Project

General

Profile

Installation on the microscope computer » History » Version 72

Anchi Cheng, 05/07/2013 06:25 PM

1 56 Anchi Cheng
h1. Installation on the microscope computer for 2.2
2 1 Amber Herold
3 65 Anchi Cheng
h2. If you are installing 2.1, see [[Installation on the microscope compute 2.1]]
4 54 Anchi Cheng
5 71 Anchi Cheng
h2. If you are installing trunk version (required for Gatan K2 Summit support development), see [[Installation on the microscope computer 3.0]]
6
7 11 Anchi Cheng
Only processing-side of Leginon system is needed
8 1 Amber Herold
9 21 Anchi Cheng
h1. Package requirement
10 1 Amber Herold
11 21 Anchi Cheng
h2.  Python and Support Packages (Note that python 2.5 must be used):
12 1 Amber Herold
13 24 Jim Pulokas
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:
14 11 Anchi Cheng
15 38 Anchi Cheng
|Python 2.5*| "http://www.python.org":http://www.python.org||
16
|Python for Windows extension (pywin32)| "http://sourceforge.net/projects/pywin32/":http://sourceforge.net/projects/pywin32/||
17
|wxPython 2.5.2.8 or newer| "http://www.wxpython.org":http://www.wxpython.org||
18 39 Anchi Cheng
|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|
19 38 Anchi Cheng
|Python Imaging Library (PIL) 1.1.4 or newer| "http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/||
20
|NumPy 1.0b5 (tested, others may work)| "http://www.scipy.org":http://www.scipy.org||
21
|SciPy 0.5.1 or newer| "http://www.scipy.org":http://www.scipy.org||
22 1 Amber Herold
23 12 Anchi Cheng
*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.
24
25 21 Anchi Cheng
h2. SVN client used for check out from our repository
26 12 Anchi Cheng
27
This required for following this instruction. We have used Tortois SVN client.  Alternatively, you may copy the required NRAMM source files from another computer.
28
29
|_.Name:|_.Download site:|
30 11 Anchi Cheng
|Tortoise SVN client| "http://tortoisesvn.tigris.org":http://tortoisesvn.tigris.org|
31
32 1 Amber Herold
33 21 Anchi Cheng
h2.  Required supporting programs for the CCD camera from camera makers
34 1 Amber Herold
35 25 Jim Pulokas
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:
36 1 Amber Herold
37
|_.Camera Make:|_.File:|
38
| Gatan|TecnaiCCD.dll|
39
| Tietz|CAMC4.exe*|
40 63 Anchi Cheng
| DirectElectronDE12|DirectElectronAPI.exe|
41 1 Amber Herold
42 21 Anchi Cheng
h2.  Supporting programs for film exposure
43 11 Anchi Cheng
44 12 Anchi Cheng
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.
45 11 Anchi Cheng
46
|_.Name:|_.File:|
47 1 Amber Herold
| exposure adaptor|adaexp.exe|
48
49 21 Anchi Cheng
h2. Packages required from NRAMM
50 11 Anchi Cheng
51 25 Jim Pulokas
h3. These are the sub-packages of myami that you will install with the python installer.
52 11 Anchi Cheng
53 1 Amber Herold
|_.Name:|_.Purpose:|
54 11 Anchi Cheng
| leginon|modular TEM image acquisition|
55
| pyami|general functions|
56
| sinedon|Leginon/database interaction|
57
| pyscope|microscope control and monitoring|
58
| imageviewer|image viewing for tomography|
59
60 47 Anchi Cheng
*For FEI Eagle Camera or Gatan Camera that uses TIA, comarray package needs to be install with python
61 46 Jim Pulokas
*[[Special Instructions for FEI Eagle Camera]]
62 1 Amber Herold
63 25 Jim Pulokas
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.
64 11 Anchi Cheng
65 65 Anchi Cheng
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.
66 1 Amber Herold
67 17 Anchi Cheng
|_.Downloadfile Name|_.Purpose:|
68
|numextension-2.0.0.win32-py2.5.exe|c extension for numerical processing|
69 45 Jim Pulokas
|comarray-2.0.0.win32-py2.5.exe|com module output conversion to array|
70 70 Anchi Cheng
|libCV-2.0.0.win32-py2.5.exe|small c library of algorithm from computer vision field|
71 11 Anchi Cheng
72 21 Anchi Cheng
h1. Installation
73 11 Anchi Cheng
74 68 Anchi Cheng
{{include(add host)}}
75 66 Anchi Cheng
76 60 Anchi Cheng
h2. Register TecnaiCCD.dll, CAMC4.exe (For Tietz camera), and adaexp.exe (For film exposure)
77 1 Amber Herold
