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FEI Talos installation specifics » History » Revision 11

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Anchi Cheng, 01/09/2016 11:01 PM


FEI Talos installation specifics

Install win32 version of python subpackages

Because all interaction with the scope uses COM interface that is only accessible through 32-bit architecture, python running Leginon component is the 32-bit version. Use the 32-bit Windows files (those marked as win32 and certainly not the ones says 64) in http://emg.nysbc.org/projects/leginon/files for these.

Talos has a 64-bit Python pre-installed unde default python location C:\Python27. Therefore, we need to name our installation with another name, such as C:\Python27-win32.

Here is the full list

Program package web site local copy of win32 installer
Python 2.7.16 https://www.python.org python-2.7.16.msi
wxPython 2.5.2.8 or newer https://www.wxpython.org wxPython2.8-win32-unicode-2.8.12.1-py27.exe
Python Imaging Library (PIL) 1.1.4 or newer http://www.pythonware.com/products/pil/ PIL-1.1.7.win32-py2.7.exe
NumPy (use only from our file to match compiled numextension numpy-1.7.0-win32-python2.7.exe
SciPy 0.5.1 or newer http://www.scipy.org scipy-0.11.0-win32-superpack-python2.7.exe
Leginon 3.5 or before
MySQL Python client 1.2 or newer http://sourceforge.net/projects/mysql-python MySQL-python-1.2.4b4.win32-py2.7.exe
Leginon 3.6 and up
pyMySQL 0.10.1 (not higher) https://pypi.org/project/PyMySQL/ pyMySQL-0.10.1-py2.py3-none-any.whl
Program package web site local copy of win32 installer
comtypes 0.6.2 http://sourceforge.net/projects/comtypes" comtypes-0.6.2.win32.exe

Important: Install Python under a custom named folder

Talos has a 64-bit Python pre-installed unde default python location C:\Python27. Therefore, we need to name our installation with another name, such as C:\Python27-win32.
This is set during python installation.

The rest of the installation is similar to other FEI systems.

(Strongly recommended) Use local myami folder to run Leginon

Because we install into FEI's framework folder, it may be erased at the next upgrade by the service engineer. To reduce the possibility of loss of local modification, we recommend using local myami checked out from NRAMM svn repository directly as follows, rather than installed into python's site packages.

Set pythonpath environment variable for local myami sandbox

For an uninstall myami svn checkout, you can set PYTHONPATH environment variable to use it directly.

  1. Control Panel\All Control Panel Items\System> click on Advanced settings
  2. System Properties\Advanced> click on Environment Variables
  3. Either create a new variable for the current user, or do it system-widely.

PYTHONPATH should incldue both the base myamipath as well as leginon

For example, myami folder is at C:\Users\vagrant\Desktop\myami, then the python path should be set as follows:

C:\Users\vagrant\Desktop\myami; C:\Users\vagrant\Desktop\myami\leginon

instruments.cfg

cs is constant for sperical abberation

For Tecnai series:

[TEM]
class: tecnai.Talos
cs: 2.7e-3

Testing with pyscope

In python command

from pyscope import tecnai
t = tecnai.Talos()
t.getMagnification()

Trouble Shooting

unable to initializ Tecnai interface error

Programs to open before Leginon Client: None

Updated by Anchi Cheng almost 9 years ago · 11 revisions