Project

General

Profile

Installation on the microscope computer » History » Version 11

Anchi Cheng, 05/20/2010 10:10 PM

1 11 Anchi Cheng
h1. Installation on the microscope computer
2 1 Amber Herold
3 11 Anchi Cheng
Only processing-side of Leginon system is needed
4 1 Amber Herold
5 11 Anchi Cheng
h2. Package requirement
6 1 Amber Herold
7 11 Anchi Cheng
h3.  Download Python and Support Packages (Note that python 2.5 must be used):
8 1 Amber Herold
9 11 Anchi Cheng
This list does not include pyton XML module because it is included in the python
10
package for window.
11 1 Amber Herold
12 11 Anchi Cheng
|_.Name:|_.Download site:|
13
|Python 2.5*| "http://www.python.org":http://www.python.org|
14
|Python for Windows extension (pywin32)| "http://sourceforge.net/projects/pywin32/":http://sourceforge.net/projects/pywin32/|
15
|wxPython 2.5.2.8 or newer| "http://www.wxpython.org":http://www.wxpython.org|
16
|MySQL Python client 1.2 or newer| "http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python|
17
|Python Imaging Library (PIL) 1.1.4 or newer| "http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/|
18
|NumPy 1.0b5 (tested, others may work)| "http://www.scipy.org":http://www.scipy.org|
19
|SciPy 0.5.1 or newer| "http://www.scipy.org":http://www.scipy.org|
20 1 Amber Herold
21 11 Anchi Cheng
|Tortoise SVN client| "http://tortoisesvn.tigris.org":http://tortoisesvn.tigris.org|
22 1 Amber Herold
23 11 Anchi Cheng
*Python 2.5 is the only python version that we have compiled numExtension. libCV and
24
comarray in. Therefore no other python version works for now.
25
*Tortoise SVN client is required with this instruction. Alternatively, you may copy the required NRAMM source files from another computer.
26 1 Amber Herold
27 11 Anchi Cheng
h3.  Required supporting programs for the CCD camera from camera makers
28 1 Amber Herold
29
Install and register the following programs for CCD cameras from the two makes:
30
31
|_.Camera Make:|_.File:|
32
| Gatan|TecnaiCCD.dll|
33
| Tietz|CAMC4.exe*|
34
35 11 Anchi Cheng
*Note:* We have experienced slowness of the CAMC4.exe comes with later version Tecnai TUI/TIA. Replacing it with an earlier version of CAMC4.exe resolved the problem
36 1 Amber Herold
37 11 Anchi Cheng
h3.  Supporting programs for film exposure
38 1 Amber Herold
39 11 Anchi Cheng
Install the following if you need film exposure on FEI Tecnai TEM through Leginon,
40
available through FEI. Please contact Max Otten: mto@feico.com and request
41
for adaexp.exe that works with your version of Tecnai user interface program.
42 1 Amber Herold
43 11 Anchi Cheng
|_.Name:|_.File:|
44
| exposure adaptor|adaexp.exe|
45 1 Amber Herold
46 11 Anchi Cheng
h4.  Register adaexep.exe
47 1 Amber Herold
48 11 Anchi Cheng
*  From the command prompt:
49
<pre>adaexp.exe /regserver</pre>
50 1 Amber Herold
51 11 Anchi Cheng
*  From the program start menu under pyScope or C:\Python25\Lib\site-packages\pyscope\
52
<pre>updatecom.py</pre>
53 1 Amber Herold
54
55 11 Anchi Cheng
h3. Packages required from NRAMM
56 1 Amber Herold
57 11 Anchi Cheng
h4. These are the sub-packages you will install with the python installer.
58 1 Amber Herold
59 11 Anchi Cheng
|_.Name:|_.Purpose:|
60
| leginon|modular TEM image acquisition|
61
| pyami|general functions|
62
| sinedon|Leginon/database interaction|
63
| pyscope|microscope control and monitoring|
64
| imageviewer|image viewing for tomography|
65
|comarray|com module output conversion to array|
66 1 Amber Herold
67 11 Anchi Cheng
*For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package need to be install
68
with python
69 1 Amber Herold
70
71 11 Anchi Cheng
Because numextension and libcv requires extra compilers, we have created window
72
installer for them for python 2.5 and made them available through  "http://www.leginon.org/":http://www.leginon.org/.
73 1 Amber Herold
74 11 Anchi Cheng