78 59 Jim Pulokas
*  From the command prompt, run the following commands.  You may need to enter the full path of the exe or dll:
79 58 Jim Pulokas
<pre>adaexp.exe /regserver
80
CAMC4.exe /regserver
81 59 Jim Pulokas
REGSVR32 TecnaiCCD.dll</pre>
82 18 Anchi Cheng
83 26 Jim Pulokas
h2. Install Python and supporting packages with their installers
84 11 Anchi Cheng
85 26 Jim Pulokas
Excute the installer files and follow the instructions.
86 11 Anchi Cheng
87 12 Anchi Cheng
88 60 Anchi Cheng
h2. Install the Windows Installer Files from Leginon website http://emg.nysbc.org/projects/leginon/files
89 1 Amber Herold
90 49 Anchi Cheng
Execute the installer files and follow the instructions. *Do not execute comarray-2.0.0.win32-py2.5.3x3 if your camera uses TIA*.  See earlier section above.
91 1 Amber Herold
92 60 Anchi Cheng
h2. Check out SVN Source Files from the repository
93 1 Amber Herold
94 11 Anchi Cheng
Use your mouse to do the following
95 65 Anchi Cheng
* Create Leginon2.2 directory somewhere at your convenience
96 1 Amber Herold
97 65 Anchi Cheng
* Change directory into Leginon2.2
98 1 Amber Herold
99
* Right-click the mouse botton in this directory window and select Tortoise svn
100
Checkout in the menu:
101
 !http://emg.nysbc.org/software/leginon/images/images/svnmenu.png!
102 11 Anchi Cheng
103 1 Amber Herold
104 65 Anchi Cheng
* Set up svn checkout window like this to check out from http://emg.nysbc.org/svn/myami/branches/myami-2.2 to Leginon2.2
105 11 Anchi Cheng
 !http://emg.nysbc.org/software/leginon/images/images/svnco.png!
106
107
108 60 Anchi Cheng
h2. Install the packages you downloaded from NRAMM svn repository
109 1 Amber Herold
110 11 Anchi Cheng
* Start a command line Window from Start Menu
111 1 Amber Herold
112 12 Anchi Cheng
* Install the package in each folder with commands such as
113 65 Anchi Cheng
<pre>cd Your_Download_Place\Leginon2.2\leginon
114 12 Anchi Cheng
c:\\python25\python.exe setup.py install</pre>
115 50 Neil Voss
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.
116 12 Anchi Cheng
117 60 Anchi Cheng
h2. Run updatecom.py
118 1 Amber Herold
119 33 Jim Pulokas
From a command line window:
120
121
<pre>cd C:\python25\Lib\Site-Packages\pyScope
122
C:\python25\python.exe updatecom.py</pre>
123
124
The python window appears should say show the required type libraries it found:
125
<pre>
126
Generating .py files from type libraries...
127
initializing TEM Scripting Error, cannot find typelib for "TEM Scripting"
128
initializing Tecnai Scripting done.
129
initializing TOM Moniker done.
130
initializing Tecnai Low Dose Kit done.
131
initializing Tecnai Exposure Adaptor done.
132
133
initializing Tietz CCD Camera done.
134
</pre>
135
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".
136
137 1 Amber Herold
You will only find Tecnai Exposure Adaptor (Scripting for film exposure) if you ask FEI for it.
138
139
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
140
141 64 Anchi Cheng
{{include(locate global config directory on Windows)}}
142 60 Anchi Cheng
143
h2. Configure leginon.cfg:
144
145 40 Anchi Cheng
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.
146
147 60 Anchi Cheng
* 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)
148 55 Anchi Cheng
149 61 Anchi Cheng
 <pre> <Global configuration directory>\leginon.cfg</pre>
150 11 Anchi Cheng
151 55 Anchi Cheng
 Example:
152 61 Anchi Cheng
 <pre> C:\Programs\myami\leginon.cfg</pre>
153 11 Anchi Cheng
154 1 Amber Herold
155 40 Anchi Cheng
* The skeleton (default) configuration file is available at:
156 55 Anchi Cheng
157 1 Amber Herold
 <pre> C:\Python25\Lib\site-packages\leginon\leginon.cfg.template</pre>
158
159 33 Jim Pulokas
160 60 Anchi Cheng
h2. Configure sinedon.cfg:
161 11 Anchi Cheng
162 1 Amber Herold
Follow instruction in [[Configure sinedon.cfg]] in the section for Linux installation but note the location of the configuration files follows.
163
164 10 Anchi Cheng
165 61 Anchi Cheng
