Tilt series alignment workflow folder

Article under construction, sorry

The folder .AWF contains different categories of files:

Workflow object

The workflow object itself appears as a file called object.mat. This is a binary file, which is used internally by Dynamo when performing alignments and reconstructions. It is rarely needed by users.

When it is needed (see examples below), It can be called into memory with the generic dread command:

w = dread('object.mat')

Remember to use the whole path if you are not in the alignment workflow folder.

Raw stack

The raw data (the stack) does not need to be physically stored inside the workflow folder. The data linked to a workflow folder can be consulted through the workflow object. If you have the workflow in memory with the variable name w (for instance, variable name is arbitrary), you can get the filename in the io area of the object w as:

w.io.datagates.items.matrix.getFilename() 

Angles

Nominal tilt angles

The nominaltilt angles of the raw stack are given as a text file with the default name:

nominal.tlt

This file is normally generated by Dynamo when the alignment workflow is created . Note that these angles can also be stored in a different location and linked to the workflow, but this procedure is exceptional.

This text file should contain an angle (in degrees) for each micrograph in the data stack, and appear in the same order.

Explicitly rejected tilt angle indices

Some micrographs might be manually rejected because of visually obvious errors, like defocus or shift jumps. An explicit decision by the user on eliminating a given (set of) micrograph(s) can be taken a priori, or during the alignment procedure with the GUI. In both cases, the indices are referred to the nominal angles seen by the workflow.