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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 v2.0 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 Leginon2.0 directory somewhere at your convenience

  • Change directory into Leginon2.0

  • Right-click the mouse botton in this directory window and select Tortoise svn Checkout in the menu:

  • Set up svn checkout window like this to check out from /svn/myami/trunk to Leginon2.0

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\Leginon2.0\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 Configuration C, 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 the instructions in Configure leginon.cfg located 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

`\Lib\site-packages\Leginon\config\leginon.cfg

Example:

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

  • Configurations for individual users

`\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 Configure sinedon.cfg 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 applies 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):

TigerVNC (http://tigervnc.org/) --- allows remote access to windows screen. If you get tired of going into the microscope room just to open the column valves.

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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