Windows Installation¶

• You need to repeat installation of the general packages for each of the computer involved in Leginon operation with addition for the camera and scope.

Install Python and supporting packages with their installers. Only Gatan K2/K3 computer uses 64-bit version of python.¶

Program	package web site	local copy of win32 installer	local copy of amd64 installer
Python > 2.7.10	http://www.python.org	python-2.7.16.msi	python-2.7.18.amd64.msi
wxPython 2.8 or newer	http://www.wxpython.org	wxPython2.8-win32-unicode-2.8.12.1-py27.exe	wxPython2.8-win64-unicode-2.8.12.1-py27.exe
MySQL Python client 1.2 or newer	http://sourceforge.net/projects/mysql-python	MySQL-python-1.2.4b4.win32-py2.7.exe	MySQL-python-1.2.3.win-amd64-py2.7.exe
Python Imaging Library (PIL) 1.1.4 or newer	http://www.pythonware.com/products/pil/	PIL-1.1.7.win32-py2.7.exe	PIL-fork-1.1.7.win-amd64-py2.7.exe
NumPy	(use only from our file to match compiled numextension	numpy-1.7.0-win32-python2.7.exe	numpy-MKL-1.6.2.win-amd64-py2.7.exe
SciPy 0.5.1 or newer	http://www.scipy.org	scipy-0.11.0-win32-superpack-python2.7.exe	scipy-0.11.0.win-amd64-py2.7.exe

Use pyMySQL for leginon 3.6 and above instead of MySQL Python client for both win32 and 64.

pyMySQL 0.10.1 (not higher)

https://pypi.org/project/PyMySQL/

pyMySQL-0.10.1-py2.py3-none-any.whl

Excute the installer files and follow the instructions.

Add the IP address and matching hostname of the microscope and digital camera computer in your host file on the main Leginon computer, and vice versa.¶

Find out what python thinks the hostname is with python command line. REPEAT this both on Linux and Windows PC¶

Run the following in python command line:

import socket
socket.gethostname()

Find out the ip address associated with the hostname¶

Run the following in python command line:

import socket
socket.gethostbyname('your_host_name')

Modify your "hosts" file on the linux Leginon computer to include the instrument hosts if the latter is not already mapped by your domain name server¶

• On Linux, this "hosts" file is at

/etc/hosts

Example of a "hosts" file:

192.000.1.222   instrument_host_name.domain_name instrument_short_host_name

Use shorter linux hostname if desired¶

If you'd like to shorten your linux hostname recognized by socket without the domain name, you may do so as root

hostname your_shorter_hostname

and also add that to the /etc/hosts as an alternative name

192.000.1.333   long_host_name.domain_name your_shorter_hostname

You will need to restart networking to make it persistent.

/etc/init.d/network restart

Test the change by finding the ip address with the hostname as in the above section.

The Linux main Leginon computer also needs to identify itself by its hostname registered on the instrument Windows computer.¶

• On Window XP and WIndows 7 this host file is

C:\\WINDOWS\system32\drivers\etc\hosts

• On Window NT, this host file is

C:\\WINNT\system32\drivers\etc\hosts

What to do if host-ip mapping still does not work: configure_pyamicfg_for_host-ip_pairings¶

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Install the Windows Installer Files from created from source by NRAMM¶

Package	win32	amd64
numextension	numextension-svn.win32-py2.7-numpy1.7.0.exe	numextension-svn.win-amd64-py2.7-numpy1.6.2.exe

Execute the installer files and follow the instructions.

Install the packages you cloned from NRAMM git repository (You will need to repeat this each time you upgdate)¶

The git checkout is a folder containing several subpackages. You will install the python packages using python installer. See the next section if you want to use directly do git checkout.

These are the subpackages¶

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

If you recall Linux processing server installation instruction, this is a bit different. Numextension and LibCV are not included. Numextension is already installed with windows installer. libcv and opencv are not required by Leginon client that this part installation is aimed for.

• Start a command line Window from Start Menu

• Install the package in each folder with commands such as
  

  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 "These are the sub-packages of myami that you will install with the python installer." section above for complete list.

(Alternative approach, easy for updating) Set environment variable PYTHONPATH to use svn checkout or git clone directly¶

Set pythonpath environment variable for local myami sandbox¶

For an uninstall myami svn checkout, you can set PYTHONPATH environment variable to use it directly.

1. Control Panel\All Control Panel Items\System> click on Advanced settings
2. System Properties\Advanced> click on Environment Variables
3. Either create a new variable for the current user, or do it system-widely.

PYTHONPATH should incldue both the base myamipath as well as leginon

For example, myami folder is at C:\Users\vagrant\Desktop\myami, then the python path should be set as follows:

C:\Users\vagrant\Desktop\myami; C:\Users\vagrant\Desktop\myami\leginon

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< Package Requirement | Additional installation specific to the microscope >

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