imageseries omega

Omega Module

This module has two classes. The OmegaImageSeries is used for the analysis. It is basically am imageseries with omega metadata (and n x 2 numpy array of rotation angle ranges for each frame) and methods for associating the frames with the omega angles. The OmegaWedges is used for setting up the omega metadata. During a scan, the specimen is rotated through an angular range while frames are being written. We call a continous angular range a wedge. We commonly use a single wedge of 360 degrees or 180 degrees, but sometimes there are multiple wedges, e.g. if there is some fixture in the way.

Examples

Start with a couple examples. In the first example, we have 3 files, each with 240 frames, going through 180 degrees in quarter degree increments. The omega array is saved into a numpy file.

nf = 3*240
omw = OmegaWedges(nf)
omw.addwedge(0, nf*0.25, nf)
omw.save_omegas('ti7-145-147-omegas')

In the second example, there are four wedges, each with 240 frames. The wedges go through angular ranges of 0 to 60, 120 to 180, 180 to 240, and 300 to 360. The omega array is then added to the imageseries metadata.

nsteps = 240
totalframes = 4*nsteps
omwedges = omega.OmegaWedges(totalframes)
omwedges.addwedge(0, 60, nsteps)
omwedges.addwedge(120, 180, nsteps)
omwedges.addwedge(180, 240, nsteps)
omwedges.addwedge(300, 360, nsteps)

ims.metadata['omega'] = omwedges.omegas

OmegaWedges Class

• __init__(self, nframes): instatiate with the number of frames.

• omegas: (property) n x 2 array of omega values

• nwedges: (property) number of wedges

• addwedge_(self, ostart, ostop, nsteps, loc=None): add a new wedge to wedge list; take starting omega, end omega, and number of steps; the keyword argument is where to insert the wedge (at the end by default)

• delwedge_(self, i): delete wedge i

• wframes: (property) number of steps in each wedge

• save_omegas(self, fname): save the omega array to a numpy file (for use with YAML-based formats)