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Anchi Cheng, 12/04/2017 01:06 PM
Windows Installation¶
- You need to repeat installation of the general packages for each of the computer involved in Leginon operation with addition for the camera and scope.
Install Python and supporting packages with their installers. Only Gatan K2 computer uses 64-bit version of python.¶
Program | package web site | local copy of win32 installer | local copy of amd64 installer |
Python > 2.7.10 | http://www.python.org | python-2.7.16.msi | python-2.7.18.amd64.msi |
wxPython 2.8 or newer | http://www.wxpython.org | wxPython2.8-win32-unicode-2.8.12.1-py27.exe | wxPython2.8-win64-unicode-2.8.12.1-py27.exe |
MySQL Python client 1.2 or newer | http://sourceforge.net/projects/mysql-python | MySQL-python-1.2.4b4.win32-py2.7.exe | MySQL-python-1.2.3.win-amd64-py2.7.exe |
Python Imaging Library (PIL) 1.1.4 or newer | http://www.pythonware.com/products/pil/ | PIL-1.1.7.win32-py2.7.exe | PIL-fork-1.1.7.win-amd64-py2.7.exe |
NumPy | (use only from our file to match compiled numextension | numpy-1.7.0-win32-python2.7.exe | numpy-MKL-1.6.2.win-amd64-py2.7.exe |
SciPy 0.5.1 or newer | http://www.scipy.org | scipy-0.11.0-win32-superpack-python2.7.exe | scipy-0.11.0.win-amd64-py2.7.exe |
pyMySQL 0.10.1 (not higher) | https://pypi.org/project/PyMySQL/ | pyMySQL-0.10.1-py2.py3-none-any.whl |
Excute the installer files and follow the instructions.
Add the IP address and matching hostname of the microscope and digital camera computer in your host file on the main Leginon computer, and vice versa.¶
Find out what python thinks the hostname is with python command line. REPEAT this both on Linux and Windows PC¶
Run the following in python command line:
import socket socket.gethostname()
Find out the ip address associated with the hostname¶
Run the following in python command line:
import socket socket.gethostbyname('your_host_name')
Modify your "hosts" file on the linux Leginon computer to include the instrument hosts if the latter is not already mapped by your domain name server¶
- On Linux, this "hosts" file is at
/etc/hosts
Example of a "hosts" file:
192.000.1.222 instrument_host_name.domain_name instrument_short_host_name
Use shorter linux hostname if desired¶
If you'd like to shorten your linux hostname recognized by socket without the domain name, you may do so as root
hostname your_shorter_hostname
and also add that to the /etc/hosts as an alternative name
192.000.1.333 long_host_name.domain_name your_shorter_hostname
You will need to restart networking to make it persistent.
/etc/init.d/network restart
Test the change by finding the ip address with the hostname as in the above section.
The Linux main Leginon computer also needs to identify itself by its hostname registered on the instrument Windows computer.¶
- On Window XP and WIndows 7 this host file is
C:\\WINDOWS\system32\drivers\etc\hosts
- On Window NT, this host file is
C:\\WINNT\system32\drivers\etc\hosts
Install the Windows Installer Files from created from source by NRAMM¶
Package | win32 | amd64 |
---|---|---|
numextension | numextension-svn.win32-py2.7-numpy1.7.0.exe | numextension-svn.win-amd64-py2.7-numpy1.6.2.exe |
Execute the installer files and follow the instructions.
Install the packages you cloned from NRAMM git repository¶
The svn checkout is a folder containing several subpackages. You will install the python packages using python installer. See the next section if you want to use directly the git/svn checkout.
These are the subpackages¶
Name: | Purpose: |
---|---|
pyami | general functions |
sinedon | database interaction |
leginon | modular TEM image acquisition |
pyscope | microscope control and monitoring |
imageviewer | image viewing for tomography |
If you recall Linux processing server installation instruction, this is a bit different. Numextension and LibCV are not included. Numextension is already installed with windows installer. libcv and opencv are not required by Leginon client that this part installation is aimed for.
- Start a command line Window from Start Menu
- Install the package in each folder with commands such as
cd path_to\myami-VERSION\myami\pyami c:\\python27\python.exe setup.py install
Then continue with the other packages, replacing pyami with the package name. See "These are the sub-packages of myami that you will install with the python installer." section above for complete list.
(Alternative approach, easy for updating) Set environment variable PYTHONPATH to use svn checkout or git clone directly¶
Set pythonpath environment variable for local myami sandbox¶
For an uninstall myami svn checkout, you can set PYTHONPATH environment variable to use it directly.
- Control Panel\All Control Panel Items\System> click on Advanced settings
- System Properties\Advanced> click on Environment Variables
- 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
< Package Requirement | Additional installation specific to the microscope >
Updated by Anchi Cheng about 7 years ago · 57 revisions