Utilities for stack creation with the Hagen scheme

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_003_-6.0_Sep07.mrc
FtsH_23_004_6.0_Sep07.mrc
FtsH_23_005_9.0_Sep07.mrc
FtsH_23_006_-9.0_Sep07.mrc
FtsH_23_007_-12.0_Sep07.mrc
FtsH_23_008_12.0_Sep07.mrc
FtsH_23_009_15.0_Sep07.mrc
FtsH_23_010_-15.0_Sep07.mrc
FtsH_23_011_-18.0_Sep07.mrc
FtsH_23_012_18.0_Sep07.mrc
FtsH_23_013_21.0_Sep07.mrc
FtsH_23_014_-21.0_Sep07.mrc
FtsH_23_015_-24.0_Sep07.mrc
FtsH_23_016_24.0_Sep07.mrc
FtsH_23_017_27.0_Sep07.mrc
FtsH_23_018_-27.0_Sep07.mrc
FtsH_23_019_-30.0_Sep07.mrc
FtsH_23_020_30.0_Sep07.mrc
FtsH_23_021_33.0_Sep07.mrc
FtsH_23_022_-33.0_Sep07.mrc
FtsH_23_023_-36.0_Sep07.mrc
FtsH_23_024_36.0_Sep07.mrc
FtsH_23_025_39.0_Sep07.mrc
FtsH_23_026_-39.0_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

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.