View source for 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.
The Hagen scheme  collects the data in the order <tt>0,angle1,-angle1,angle2,-angle2,...</tt>, which frequently leads to inconveniently formatted raw data folders after a data collection session.

This utility just:
* parses the structure of the input folder
* creates a correctly formatted input for the Imod command <tt>alignframes</tt>
* 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. 

An example:
 <nowiki>
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
</nowiki>

== Imod wrappers ==

== Creates the wrapper object ==

 <nowiki>p = <full path to your directory>;
a = dpcomp.hagen.StackConverter();
a.parseSourcePath(p); </nowiki>

It will detect the contents of the file, and check that it can understand the ordering of the micrographs.

== Order the projection files==
You can display if the files where correctly parsed:

 <tt>a.listFiles();</tt>

and, if so, you can then create a text file for them 
 <tt>a.writeList();</tt>

which will be called by default <tt>orderedFiles.list</tt> and will be located on the same directory. You can also create text file for the tilt angles with 
<tt>a.writeTiltList();</tt>
This will create by default the file <tt>stack.tlt</tt>

== Align the frames ==

=== Imod order ===

The created order for imod will have the structure:

 <tt>alignframes -gain GAINFILE -defect DEFECTFILE -mode 2 -list LIST STACK</tt>

By default, the target <tt>STACK</tt> will be called <tt>stack.mcr</tt>.

To create and run it, type:

 <tt>a.imodAlignFrames('execute',1);</tt>

If the target <tt>STACK</tt> already exist in disk, ''Dynamo'' will show the formatted order, but will abort before submitting it to Imod. The 'execute' flag indicates ''Dynamo'' to submit the order (not only create the string). Other default values can be changed with the flags <tt> 'gain','defect','list','mode','target'</tt>

=== Troubleshouting ===
You need to activate Imod before opening Matlab (or before starting the ''Dynamo'' [[standalone]] session).

== Batched operation ==

=== Single folder ===
To operate all the steps with default values on a single folder, use:
 <tt> check = dpcomp.hagen.StackConverter.processFolder(path) </tt>

=== Cell array of folders ===

If you have the names of identically structured folders in a [[Matlab cell array | array]] (say, <tt>myFolders</tt>), you can operate the order: 
 <tt> check = dpcomp.hagen.StackConverter.processFolderArray(myFolders) </tt>
to create the stacks for all of them.