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