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Anchi Cheng, 10/31/2013 04:35 PM
Installation on the microscope computer (svn trunk)¶
If you are installing 2.2, see Installation on the microscope computer¶
Only processing-side of Leginon system is needed
Package Requirement and Download¶
Installation¶
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
Register TecnaiCCD.dll (Gatan 32-bit DM on FEI microscope), CAMC4.exe (For Tietz camera), and adaexp.exe (For film exposure)¶
- From the command prompt, run the following commands. You may need to enter the full path of the exe or dll:
adaexp.exe /regserver CAMC4.exe /regserver REGSVR32 TecnaiCCD.dll
Install Python and supporting packages with their installers¶
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.
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 downloaded from NRAMM svn repository¶
The svn checkout is a folder containing several subpackages. You will install the python packages using python installer
These are the sub-packages¶
Name: | Purpose: |
---|---|
leginon | modular TEM image acquisition |
pyami | general functions |
sinedon | Leginon/database interaction |
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 is 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 Your_Download_Place\LeginonTrunk\leginon c:\\python27\python.exe setup.py install
Then continue with the other packages, replacing leginon 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.
Modify comtypes if TIA controlling camera is used or Gatan camera is controlled by older, 32-bit computer.¶
IMPORTANT: After installing comtypes, you must make one modification to it. The module "safearray.py" that comes with comtypes must be replaced with a modified version that we provide. You can find the custom version of safearray.py in the pyscope package. Please copy this module from pyscope into the installed comtypes folder: C:\Python2*\Lib\site-packages\comtypes\. It should replace the safearray.py that is included in comtypes.
TIA controlling camera only:¶
(Reported by a user as a necessary step on his system. May not be necessary) Copy TecnaiCCD.dll and stdscript.dll into pyscope folder
Run updatecom.py¶
From a command line window:
cd C:\python27\Lib\Site-Packages\pyScope C:\python27\python.exe updatecom.py
The python window appears should say show the required type libraries it found:
Generating .py files from type libraries... initializing TEM Scripting Error, cannot find typelib for "TEM Scripting" initializing Tecnai Scripting done. initializing TOM Moniker done. initializing Tecnai Low Dose Kit done. initializing Tecnai Exposure Adaptor done. initializing Tietz CCD Camera done.
The output is of course depending on what is available on your microscope computer. You should have either "Tecnai Scripting" or the pairing of "TEM Scripting" and "TOM Moniker".
You will only find Tecnai Exposure Adaptor (Scripting for film exposure) if you ask FEI for it.
The script should generate a few files in C:\\python27\Lib\win32com\gen_py with seemly scrambled names such as BC0A2B03-19FF-11D3-AE00-00A024CBA50Cx0x1x9.py
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:
- go to C:\\python27\Lib\site-packages\leginon
- 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.
Configure leginon.cfg:¶
Follow the instructions in Configure leginon.cfg located in the section for Linux installation but note the location of the configuration files follows. In addition, if the storage disk is mapped onto the Windows PC as drive Z, this mapping should be included in leginon.cfg. See below.
- Configurations for all users and all local copy and installation of leginon (Recommended on the microscope computer since users are not expected to start the main processing here)
<Global configuration directory>\leginon.cfg
Example:
C:\Programs\myami\leginon.cfg
- The skeleton (default) configuration file is available at:
C:\Python27\Lib\site-packages\leginon\leginon.cfg.template
Configure sinedon.cfg:¶
Follow instruction in Configure sinedon.cfg in the section for Linux installation but note the location of the configuration files follows.
- (Recommanded on microscope computer) For all users, put sinedon.cfg in the global configuration directory such as
C:\Programs\myami\sinedon.cfg
- the skeleton sinedon configuration file is
C:\Python27\Lib\site-packages\sinedon\examples\sinedon.cfg
Configure instruments.cfg:¶
- A template for instruments.cfg is in the installed pyscope directory as "instruments.cfg.template". Copy it to
C:\Programs\myami\instruments.cfg
- Remove the Sim Tem and Sim Cam modules in the configuration.
- Add the modules for your microscope and camera.
- If you have Direct Electron camera DE12, your camera module.class is de.DE12
- If your microscope uses Tecnai Scripting Interface, youe scope module.class is tecnai.Tecnai
- If you have a Gatan camera running on the microscope computer that you interface through DigitalMicrograph, your camera module.class is gatan.Gatan
- If you have a Gatan K2 Summit running on its only 64-bit computer, your camera module is dmsem and three cameras are added. See Gatan K2 Installation Notes
- If you have a Tietz camera, there are several choices for the "class" field. Run the tietztest.py script that comes in pyscope to tell you your available options.
TEM¶
cs is the coefficient of spherical aberration in meters. Find out from TEM manufacture the proper value for your tem.
