Programmatic control of alignment and reconstruction workflows

Article in progress. These functionalities will be released in the Dynamo 1.2 series.

Alignment and reconstruction workflows can be used with the GUI or on a totally programmatic manner. Programmatic control allows for batched reconstructions of sets of several tilt series.

Description

The workflow folder

Workflows in Dynamo are stored typically in folders (named with a capital case extension) that contain:

• a file that represents the workflow object itself. You kind think of it as a lightweight database that keeps track of every operation and parameter value.
• files and folders containing intermediate results.

Alignment and reconstruction workflow folders are marked with the extension .AWF

The workflow object

The workflow object is contained in a file called object.mat inside the .AWF folder.

If you need to perform low-level operations on the object, your can bring it to memory through dread

w = dread(<my workflow folder>);

or

w = dread(<my workflow folder>/object.mat);

which will create a memory a variable w that represents the workflow object. Most users, however, do not need to operate directly on the object, and can use instead

• dtsa for invoking a GUI that controls a workflow and allows on-screen design of steps and parameter selection.
• dtsar (dynamo_tilt_series_alignment_run) for running a workflow, i.e. executing all or part of their steps in non-interactive mode.

Both commands are valid for creating new workflows or manipulating existing ones.

Results

By default, intermediate and final results will be stored as fixed locations inside the workflow folder. This is the recommended behaviour for starting users.

Data

Data does not need to be stored physically