Windows Installation¶

Processing-side Leginon Windows Installation¶

Install Python and Support Packages (Note that python 2.5 must be used):¶

This list does not include pyton XML module because it is included in the python
package for window.

Name:	Download site:
Python 2.5*	http://www.python.org
Python for Windows extension (pywin32)	http://sourceforge.net/projects/pywin32/
wxPython 2.5.2.8 or newer	http://www.wxpython.org
MySQL Python client 1.2 or newer	http://sourceforge.net/projects/mysql-python
Python Imaging Library (PIL) 1.1.4 or newer	http://www.pythonware.com/products/pil/
NumPy 1.0b5 (tested, others may work)	http://www.scipy.org
SciPy 0.5.1 or newer	http://www.scipy.org
Tortoise SVN client	http://tortoisesvn.tigris.org

*Python 2.5 is the only python version that we have compiled numExtension. libCV and
comarray in. Therefore no other python version works for now.

Execute the installer file and follow the directions.

Packages required from NRAMM¶

These are the packages you will install with the python installer.

Name:	Purpose:
Leginon	modular TEM image acquisition
pyami	general functions
sinedon	Leginon/database interaction
pyScope	microscope control and monitoring
ImageViewer	image viewing for tomography

Because numextension and libCV requires extra compilers, we have created window
installer for them for python 2.5 and made them available through http://www.leginon.org/.

These are the Leginon v1.6 python 2.5 compiled packages installed through python installer on Windows.

Downloadfile Name	Installed Python Package File	Purpose:
NumExtension-1.2.0.win32-py2.5.exe	numextension.pyd	c extension for numerical processing
libCV-0.2.win32-py2.5.exe	libCV.pyd	small c library of algorithm from computer vision field

Check out SVN Source Files from the depository¶

Use your mouse to do the following

• Create Leginon-1.6-ALL directory somewhere at your convenience

• Change directory into Leginon-1.6-ALL

• Right-click the mouse botton in this directory window and select Tortoise svn
  Checkout in the menu:!http://emg.nysbc.org/software/leginon/images/images/svnmenu.png!

• Set up svn checkout window like this for <link linkend="windows_packages">EACH
  of the leginon packages</link>.!http://emg.nysbc.org/software/leginon/images/images/svnco.png!

Install the packages you downloaded from NRAMM svn depository¶

• Start a command line Window from Start Menu

• Install the package in each folder with commands such as
  

  cd Your_Download_Place\Leginon-1.6-ALL\leginon
  c:\\python25\python.exe setup.py install

Download the two Window Installer Files from Leginon website¶

http://www.leginon.org/

Install individual packages¶

Excute the installer files and follow the instruction.

Mapping Drives:¶

If you plan to run Leginon directly on the Windows machine, such as in <link
linkend="config_C">configuration C</link>, and your data files are served through a
Samba server on a Linux machine, you will need to map the network drive. For example, if
your Samba server has a hostname your_smbserver, and you have set up a share called
[your_share_point] which points to /your_data_path/ and leginon data will be saved under a
folder in /your_data_path/leginon/

• Start, My Computer

• Tools menu, Map network drive

• Use an unmapped drive such as Z:

Enter shared path in Windows format
as

\\your_smbserver\your_share_point

• Add the drive and the Linux path to leginon.cfg on the Windows machine
  as

  [Drive Mapping]
  Z:/your_data_path

• Add image path to leginon.cfg on the Windows machine in Linux format
  as

  [Images]
  path:/your_data_path/leginon

Configure leginon.cfg:¶

Follow instruction in "<link linkend="leginon_cfg">Configure leginon.cfg</link>" in
the section for Linux installation but note the location of the configuration files
follows. In addition, if the storage disk is mapped onto the Windows PC as drive Z, this
mapping should be included in leginon.cfg. See above.

• Configurations for all users

 <Python directory>\Lib\site-packages\Leginon\config\leginon.cfg

Example:

 C:\Python25\Lib\site-packages\Leginon\config\leginon.cfg

• Configurations for individual users

 <Home directory>\leginon.cfg

Example:

 C:\Documents and Settings\Leginon User\leginon.cfg 

• A skeleton (default) configuration file is available:

 C:\Python25\Lib\site-packages\Leginon\config\default.cfg

Configure sinedon.cfg:¶

Sinedon is designed to be able to interact with multiple databases.

Follow instruction in "<link linkend="sinedon_cfg">Configure sinedon.cfg</link>" in
the section for Linux installation but note the location of the configuration files
follows.

• For all users, put sinedon.cfg with the installed package
  as

  C:\Python25\Lib\site-packages\sinedon\sinedon.cfg

• Your home directory on
  Windows:

  C:\Documents and Settings\your_name>

• the skeleton sinedon configuration file
  is

  C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg

Create Leginon and Leginon Client shortcut in Start menu menu under Leginon¶

This instruction refers to Windows XP

• Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new
  folder named Leginon.

• In another window, go
  to

  C:\Python25\Lib\site-packages\Leginon

• Create a shortcut from start-leginon.py as Leginon and a shortcut from
  launcher.py as Leginon Client.

• Move the two shortcuts into
  

  C:\Documents and Settings\All Users\Start Menu\Programs\Leginon

Additional Software (Optional):¶

TightVNC (http://www.tightvnc.com)

Database server Windows Installation¶

We do not do this at NRAMM. Please follow the instruction in Linux installation and
modify it for Windows at your own risk.¶

For a good Windows specific instruction for general PHP configuration with MySQL for
Apache 2 in Windows, try http://www.artfulsoftware.com/php_mysql_win.html.

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