How to Update from v30 (Instrument Windows Computer)¶

The changes to v3.1 DOES require upgrade at the microscope and camera computers.

See Installation Troubleshooting and Leginon Bulletin Board searching
for "install" if you run into problems.

Download myami-3.1 source code¶

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 myami3.1 directory somewhere at your convenience
• Change directory into myami3.1
• Right-click the mouse botton in this directory window and select Tortoise svn
  Checkout in the menu:
• 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

Otherwise, you can copy the files from your linux myami-3.1 source.

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

Go to C\\python27\site-packages
Create Leginon3_0_backup folder
Move Leginon folder into Leginon3_0_backup folder

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

cd Your_Download_Place\myami3.1_folder
c:\\python27\python.exe setup.py install

Locate global configuration directory following standard on Windows¶

Saving cfg files in a global location reduces future need for copying old configuration to updated installation. The location is different for different versions of Windows. To locate the one for your Windows version:

1. go to C:\\python27\Lib\site-packages\leginon
2. run configcheck.py

The script gives the three search directories of the cfg files and the loaded file if present. Note the first search directory that with a name most likely start with C:\\Programs and ends with \myami. This is the global configuration directory we will use.

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

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

[camera]
tietz.TietzPXL
zplane:10
height: 2048
width: 2048

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.

Gatan K2 Summit camera with GMS 2.3.0¶

Check and modify pyscope/dmsem.py for new configuration needed for the camera to indicate its DM version, orientation, and file saving location. More details in Gatan_K2_installation_and_setup

# DM Version
DM_VERSION = '2.30.542.0'
# the value in DM camera config
K2_CONFIG_FLIP = True
# multiple of 90 degrees (i.e. put 1 if 90 degrees, 3 if 270 degrees)
K2_CONFIG_ROTATE = 3
# raw frame base directory. Use '\\' as path separator
RAW_FRAME_DIR = 'D:\\frames\\'

Gatan K2 Summit camera changes upon GMS upgrade to 2.3.1¶

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:

# DM Version
DM_VERSION = '2.31.734.0'

If you have acquired data in one or more session in Leginon 3.0 with GMS 2.3.1, gain correction in appion frame processing will not work properly once you are upgraded to Leginon/Appion 3.1. You need to record the start of GMS 2.3.1 frame-saving session by running dbschema/schema-dm231.py

< How to Update from v3.0 (Linux)

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