For example
[tem] class: fei.Tecnai cs: 2.0e-3
Camera¶
height and width are number of pixels based on the orientation presented in Leginon image viewer- Some Tietz camera may have an odd physical dimension. Use TCL/EMMenu program to find out the good dimension used in Tietz's own software and entered in this configuration.
For example
[camera] class: gatan.Gatan zplane: 50 height: 4096 width: 4096
zplane is a number that gives the order of camera. If a camera with low zplane value is going to acquire an image, Leginon will attempt to retract all cameras at higher zplane values.
HEIGHT and WIDTH are not shown in these examples for simplicity- One computer for both tem and digital camera:
[tem] class: fei.Tecnai cs: 2.0e-3 [camera] class: gatan.Gatan zplane: 50
- Separate computers for the two instruments: configure only the instrument reside on the particular computer
- On the computer that controls the tem:
[tem] class: fei.Tecnai cs: 2.0e-3
- On the computer that controls the digital camera:
[camera] class: gatan.Gatan zplane: 50
- On the computer that controls the tem:
- Two camera at the same plane:
- On the computer that controls the digital camera:
DE12 and DE Survey camera are retract/extend together, with the survey camera at off-axis. Therefore zplane should be set at the same value
For example,[camera1] class: de.DE12 zplane: 50 [camera2] class: de.DESurvey zplane: 50
- On the computer that controls the digital camera:
- Gatan Orius camera that is installed typically with Gatan K2/Falcon camera is technically on the same plane but is not capable of insertion unless K2 is retracted. On the other hand, K2 camera insertion includes a retraction of Orius at lower level of the function call in DM. Therefore, Orius is considered as a camera at lower zplane.
[camera1] class: dmsem.GatanK2Base zplane: 50 [camera2] class: dmsem.GatanOrius zplane: 49
The file contains other examples of microscope and camera drivers that we distribute from NRAMM.
Additional setup on Tietz cameras¶
Register the Tietz ping callback function. From a command line window:
cd C:\python27\Lib\Site-Packages\pyscope C:\python27\python.exe tietzping.py
Troubleshooting Tietz cameras:
When Leginon initializes the camera, a program called CAMC4 should start automatically in the backgound. This is confirmed by the little camera icon showing up in the system tray in the lower right of the screen. Also, task manager can be started to confirm CAMC4 is running. Sometimes problems occur if more than one CAMC4 is running at the same time, so task manager will help identify this.
CAMC4 has its own configuration file "CAMC.ini" that will normally be set up already, but you can search for it on your computer and confirm that everything looks right. It will have configuration parameters for several cameras and only one of them will be activated. The only parameter that may need some adjustment is the readout geometry, which affects the rotation and mirror of the image.
If Leginon is not initializing the camera or not getting proper images, you should first test image acquisition using TVIPS software to make sure it is not a hardware issue. Use TCL or there is a test program called TestMFCCamera that can acquire an image and test the CAMC4 operation.
For strange dimension cameras¶
Unless it is Gatan K2 where it uses flooring when dealing determining camera dimension when binning, you will do better specify a value that can be divided by power of 2 in width and height in instruments.cfg. Examples of this type of configuration can be found in some Tietz camera. Use Tietz's image acquisition software to find out what they use as a guide.
Create Leginon Admin and Leginon Client shortcut in Start menu menu under Leginon¶
This instruction applies to Windows XP.
- Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new
folder named Leginon.
- In another window, go to
C:\Python27\Lib\site-packages\leginon
- Create a shortcut from start-leginon.py as "Leginon Admin" and a shortcut from launcher.py as "Leginon Client".
- Move the two shortcuts into
C:\Documents and Settings\All Users\Start Menu\Programs\Leginon
Mapping Drives (Optional):¶
Although we don't recommend it, it is possible to run minimal Leginon directly on the Windows machine, Since the database and web servers are not there, you probably will be saving the images through a Samba server on a network drive also available to the Linux machine. If you do so, you will need to map the network drive. For example, if your Samba server has a hostname your_smbserver, and you have set up a share called [your_share_point] which points to /your_data_path/ and leginon data will be saved under a folder in /your_data_path/leginon/.
- Start, My Computer
- Tools menu, Map network drive
- Use an unmapped drive such as Z:
Enter shared path in Windows format as
\\your_smbserver\your_share_point
- Add the drive and the Linux path to leginon.cfg on the Windows machine as
[Drive Mapping] Z:/your_data_path
- Add image path to leginon.cfg on the Windows machine in Linux format as
[Images] path:/your_data_path/leginon
Additional Software (Optional):¶
TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room just to open the column valves.
Gatan K2 Experimental support:¶
Falcon/Orius Combination Suport:¶
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Updated by Anchi Cheng about 11 years ago · 35 revisions