Upgrade at the computer controlling the microscope and camera (Window)¶

By switching to svn package check out, you now need to install svn on Windows to get the
updated packages. Because numextension and libCV requires extra compiler, we have created
window installer for them for python 2.5 and made them available through http://www.leginon.org/

See Installation Troubleshooting and the Leginon Forum searching
for "install" if you run into problems.

Packages required from NRAMM¶

Here are the packages you need to install with python installer

SVN Package Name	Installed Python Package Name	Reason for update:
leginon	Leginon	new features
pyami	pyami	clean up
sinedon	sinedon	new stuff
pyScope	pyScope	new instrument configuration
ImageViewer	ImageViewer	updated and required for tomography
comarray	comarray	new for Gatan and Eagle camera

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

Downloadfile Name	Installed Python Package File	Reason for update:
NumExtension-1.2.0.win32-py2.5.exe	numextension.pyd	clean up
libCV-0.2.win32-py2.5.exe	libCV.pyd	bug fixes

Uninstall your existing packages:¶

Although new installation overwrite the old in most cases, problem has been observed in
the past. Therefore, it is best to remove the old files before new installation.

Use "Add or Remove Programs" application in "Control Panel" to do this. Leginon related
packages are shown with prefix "Python 2.5"

If you didn't use Installer to install previously, the packages may not show up in the
Programs list. Simply remove the folder containing the old packages in this case.

Download and install SVN client program:¶

By switching to svn package check out, you now need to install svn client on Windows to
get the updated packages. We recommand TortoiseSVN http://tortoisesvn.tigris.org/ .

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:
• Set up svn checkout window like this for each of the leginon package!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

• Reinstall 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.

Additional Package required from NRAMM for Gatan camera or camera that uses TIA

comarray package need to be install with python

Modify instruments.cfg:¶

Modify the file instruments.cfg in the installed pyScope directory.

• Remove the "Sim TEM" and "Sim Cam" modules. These are not needed on the microscope and could cause problem during operation if not checked every time.

• Add the real tem and camera. For example, if your microscope uses FEI TEM Scripting Interface and you have a Gatan camera that you interface through DigitalMicrograph:

[tem]
class: tecnai.Tecnai
[camera]
class: gatan.Gatan
The file contains other examples of microscope and camera drivers that we distribute from NRAMM.

Run updatecom.py¶

From a command line window:

cd C:\python25\Lib\Site-Packages\pyScope
C:\python25\python.exe updatecom.py

This should generate a few files, including tecnaicom.py, gatancom.py and tietzcom.py, in the same directory.