Leginon

h1. How to Update from v35 (Instrument Windows Computer)

h2. 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|

h2. 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 [[Download_Appion_Files|Acquiring NRAMM GIT Repository files]] for different examples and match the repository with what you do on the Linux side.

*OR*

h2. With internet access

h3. Clone the proper branch from git repository.  You will want myami-3.6

{{include(git_for_windows_cloning)}}

h2. Install

h3. install pymysql

<pre>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

</pre>

* 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

h3. Move the cloned folder according to your environment variable PYTHONPATH if you use that during the original installation.

*OR*

h3. Install to default python site-packages

* Start a command line Window from Start Menu

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

<pre>cd path_to\myami-VERSION\myami\pyami

c:\\python27\python.exe setup.py install</pre>

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

h2. Configure

[[locate global config directory on Windows]]

h1. FEI scopes

h2. 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.

h3. If you set for your Talos column

<pre>

FORCE_NORMALIZE_ALL_LENS_AFTER_MAG_SETTING = True

</pre>

please change it to use

<pre>

FORCE_NORMALIZE_ALL_AFTER_SETTING = True

</pre>

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

h1. GatanK2Summit or K3

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

h1. New Features

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