Leginon

h1. Installation on the microscope computer for 2.2

h2. If you are installing 2.1, see [[Installation on the microscope compute 2.1]]

h2. If you are installing pre-released 3.0 version (required for Gatan K2 Summit and FEI Falcon support), see [[Installation on the instrument computers]]

Only processing-side of Leginon system is needed

h1. Package requirement

h2.  Python and Support Packages (Note that python 2.5 must be used):

This list does not include the python XML module because it is included in the python package for Windows.  You should generally be able to use the most recent versions of these packages that are available from their respective web sites.  Just be sure to always get the version that is compatible with Python 2.5.  If you are having trouble with the most recent version, try to use the specific versions listed here:

|Python 2.5*| "http://www.python.org":http://www.python.org||

|Python for Windows extension (pywin32)| "http://sourceforge.net/projects/pywin32/":http://sourceforge.net/projects/pywin32/||

|wxPython 2.5.2.8 or newer| "http://www.wxpython.org":http://www.wxpython.org||

|MySQL Python client 1.2 or newer| "http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python|1.2.3 doesn't have window installer, yet, use 1.2.2|

|Python Imaging Library (PIL) 1.1.4 or newer| "http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/||

|NumPy 1.0b5 (tested, others may work)| "http://www.scipy.org":http://www.scipy.org||

|SciPy 0.5.1 or newer| "http://www.scipy.org":http://www.scipy.org||

*Python 2.5 is the only python version that we have compiled numExtension. libCV and comarray in. Therefore no other python version works for now.

h2. SVN client used for check out from our repository

This required for following this instruction. We have used Tortois SVN client.  Alternatively, you may copy the required NRAMM source files from another computer.

|_.Name:|_.Download site:|

|Tortoise SVN client| "http://tortoisesvn.tigris.org":http://tortoisesvn.tigris.org|

h2.  Required supporting programs for the CCD camera from camera makers

Install and register the following programs for CCD cameras from the two makes.  Most likely, you already have these installed when the camera and TEM software was installed:

|_.Camera Make:|_.File:|

| Gatan|TecnaiCCD.dll|

| Tietz|CAMC4.exe*|

| DirectElectronDE12|DirectElectronAPI.exe|

h2.  Supporting programs for film exposure

Install the following if you need film exposure on FEI Tecnai TEM through Leginon, available through FEI. Please contact Max Otten: mto@feico.com and request for adaexp.exe that works with your version of Tecnai user interface program.

|_.Name:|_.File:|

| exposure adaptor|adaexp.exe|

h2. Packages required from NRAMM

h3. These are the sub-packages of myami that you will install with the python installer.

|_.Name:|_.Purpose:|

| leginon|modular TEM image acquisition|

| pyami|general functions|

| sinedon|Leginon/database interaction|

| pyscope|microscope control and monitoring|

| imageviewer|image viewing for tomography|

* For FEI Eagle Camera or Gatan Camera that uses TIA, comarray package needs to be install with python

* [[Special Instructions for FEI Eagle Camera]]

* In Testing:  Comarray will soon be retired.  We will be using the third party package "comtypes" instead.  See instructions here: [[Installing comtypes]].

Because numextension, comarray and libcv would require extra compilers if you build them yourself, we have created Windows installers for them for python 2.5 and made them available at http://emg.nysbc.org/projects/leginon/files.

h3. These are the Leginon v2.0 python 2.5 compiled packages installed through python installer on Windows. Leginon v2.2 uses the same files.

|_.Downloadfile Name|_.Purpose:|

|numextension-2.0.0.win32-py2.5.exe|c extension for numerical processing|

|comarray-2.0.0.win32-py2.5.exe|com module output conversion to array|

|libCV-2.0.0.win32-py2.5.exe|small c library of algorithm from computer vision field|

h1. Installation

{{include(add host)}}

h2. Register TecnaiCCD.dll, 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:

<pre>adaexp.exe /regserver

CAMC4.exe /regserver

REGSVR32 TecnaiCCD.dll</pre>

h2. Install Python and supporting packages with their installers

Excute the installer files and follow the instructions.