 * (Recommanded on microscope computer) For all users, put sinedon.cfg in the *global configuration directory* such as
166
 <pre>C:\Programs\myami\sinedon.cfg</pre>
167 1 Amber Herold
168
 * the skeleton sinedon configuration file is
169 10 Anchi Cheng
 <pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre>
170 1 Amber Herold
171
h2. Configure instruments.cfg:
172
173 61 Anchi Cheng
* A template for instruments.cfg is in the installed pyscope directory as "instruments.cfg.template".  Copy it to
174
 <pre>C:\Programs\myami\instruments.cfg</pre>
175 60 Anchi Cheng
176 1 Amber Herold
* Remove the Sim Tem and Sim Cam modules in the configuration.
177
178 61 Anchi Cheng
* Add the modules for your microscope and camera. 
179
** If you have Direct Electron camera DE12, your camera module.class is de.DE12
180
** If your microscope uses Tecnai Scripting Interface, youe scope module.class is tecnai.Tecnai
181
** If you have a Gatan camera that you interface through DigitalMicrograph, your camera module.class is gatan.Gatan
182 62 Anchi Cheng
** 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.
183
184 55 Anchi Cheng
{{include(instruments.cfg for 2.2)}}
185 1 Amber Herold
186
The file contains other examples of microscope and camera drivers that we distribute from NRAMM.
187
188 60 Anchi Cheng
h2. Additional setup on Tietz cameras
189 1 Amber Herold
190 42 Anchi Cheng
Register the Tietz ping callback function.  From a command line window:
191 29 Jim Pulokas
192 1 Amber Herold
<pre>cd C:\python25\Lib\Site-Packages\pyscope
193
C:\python25\python.exe tietzping.py</pre>
194 57 Jim Pulokas
195 1 Amber Herold
Troubleshooting Tietz cameras:
196 57 Jim Pulokas
197
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.
198
199
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.
200
201
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.
202
203 60 Anchi Cheng
h2. For strange dimension cameras
204 1 Amber Herold
205 36 Anchi Cheng
{{include(strange dimension cameras)}}
206 1 Amber Herold
207 60 Anchi Cheng
h2. Create Leginon Admin and Leginon Client shortcut in Start menu menu under Leginon
208 1 Amber Herold
209
210 11 Anchi Cheng
This instruction applies to Windows XP.
211 1 Amber Herold
212
213
 * Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new
214 11 Anchi Cheng
folder named Leginon.
215
216 1 Amber Herold
217
 * In another window, go to
218
 <pre>C:\Python25\Lib\site-packages\leginon</pre>
219 11 Anchi Cheng
220
221 51 Neil Voss
 * Create a shortcut from start-leginon.py as "Leginon Admin" and a shortcut from launcher.py as "Leginon Client".
222 11 Anchi Cheng
223 1 Amber Herold
224 11 Anchi Cheng
 * Move the two shortcuts into
225
 <pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre>
226
227
228
229 60 Anchi Cheng
h2. Mapping Drives (Optional):
230 11 Anchi Cheng
231 40 Anchi Cheng
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/.
232 11 Anchi Cheng
233
*  Start, My Computer
234
235
236
*  Tools menu, Map network drive
237
238
239
*  Use an unmapped drive such as Z:
240
241 12 Anchi Cheng
 Enter shared path in Windows format as
242 11 Anchi Cheng
 <pre>\\your_smbserver\your_share_point</pre>
243
244
245 12 Anchi Cheng
*  Add the drive and the Linux path to leginon.cfg on the Windows machine as
246 11 Anchi Cheng
 <pre>[Drive Mapping]
247
Z:/your_data_path</pre>
248
249
250 12 Anchi Cheng
*  Add image path to leginon.cfg on the Windows machine in Linux format as
251 11 Anchi Cheng
 <pre>[Images]
252
path:/your_data_path/leginon</pre>
253
254
255
h2.  Additional Software (Optional):
256 3 Amber Herold
257 12 Anchi Cheng
TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room just to open the column valves.
258 1 Amber Herold
259 69 Jim Pulokas
h2. Gatan K2 Experimental support:
260
261
* [[Gatan K2 Installation Notes]]
262 3 Amber Herold
263 72 Anchi Cheng
* [[Gatan K2 Support Update of trunk from before r17514 to higher than r17561]] 
264
265 1 Amber Herold
______
266
267 41 Anchi Cheng
[[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 >]]
268 1 Amber Herold
269
270
______