Utilities for stack creation with the Hagen scheme
Revision as of 11:14, 10 March 2017 by Daniel Castaño (talk | contribs)
Here we describe some parsers we frequently use to organize the data folders delivered by the microscope operators into single stack files. This utility just:
- parses the structure of the input folder
- creates a correctly formatted input for the Imod command alignframes
- creates the corresponding Imod order and
- submits it to Imod
Thus, you'll need to have Imod activated in your session to use this parser
Input raw data folder
A typical input raw data folder contains
- a gain reference file (with extension .dm4)
- a defect file (with extension .txt)
- a series of files, each one for each tilt angle.
CountRef_FtsH_23_000_-0.0_Sep07.dm4 defects_FtsH_000_0.0_Sep06.txt FtsH_23_000_-0.0_Sep07.mrc FtsH_23_001_3.0_Sep07.mrc FtsH_23_002_-3.0_Sep07.mrc . . . . FtsH_23_027_-42.0_Sep07.mrc FtsH_23_028_42.0_Sep07.mrc FtsH_23_029_45.0_Sep07.mrc FtsH_23_030_-45.0_Sep07.mrc
Imod wrappers
Creates the wrapper object
p = <full path to your directory>; a = dpcomp.hagen.StackConverter(); a.parseSourcePath(p);
It will detect the contents of the file, and check that it can understand the ordering of the micrographs.