h2. Install the Windows Installer Files from Leginon website http://emg.nysbc.org/projects/leginon/files

Execute the installer files and follow the instructions. *Do not execute comarray-2.0.0.win32-py2.5.exe if your camera is only controlled by TIA, such as an FEI Eagle camera*.  See [[Special_Instructions_for_FEI_Eagle_Camera]].

h2. Check out SVN Source Files from the repository

Use your mouse to do the following

* Create Leginon2.2 directory somewhere at your convenience

* Change directory into Leginon2.2

* 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 to check out from http://emg.nysbc.org/svn/myami/branches/myami-2.2 to Leginon2.2

 !http://emg.nysbc.org/software/leginon/images/images/svnco.png!

h2. Remove tifffile.py from pyami suppackage

This file, needed by DE camera frame processing with Appion can not be compiled with python 2.5.  Therefore, you should remove it from your download before installation.

<pre>

cd Your_Download_Place\Leginon2.2\pyami

del tifffile.py

</pre>

h2. Install the packages you downloaded from NRAMM svn repository

* Start a command line Window from Start Menu

* Install the package in each folder with commands such as

<pre>cd Your_Download_Place\Leginon2.2\leginon

c:\\python25\python.exe setup.py install</pre>

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.

h2. Run updatecom.py

From a command line window:

<pre>cd C:\python25\Lib\Site-Packages\pyScope

C:\python25\python.exe updatecom.py</pre>

The python window appears should say show the required type libraries it found:

<pre>

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.

</pre>

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:\\python25\Lib\win32com\gen_py with seemly scrambled names such as BC0A2B03-19FF-11D3-AE00-00A024CBA50Cx0x1x9.py

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

h2. Configure leginon.cfg:

Follow the instructions in [[Configure leginon.cfg|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)

 <pre> <Global configuration directory>\leginon.cfg</pre>

 Example:

 <pre> C:\Programs\myami\leginon.cfg</pre>

* The skeleton (default) configuration file is available at:

 <pre> C:\Python25\Lib\site-packages\leginon\leginon.cfg.template</pre>

h2. 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

 <pre>C:\Programs\myami\sinedon.cfg</pre>

 * the skeleton sinedon configuration file is

 <pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre>

h2. Configure instruments.cfg:

* A template for instruments.cfg is in the installed pyscope directory as "instruments.cfg.template".  Copy it to

 <pre>C:\Programs\myami\instruments.cfg</pre>

* 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 that you interface through DigitalMicrograph, your camera module.class is gatan.Gatan

** 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.

{{include(instruments.cfg for 2.2)}}

The file contains other examples of microscope and camera drivers that we distribute from NRAMM.

h2. Additional setup on Tietz cameras

Register the Tietz ping callback function.  From a command line window:

<pre>cd C:\python25\Lib\Site-Packages\pyscope

C:\python25\python.exe tietzping.py</pre>

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.

h2. For strange dimension cameras

{{include(strange dimension cameras)}}

h2. 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

 <pre>C:\Python25\Lib\site-packages\leginon</pre>

 * Create a shortcut from start-leginon.py as "Leginon Admin" and a shortcut from launcher.py as "Leginon Client".

 * Move the two shortcuts into

 <pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre>

h2. 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

 <pre>\\your_smbserver\your_share_point</pre>

*  Add the drive and the Linux path to leginon.cfg on the Windows machine as

 <pre>[Drive Mapping]

Z:/your_data_path</pre>

*  Add image path to leginon.cfg on the Windows machine in Linux format as

 <pre>[Images]

path:/your_data_path/leginon</pre>

h2.  Additional Software (Optional):

TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room just to open the column valves.

h2. Gatan K2 Experimental support:

* [[Gatan K2 Installation Notes]]

* [[Gatan K2 Support Update of trunk from before r17514 to higher than r17561]] 

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[[Additional Database Server Setup after Web Server Installation|< Additional Database Server Setup]] | [[Steps involved in the installation| Steps needed for Installation Using Database Administration Tools >]]

If you used *autoinstaller*:  [[Autoinstaller for CentOS| < Autoinstaller for CentOS]] | [[Start_Leginon|Perform Microscope Setup and Test run >]]

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