How to Update from v33 (Instrument Windows Computer)¶

Preparation¶

You will need these myami subpackages from the branch you want from our git repository.

Name:	Purpose:
leginon	modular TEM image acquisition
pyami	general functions
myami_test	test suite that is called before starting leginon
sinedon	database interaction
pyscope	microscope control and monitoring
imageviewer	image viewing for tomography

No internet access - copy from linux Leginon workstation the python files.¶

If your Windows computer has no access to internet, copy from your linux processing server the git clone of myami super package of the right branch for the installation which you used to upgrade there.

See Acquiring NRAMM GIT Repository files for different examples and match the repository with what you do on the Linux side.

OR

With internet access¶

Install Git-for-Windows¶

We have switched to git revision control recently. If you want to install the newest changes, you need to use the files from git repository.

You can clone our repository with

Name:	Download site:
git for Windows	https://git-for-windows.github.io

• During the installation, select "Checkout as-is, commit as-is" option at the step regarding automated translation of CRLF and LF line endings if you are a developer and may commit changes.
• Default is fine with the rest of the options.

Clone the proper branch from git repository. You will want myami-3.4¶

Start Git Bash Window¶

• Right Click at the folder where it will contain your clone and choose "Git Bash Here" to start the shell window.

• With Windows XP "Git Bash Here" does not appear with right-click. In this case, you can start git bash from Start menu/Programs/Git/Git Bash and move the folder created to where you want it to be.

To checkout (called clone in git) the package from NRAMM:
See Acquiring NRAMM GIT Repository files for different examples and match the repository with what you do on the Linux side.¶

Install¶

Move the cloned folder according to your environment variable PYTHONPATH if you use that during the original installation.¶

OR

Install to default python site-packages¶

• Start a command line Window from Start Menu

• Install the package in each folder (must starts with pyami)
  

  cd path_to\myami-VERSION\myami\pyami
  c:\\python27\python.exe setup.py install

  
  Then continue with the other packages, replacing pyami with the package name. See the packages listed above for the complete list.

Configure¶

FEI scopes¶

fei.cfg¶

Locate global configuration directory following standard on Windows¶

Saving cfg files in a global location reduces future need for copying old configuration to updated installation. The location is different for different versions of Windows. To locate the one for your Windows version:

1. go to C:\\python27\Lib\site-packages\leginon
2. run configcheck.py

The script gives the three search directories of the cfg files and the loaded file if present. Note the first search directory that with a name most likely start with C:\\Programs and ends with \myami. This is the global configuration directory we will use.

Compare yours_git_clone\pyscope\fei.cfg.template with your active fei.cfg There are additional configuration that you may want to add. Especially if you have Falcon 3.

GatanK2Summit¶

Compare pyscope/dmsem.cfg.template with your active dmsem.cfg There are additional configuration that you may want to add.