API¶
Project object¶
-
class
relion.
Project
(path)[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.
-
property
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)¶ Contrast Transfer Function stage.
-
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
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.
-
property
-
class
relion._parser.motioncorrection.
MCMicrograph
(micrograph_name, total_motion, early_motion, late_motion)¶ Motion Correction stage.
-
property
early_motion
¶ Early motion.
-
property
late_motion
¶ Late motion.
-
property
micrograph_name
¶ Micrograph name. Useful for reference.
-
property
total_motion
¶ Total motion. The amount the sample moved during exposure. Units angstrom (A).
-
property
-
class
relion._parser.class2D.
Class2DParticleClass
(particle_sum, reference_image, class_distribution, accuracy_rotations, accuracy_translations_angst, estimated_resolution, overall_fourier_completeness)¶ 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
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.
-
property
-
class
relion._parser.class3D.
Class3DParticleClass
(particle_sum, reference_image, class_distribution, accuracy_rotations, accuracy_translations_angst, estimated_resolution, overall_fourier_completeness)¶ 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
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.
-
property