h4. These are the Leginon v2.0 python 2.5 compiled packages installed through python installer on Windows.
75 1 Amber Herold
76 11 Anchi Cheng
|_.Downloadfile Name|_.Installed Python Package File|_.Purpose:|
77
|NumExtension-1.2.0.win32-py2.5.exe|numextension.pyd|c extension for numerical processing|
78
|libCV-0.2.win32-py2.5.exe|libCV.pyd|small c library of algorithm from computer vision field|
79 1 Amber Herold
80 11 Anchi Cheng
h2. Installation
81 1 Amber Herold
82 11 Anchi Cheng
h3. Install Python and supporting packages with their installer
83 1 Amber Herold
84 11 Anchi Cheng
Excute the installer files and follow the instruction.
85 1 Amber Herold
86 11 Anchi Cheng
h3. Install the two Window Installer Files from Leginon website "http://www.leginon.org/":http://www.leginon.org/
87 1 Amber Herold
88 11 Anchi Cheng
Excute the installer files and follow the instruction.
89 1 Amber Herold
90 11 Anchi Cheng
h3. Check out SVN Source Files from the depository
91 1 Amber Herold
92 11 Anchi Cheng
Use your mouse to do the following
93
* Create Leginon2.0 directory somewhere at your convenience
94 1 Amber Herold
95 11 Anchi Cheng
* Change directory into Leginon2.0
96 1 Amber Herold
97 11 Anchi Cheng
* Right-click the mouse botton in this directory window and select Tortoise svn
98
Checkout in the menu:
99
 !http://emg.nysbc.org/software/leginon/images/images/svnmenu.png!
100 1 Amber Herold
101
102 11 Anchi Cheng
* Set up svn checkout window like this to check out from http://emg.nysbc.org/svn/myami/trunk to Leginon2.0
103
 !http://emg.nysbc.org/software/leginon/images/images/svnco.png!
104 1 Amber Herold
105
106 11 Anchi Cheng
h3. Install the packages you downloaded from NRAMM svn depository
107 1 Amber Herold
108 11 Anchi Cheng
* Start a command line Window from Start Menu
109 1 Amber Herold
110 11 Anchi Cheng
* Install the package in each folder with commands such as
111
<pre>cd Your_Download_Place\Leginon2.0\leginon
112
c:\\python25\python.exe setup.py install</pre>
113 9 Amber Herold
114 11 Anchi Cheng
h2.  Configure leginon.cfg:
115 1 Amber Herold
116 11 Anchi Cheng
Follow the instructions in [[Configure leginon.cfg|Configure leginon.cfg]] located in
117
the section for Linux installation but note the location of the configuration files
118
follows. In addition, if the storage disk is mapped onto the Windows PC as drive Z, this
119
mapping should be included in leginon.cfg. See above.
120 1 Amber Herold
121 11 Anchi Cheng
* Configurations for all users
122 1 Amber Herold
123 11 Anchi Cheng
 <pre> <Python directory>\Lib\site-packages\Leginon\config\leginon.cfg</pre>
124 1 Amber Herold
125 11 Anchi Cheng
 Example:
126
 <pre> C:\Python25\Lib\site-packages\Leginon\config\leginon.cfg</pre>
127 1 Amber Herold
128
129 11 Anchi Cheng
* Configurations for individual users
130 1 Amber Herold
131 11 Anchi Cheng
 <pre> <Home directory>\leginon.cfg</pre>
132 1 Amber Herold
133 11 Anchi Cheng
 Example:
134
 <pre> C:\Documents and Settings\Leginon User\leginon.cfg </pre>
135 1 Amber Herold
136 10 Anchi Cheng
137 11 Anchi Cheng
* A skeleton (default) configuration file is available:
138 1 Amber Herold
139 11 Anchi Cheng
 <pre> C:\Python25\Lib\site-packages\Leginon\config\default.cfg</pre>
140 1 Amber Herold
141
142 11 Anchi Cheng
h2.  Configure sinedon.cfg:
143 1 Amber Herold
144 11 Anchi Cheng
Follow instruction in [[Configure sinedon.cfg]] in
145
the section for Linux installation but note the location of the configuration files
146
follows.
147 1 Amber Herold
148
149 11 Anchi Cheng
 * For all users, put sinedon.cfg with the installed package as
150
 <pre>C:\Python25\Lib\site-packages\sinedon\sinedon.cfg</pre>
151 1 Amber Herold
152
153 11 Anchi Cheng
 * Your home directory on Windows:
154
 <pre>C:\Documents and Settings\your_name></pre>
155 1 Amber Herold
156
157 11 Anchi Cheng
 * the skeleton sinedon configuration file is
158
 <pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre>
