Leginon

h1. How to Update from v31 (Instrument Windows Computer)

The changes to v3.2 DOES require upgrade at the microscope and camera computers.

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

for "install" if you run into problems.

h2. Download myami-3.2 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 myami3.2 directory somewhere at your convenience

* Change directory into myami3.2

* 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-3.2 and save it to myami3.2 folder !http://emg.nysbc.org/software/leginon/images/images/svnco.png!

Otherwise, you can copy the files from your linux myami-3.2 source.

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 installed Leginon folder is at C:\\python27\Lib\site-packages\leginon

<pre>Go to C\\python27\site-packages

Create Leginon3_1_backup folder

Move Leginon folder into Leginon3_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\myami3.2_folder

c:\\python27\python.exe setup.py install</pre>

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

h2. copy the old config files to the global location if you still use local files

h2. Install comtypes on FEI scope controlling computer

We have switched to use comtypes exclusively in 3.2.

See [[FEI_TecnaiTitan_installation_specifics|32-bit]] or [[FEI_Talos_installation_specifics|64-bit]] computer instruction depending on your system although know that to communicate with the instrument, the 32-bit python and subpackages are always installed.

h2. Enter Tietz PXL camera imaging size in instruments.cfg if needed in this format:

<pre>

[camera]

tietz.TietzPXL

zplane:10

height: 2048

width: 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. Gatan K2 Summit camera

We moved the configuration from dmsem.py to a configuration file parsed with standard parser.

# Check your 3.1 pyscope/dmsem.py for the old configuration needed for the camera to indicate its DM version, orientation, and file saving location.

# Copy Your_Download_Place\myami3.2\pyscope\dmsem.cfg.template to the standard myami config path C:\Program File\myami\dmsem.cfg

# Modify dmsem.cfg according to your old configuration

  More details in [[Gatan_K2_installation_and_setup#(Version-3.2)-Define-local-configuration-in-dmsemcfg]]

<pre>

### general dm configurations

[dm]

# DM Version

DM_VERSION = 2.31.734.0

### K2 Summit configuration through SERIALEMCCD plugin

[k2]

# Camera ID

CAMERA_ID = 0

# the value in DM camera config

FLIP = True

# multiple of 90 degrees (i.e. put 1 if 90 degrees, 3 if 270 degrees)

ROTATE = 1

# raw frame base directory. Use '\' as path separator

RAW_FRAME_DIR = D:\frames\

# max number of frames to sum in order to return early

EARLY_RETURN_FRAME_COUNT = 0

</pre>

h2. Gatan K2 Summit camera changes upon GMS upgrade

A change in GMS 2.3.1 and SerialEMCCD which we use at the backend causes the frame saved at different orientation from the reference images saved in standard Leginon orientation. An up-down flip is required in general.

You must change dmsem.py to reflect this:

GMS upgrade to 3.0 is now tested in the field, and confirmed that functions are not affected.

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[[How_to_Update_from_v30_(Linux)|< How to Update from v3.0 (Linux) ]] 

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