Leginon

h1. How to Update from v21 (Microscope Windows Computer)

The changes from v2.1 DOES require upgrade at the microscope

See [[Installation Troubleshooting]] and  "Leginon Bulletin Board":http://emg.nysbc.org/projects/leginon/boards  searching

for "install" if you run into problems.

h2. Packages required from NRAMM

All Leginon (and Appion) packages distributed from NRAMM are under one svn control.

Recommended minimal subpackage upgrade:

|pyscope|change in configuration|

|pyami|new function related to configuration search|

|leginon|change in configuration reading|

|sinedon|change in configuration reading|

h2. Download myami-2.2 source code

h3. Check out SVN Source Files from the repository

Assuming that you have installed some kind of svn client such as TortoiseSVN "http://tortoisesvn.tigris.org/", you can use your mouse to do the following

* Create myami2.2 directory somewhere at your convenience

* Change directory into myami2.2

* 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, but check out from http://emg.nysbc.org/svn/myami/branches/myami-2.2 and save it to myami2.2 folder !http://emg.nysbc.org/software/leginon/images/images/svnco.png!

Otherwise, you can copy the files from your linux myami-2.2 source.

h2. Perform system check if you can't remember where you have installed your Leginon before.

* Go to ~/myami2.2/leginon

* Double click on syscheck.py

You should have all the supporting packages installed for v2.1. If you see any lines like "*** Failed...", then you have something missing. Otherwise, everything should result in "OK".

h2. Move your existing packages to a backup directory (Optional):

At the beginning of the syscheck.py output, the location of the exisiting Leginon folder is shown. 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 from the path before new installation.  Better yet, copy into a backup folder because we need some configuration files from them.

You may find these folders here:

|leginon|

|pyscope|

|sinedon|

|pyami|

For example, your Leginon folder is at C:\\python25\Lib\site-packages\leginon

<pre>Go to C\\python25\site-packages

Create Leginon2_1_backup folder

Move Leginon folder into Leginon2_1_backup folder</pre>

h2. Install subpackages you downloaded from NRAMM svn repository.  *You should not install numextension, libcv and comarray using this instruction*

* Start a command line Window from Start Menu

* Reinstall the package in EACH of the following folders using the included setup.py

|leginon|

|pyscope|

|sinedon|

|pyami|

<pre>cd Your_Download_Place\myami2.2_folder

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

h2. copy the old config files to the new location.

*If you want to avoid copying cfg files to new installation in the future, copy them from where you had it in the 2.1 backup to the global config directory*

{{include(locate global config directory on Windows)}}

|_config file_|likely location in 2.1 installation if not in your hoe directory|

|sinedon.cfg|C:\\python25\Lib\site-packages\sinedon_2.1_backup\|

|leginon.cfg|C:\\python25\Lib\site-packages\leginon_2.1_backup\config\|

|instruments.cfg|C:\\python25\Lib\site-packages\pyscope_2.1_backup\|

h2. modify Tietz PXL camera imaging size if you did so before for Leginon 2.2

*You should not copy the old one in this case since the file has been changed*

*  Go to C:\Python25\Lib\site-packages\pyscope\

*  Edit tietz.py with a plain text editor

*  Find the lines:

<pre> def getCameraSize(self):

# {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}}

x = self._getParameterValue('cpTotalDimensionX')

y = self._getParameterValue('cpTotalDimensionY')

return {'x': x, 'y': y}

</pre>

*  Change the last line to:

<pre>    return {'x': 2048, 'y': 2048}</pre>

h2. About [[TEM Scripting Beam Tilt Calibration]]

* If you have done [[TEM_Scripting Beam Tilt Calibration]] and have changed the scale factor in tecnai.py, you should copy the value to your new installation.

h2. Modify pyscope/instruments.cfg

Starting from 2.2, Cs values are saved with the scope in instruments.cfg that need to match the value saved in the database.  Also a z-plane needs to be assigned to each camera

{{include(Instrumentscfg_for_22)}}

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[[How_to_Update_from_v21_(Linux)|< How to Update from v2.1 (Linux) ]] | [[Check Cs value match before using Leginon after update|Check Cs value match before using Leginon after upgrade >]]

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