159 1 Amber Herold
160
h2. Modify instruments.cfg:
161
162
* Modify the file instruments.cfg in the installed pyScope directory to that for
163
your microscope and camera. For example, if your microscope uses Tecnai Scripting
164
Interface and you have a Gatan camera that you interface through DigitalMicrograph:
165
166
<pre>[tem]
167 10 Anchi Cheng
class: tecnai.Tecnai
168
[camera]
169
class: gatan.Gatan</pre>
170
171
The file contains other examples of microscope and camera drivers that we distribute from NRAMM.
172
173
h2. Run updatecom.py
174
175 1 Amber Herold
From a command line window:
176 10 Anchi Cheng
177
<pre>cd C:\python25\Lib\Site-Packages\pyScope
178
C:\python25\python.exe updatecom.py</pre>
179 1 Amber Herold
180
The python window appears should say show the required type libraries it found:
181
<pre>
182 10 Anchi Cheng
Generating .py files from type libraries...
183 1 Amber Herold
initializing TEM Scripting Error, cannot find typelib for "TEM Scripting"
184
initializing Tecnai Scripting done.
185
initializing TOM Moniker done.
186
initializing Tecnai Low Dose Kit done.
187
initializing Tecnai Exposure Adaptor done.
188
189
initializing Tietz CCD Camera done.
190
</pre>
191
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".
192
193
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
194
195
196
h2. Additional setup on Tietz PXL camera (optional)
197
198
199
The actual Tietz PXL camera dimension is slightly larger than 2048 x 2048. If you'd like
200
to take the images using the maximum of 2048 x 2048 pixels, you may modify the function that
201
get camera dimension in tietz.py of pyScope package.
202
203
204
*  Go to C:\Python25\Lib\site-packages\pyScope\
205
206
207
*  Edit tietz.py with a plain text editor
208
209
210
*  Find the lines:
211
212
<pre> def getCameraSize(self):
213
# {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}}
214
x = self._getParameterValue('cpTotalDimensionX')
215
y = self._getParameterValue('cpTotalDimensionY')
216
return {'x': x, 'y': y}
217
</pre>
218
219
*  Change the last line to:
220
221 11 Anchi Cheng
<pre>    return {'x': 2048, 'y': 2048}</pre>
222 1 Amber Herold
223 11 Anchi Cheng
h2.  Create Leginon and Leginon Client shortcut in Start menu menu under Leginon
224 1 Amber Herold
225
226 11 Anchi Cheng
This instruction applies to Windows XP.
227 1 Amber Herold
228
229 11 Anchi Cheng
 * Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new
230
folder named Leginon.
231 1 Amber Herold
232 11 Anchi Cheng
233
 * In another window, go to
234
 <pre>C:\Python25\Lib\site-packages\leginon</pre>
235
236
237
 * Create a shortcut from start-leginon.py as Leginon and a shortcut from launcher.py as Leginon Client.
238
239
240
 * Move the two shortcuts into
241
 <pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre>
242
243
244
245
h2.  Mapping Drives:
246
247
If you plan to run Leginon directly on the Windows machine, and your data files are served through a Samba server on a Linux machine, 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/.
248
249
*  Start, My Computer
250
251
252
*  Tools menu, Map network drive
253
254
255
*  Use an unmapped drive such as Z:
256
257
 Enter shared path in Windows format
258
as
259
 <pre>\\your_smbserver\your_share_point</pre>
260
261
262
*  Add the drive and the Linux path to leginon.cfg on the Windows machine
263
as
264
 <pre>[Drive Mapping]
265
Z:/your_data_path</pre>
266
267
268
*  Add image path to leginon.cfg on the Windows machine in Linux format
269
as
270
 <pre>[Images]
271
path:/your_data_path/leginon</pre>
272
273
274
h2.  Additional Software (Optional):
275
276 3 Amber Herold
TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room
277
just to open the column valves.
278
279 1 Amber Herold
280
______
281
282 11 Anchi Cheng
[[Linux Installation|< Linux Installation]] | [[Next Steps|Next Steps >]]
283 1 Amber Herold
284
285
______