How to Update from v35 (Instrument Windows Computer)¶

Preparation¶

Pymysql replaces MySQL-python in this version. There is no Windows installer exe file for this.

You can find [[https://emg.nysbc.org/attachments/20299/PyMySQL-0.10.1-py2.py3-none-any.whl|PyMySQL-0.10.1-py2.py3-none-any.whl]] under Files tab at this redmine site. Copy the file to the microscope scope if you don't have internet access on the instruments.

You will need these myami subpackages updated.

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

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¶

Clone the proper branch from git repository. You will want myami-3.6¶

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¶

install pymysql¶

cd path_to\PyMySQL-0.10.1-py2.py3-none-any.wh
C:\Python27\Scripts\pip.exe install PyMySQL-0.10.1-py2.py3-none-any.wh

• If you have older python2.7 mirnor method, pip might not be available. In this case, it is best reinstall newer version. We know it needs to at least 2.7.11

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¶

locate global config directory on Windows

FEI scopes¶

fei.cfg¶

Compare yours_git_clone\pyscope\fei.cfg.template with your active fei.cfg. Especially if you plan to use new featured instruments or have had a TEMServer upgrade to recent versions.

If you set for your Talos column¶

FORCE_NORMALIZE_ALL_LENS_AFTER_MAG_SETTING = True

please change it to use

FORCE_NORMALIZE_ALL_AFTER_SETTING = True

This is more generalized and produces better results. See Issue #7076 for more details.

GatanK2Summit or K3¶

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

New Features¶

Follow PyScope_Changes_36 on the installation and setup of the specific feature you want to activate.