles, job)
3D Classification stage.
- property accuracy_rotations
Accuracy rotations.
- property accuracy_translations_angst
Accuracy translations angst.
- property class_distribution
Class Distribution. Proportional to the number of particles per class.
- property estimated_resolution
Estimated resolution.
- property initial_model_num_particles
The number of particles used to generate the initial model.
- property job
Job number of the Class3D job.
- property overall_fourier_completeness
Overall Fourier completeness.
- property particle_sum
Sum of all particles in the class. Gives a tuple with the class number first, then the particle sum.
- property reference_image
Reference image.