Difference between revisions of "Tilt series alignment workflow folder"
| Line 26: | Line 26: | ||
<tt>nominal.tlt</tt> | <tt>nominal.tlt</tt> | ||
| − | This file is normally generated by ''Dynamo'' when the alignment workflow is created . Note that these angles | + | This file is normally generated by ''Dynamo'' when the alignment workflow is created. Note that these angles could also be stored in a different location and linked to the workflow, but this procedure is non-standard. |
| − | + | In any case, the 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 === | === Explicitly rejected tilt angle indices === | ||
| Line 36: | Line 36: | ||
=== Tilts rejected a priori === | === Tilts rejected a priori === | ||
| + | |||
| + | This option is normally used for batch processing using unsupervised alignment. Before launching the automatic alignment process, the user quickly supervises the different tilt series in the batch and marks the tilts that are . | ||
=== Tilts rejected during manual alignment === | === Tilts rejected during manual alignment === | ||
Revision as of 12:53, 6 February 2019
Article under construction, sorry
The folder .AWF contains different categories of files:
Contents
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 could also be stored in a different location and linked to the workflow, but this procedure is non-standard.
In any case, the 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
This option is normally used for batch processing using unsupervised alignment. Before launching the automatic alignment process, the user quickly supervises the different tilt series in the batch and marks the tilts that are .
