Falcon 3 support¶

Requirement from camera manufacture:¶

• Krios 2.12 or Talos/Arctica 1.12 software version.
• Advanced TEM Scripting

Required leginon version:¶

• 3.4 and above

Extra Package and Installation¶

program/package	notes
TEMAdvancedScripting.dll	(Should come with the microscope)

Program	package web site	local copy of win32 installer
comtypes 0.6.2	http://sourceforge.net/projects/comtypes"	comtypes-0.6.2.win32.exe

Comtypes installation¶

THIS INSTRUCTION IS FOR comtypes 0.6.2. If you install newer version, this may not work.¶

Double click on the installer¶

Modify comtypes¶

IMPORTANT: After installing comtypes, you must make one modification to it. The module "safearray.py" that comes with comtypes must be replaced with a modified version that we provide. You can find the custom version of safearray.py in the pyscope package. Please copy this module from pyscope into the installed comtypes folder: C:\Python2*\Lib\site-packages\comtypes\. It should replace the safearray.py that is included in comtypes.

Remove safearray.pyc in C:\Python2*\Lib\site-packages\comtypes\ if it does not appear to recompile (timestamp of the file change) when you import comtype in python command line

import comtypes

Run checkcom.py¶

• From a command line window:
  

  cd C:\python27\Lib\site-packages\pyscope
  C:\python27\python.exe checkcom.py

The module it finds depends on the module.

You should have

TEMAdvancedScripting

instruments.cfg¶

• Falcon3 class is for linear mode and Falcon3EC class is for electron counting mode. You want to have both.
  

  [camera]
  class: feicam.Falcon3
  zplane: 50
  height: 4096
  width: 4096
  

  
  

  [camera]
  class: feicam.Falcon3EC
  zplane: 50
  height: 4096
  width: 4096
  

Setup¶

• Set dose rate and acquire References using TUI Reference manager. Don't do it in Leginon.
• Set up in fei.cfg (See FEI scope installation instruction)
  

  [camera]
  FRAME_SUBPATH = leginonframes
  

  
  In this case, you will need to create a directory called leginonframes on your Falcon image storage server (called OffloadData on your scope PC) with these parent directories
  

  OffloadData\TemScripting\BM-Falcon\leginonframes
  

This leginonframes directory can then mounted on your permanent storage system and allow rawtransfer.py to rsync the files.

Programs to open before Leginon Client: TIA.¶

Testing with pyscope¶

In python command

form pyscope import feicam
g = feicam.Falcon3()
g.setExposureTime(200)
g.getImage()

You should expect these to run without error. The getImage() command should give a 2D numpy array like

array([[1000, 3400, 2300, ..., 1000,1200,3000],
         [1000, 3400, 2300, ..., 1000,1200,3000],
         [1000, 3400, 2300, ..., 1000,1200,3000],
         ...,
         [1000, 3400, 2300, ..., 1000,1200,3000],
         [1000, 3400, 2300, ..., 1000,1200,3000],
         [1000, 3400, 2300, ..., 1000,1200,3000],dtype=int16)

The number and dtype depends on the camera.

a.shape command should give a tuple of the camera dimension matching your camera.
For example, (4096,4096)

If you use python shell to do this test, some of the error will cause the shell window to close immediately. Use Python IDLE instead in that case

Trouble shooting¶

If TEM Advanced Scripting is not setup correctly by the manufacture, a configuration error will appear similar to this:

_ctypes.COMError: (-2147467259, 'Unspecified error.', (u"Could not load Storage Server configuration file: C:\\ProgramData\\FEI||AcquisitionStorageServer||StorageServer.config', u'',u'', 0, None))