Leginon

h1. Windows Installation

h2.  Processing-side Leginon Windows Installation

h2.  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":http://www.python.org|

|Python for Windows extension (pywin32)| "http://sourceforge.net/projects/pywin32/":http://sourceforge.net/projects/pywin32/|

|wxPython 2.5.2.8 or newer| "http://www.wxpython.org":http://www.wxpython.org|

|MySQL Python client 1.2 or newer| "http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python|

|Python Imaging Library (PIL) 1.1.4 or newer| "http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/|

|NumPy 1.0b5 (tested, others may work)| "http://www.scipy.org":http://www.scipy.org|

|SciPy 0.5.1 or newer| "http://www.scipy.org":http://www.scipy.org|

|Tortoise SVN client| "http://tortoisesvn.tigris.org":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.

h2. 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/":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|

h2. 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 EACH

of the leginon packages listed above.

 !http://emg.nysbc.org/software/leginon/images/images/svnco.png!

h2. 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

<pre>cd Your_Download_Place\Leginon-1.6-ALL\leginon

c:\\python25\python.exe setup.py install</pre>

h2. Download the two Window Installer Files from Leginon website

"http://www.leginon.org/":http://www.leginon.org/

h2. Install individual packages

Excute the installer files and follow the instruction.

h2.  Mapping Drives:

If you plan to run Leginon directly on the Windows machine, such as in [[Possible Computer Set-up Configurations#Configuration-C|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

 <pre>\\your_smbserver\your_share_point</pre>

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

as

 <pre>[Drive Mapping]

Z:/your_data_path</pre>

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

as

 <pre>[Images]

path:/your_data_path/leginon</pre>

h2.  Configure leginon.cfg:

Follow the instructions in [[Configure leginon.cfg|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

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

Example:

<pre> C:\Python25\Lib\site-packages\Leginon\config\leginon.cfg</pre>

*  Configurations for individual users

<pre> <Home directory>\leginon.cfg</pre>

Example:

<pre> C:\Documents and Settings\Leginon User\leginon.cfg </pre>

*  A skeleton (default) configuration file is available:

<pre> C:\Python25\Lib\site-packages\Leginon\config\default.cfg</pre>

h2.  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<pre>C:\Python25\Lib\site-packages\sinedon\sinedon.cfg</pre>

*  Your home directory on

Windows:<pre>C:\Documents and Settings\your_name></pre>

* the skeleton sinedon configuration file

is<pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre>

h2.  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<pre>C:\Python25\Lib\site-packages\Leginon</pre>

* Create a shortcut from start-leginon.py as Leginon and a shortcut from

launcher.py as Leginon Client.

* Move the two shortcuts into

<pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre>

h2.  Additional Software (Optional):

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

h2. Database server Windows Installation

h2. 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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[[Web Server Installation|< Web Server Installation]] | [[Additional installation on the microscope computer|Additional installation on the microscope computer >]]

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