View source for 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 <tt>object.mat</tt>. 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 <tt>dread</tt> command:

 <tt>w = dread('object.mat')</tt>

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 <tt>w</tt> (for instance, variable name is arbitrary), you can get the filename in the <tt>io</tt> area of the object <tt>w</tt> as:

 <tt>w.io.datagates.items.matrix.getFilename()</tt> 

== Angles ==

=== Nominal tilt angles ===
The '''nominal'''tilt angles of the raw stack are given as a text file with the ''default'' name:
 <tt>nominal.tlt</tt>

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.

=== Tilts rejected a priori ===

=== Tilts rejected during manual alignment ===

== Stacks ==
==Reconstructions ==
==Metadata ==