i3assist.Position

class i3assist.Position(position_line)

A single particle transform in old I3.

The fields in the position are broken down as follows:

1. Particle’s X coordinate in the tomogram not used in alignment
2. Particle’s Y coordinate in the tomogram not used in alignment
3. Particle’s Z coordinate in the tomogram not used in alignment
4. Particle’s 4D index in the stack of particles
5. Particle’s displacement (shift) along X from center of volume.
6. Particle’s displacement (shift) along Y from center of volume.
7. Particle’s displacement (shift) along Z from center of volume.
8. First euler angle in degrees about Z axis in range [-180, 180].
9. Second euler angle in degrees about X axis in range [0, 180].
10. Third euler angle in degrees about Z axis in range [-180, 180].
11. Class number the particle belongs to.
12. Max correlation coefficient between the particle and reference
13. Unknown reserved value.

Parameters:positionLine (str) – A string with the transform data.

__init__(position_line)

Methods

__init__(position_line)
copy()	Returns a copy of the position.
to_trf()	Returns the equivalent new I3 transform.

Attributes

class_number	int Class number that the particle belongs to.
coordinates	list of int Particles integer coordinates in tomogram.
rotation	i3assist.Euler Euler angles rotating reference to particle.
score	float Correlation score of particle alignment to reference.
shifts	list of float Particle displacements from box center.
stack_index	int Fourth dimension coordinate of particle in stack.