Installation on the microscope computer » History » Version 17
Anchi Cheng, 05/28/2010 05:44 PM
1 | 11 | Anchi Cheng | h1. Installation on the microscope computer |
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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 | 12 | Anchi Cheng | h3. Python and Support Packages (Note that python 2.5 must be used): |
8 | 1 | Amber Herold | |
9 | 13 | Anchi Cheng | This list does not include pyton XML module because it is included in the python package for window. |
10 | 11 | Anchi Cheng | |
11 | |Python 2.5*| "http://www.python.org":http://www.python.org| |
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12 | |Python for Windows extension (pywin32)| "http://sourceforge.net/projects/pywin32/":http://sourceforge.net/projects/pywin32/| |
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13 | |wxPython 2.5.2.8 or newer| "http://www.wxpython.org":http://www.wxpython.org| |
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14 | |MySQL Python client 1.2 or newer| "http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python| |
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15 | |Python Imaging Library (PIL) 1.1.4 or newer| "http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/| |
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16 | |NumPy 1.0b5 (tested, others may work)| "http://www.scipy.org":http://www.scipy.org| |
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17 | 1 | Amber Herold | |SciPy 0.5.1 or newer| "http://www.scipy.org":http://www.scipy.org| |
18 | |||
19 | 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. |
20 | |||
21 | h3. SVN client used for check out from our repository |
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22 | |||
23 | This required for following this instruction. We have used Tortois SVN client. Alternatively, you may copy the required NRAMM source files from another computer. |
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24 | |||
25 | |_.Name:|_.Download site:| |
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26 | 11 | Anchi Cheng | |Tortoise SVN client| "http://tortoisesvn.tigris.org":http://tortoisesvn.tigris.org| |
27 | |||
28 | 1 | Amber Herold | |
29 | 11 | Anchi Cheng | h3. Required supporting programs for the CCD camera from camera makers |
30 | 1 | Amber Herold | |
31 | Install and register the following programs for CCD cameras from the two makes: |
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32 | |||
33 | |_.Camera Make:|_.File:| |
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34 | | Gatan|TecnaiCCD.dll| |
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35 | 11 | Anchi Cheng | | Tietz|CAMC4.exe*| |
36 | 1 | Amber Herold | |
37 | 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 |
38 | 1 | Amber Herold | |
39 | 11 | Anchi Cheng | h3. Supporting programs for film exposure |
40 | |||
41 | 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. |
42 | 11 | Anchi Cheng | |
43 | |_.Name:|_.File:| |
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44 | 1 | Amber Herold | | exposure adaptor|adaexp.exe| |
45 | |||
46 | h3. Packages required from NRAMM |
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47 | 11 | Anchi Cheng | |
48 | 1 | Amber Herold | h4. These are the sub-packages you will install with the python installer. |
49 | 11 | Anchi Cheng | |
50 | 1 | Amber Herold | |_.Name:|_.Purpose:| |
51 | 11 | Anchi Cheng | | leginon|modular TEM image acquisition| |
52 | | pyami|general functions| |
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53 | | sinedon|Leginon/database interaction| |
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54 | | pyscope|microscope control and monitoring| |
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55 | | imageviewer|image viewing for tomography| |
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56 | |||
57 | 13 | Anchi Cheng | *For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package need to be install with python |
58 | 1 | Amber Herold | |
59 | |||
60 | 17 | Anchi Cheng | Because numextension and libcv requires extra compilers, we have created window installer for them for python 2.5 and made them available at http://emg.nysbc.org/projects/leginon/files. |
61 | 11 | Anchi Cheng | |
62 | 1 | Amber Herold | h4. These are the Leginon v2.0 python 2.5 compiled packages installed through python installer on Windows. |
63 | |||
64 | 17 | Anchi Cheng | |_.Downloadfile Name|_.Purpose:| |
65 | |numextension-2.0.0.win32-py2.5.exe|c extension for numerical processing| |
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66 | |comarray-2.0.0.win32-py2.5.exe|com module output conversion to array| |
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67 | |libCV-0.2.win32-py2.5.exe|small c library of algorithm from computer vision field| |
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68 | 11 | Anchi Cheng | |
69 | 1 | Amber Herold | h2. Installation |
70 | 11 | Anchi Cheng | |
71 | 1 | Amber Herold | h3. Install Python and supporting packages with their installer |
72 | 11 | Anchi Cheng | |
73 | 1 | Amber Herold | Excute the installer files and follow the instruction. |
74 | 11 | Anchi Cheng | |
75 | 12 | Anchi Cheng | |
76 | 17 | Anchi Cheng | h3. Install the two Window Installer Files from Leginon website http://emg.nysbc.org/projects/leginon/files |
77 | 1 | Amber Herold | |
78 | 11 | Anchi Cheng | Excute the installer files and follow the instruction. |
79 | 1 | Amber Herold | |
80 | 11 | Anchi Cheng | h3. Check out SVN Source Files from the depository |
81 | 1 | Amber Herold | |
82 | 11 | Anchi Cheng | Use your mouse to do the following |
83 | * Create Leginon2.0 directory somewhere at your convenience |
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84 | 1 | Amber Herold | |
85 | * Change directory into Leginon2.0 |
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86 | |||
87 | * Right-click the mouse botton in this directory window and select Tortoise svn |
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88 | Checkout in the menu: |
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89 | !http://emg.nysbc.org/software/leginon/images/images/svnmenu.png! |
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90 | 11 | Anchi Cheng | |
91 | 1 | Amber Herold | |
92 | * Set up svn checkout window like this to check out from http://emg.nysbc.org/svn/myami/trunk to Leginon2.0 |
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93 | 11 | Anchi Cheng | !http://emg.nysbc.org/software/leginon/images/images/svnco.png! |
94 | |||
95 | |||
96 | 1 | Amber Herold | h3. Install the packages you downloaded from NRAMM svn depository |
97 | |||
98 | 11 | Anchi Cheng | * Start a command line Window from Start Menu |
99 | 1 | Amber Herold | |
100 | 11 | Anchi Cheng | * Install the package in each folder with commands such as |
101 | 1 | Amber Herold | <pre>cd Your_Download_Place\Leginon2.0\leginon |
102 | 11 | Anchi Cheng | c:\\python25\python.exe setup.py install</pre> |
103 | |||
104 | 12 | Anchi Cheng | h4. Register TecnaiCCD.dll, CAMC4.exe, and adaexep.exe |
105 | |||
106 | * For example, from the command prompt: |
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107 | <pre>adaexp.exe /regserver</pre> |
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108 | |||
109 | 11 | Anchi Cheng | h2. Configure leginon.cfg: |
110 | |||
111 | 12 | 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 above. |
112 | 1 | Amber Herold | |
113 | * Configurations for all users |
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114 | 11 | Anchi Cheng | |
115 | 1 | Amber Herold | <pre> <Python directory>\Lib\site-packages\Leginon\config\leginon.cfg</pre> |
116 | 11 | Anchi Cheng | |
117 | 1 | Amber Herold | Example: |
118 | 11 | Anchi Cheng | <pre> C:\Python25\Lib\site-packages\Leginon\config\leginon.cfg</pre> |
119 | |||
120 | 1 | Amber Herold | |
121 | 11 | Anchi Cheng | * Configurations for individual users |
122 | 1 | Amber Herold | |
123 | 11 | Anchi Cheng | <pre> <Home directory>\leginon.cfg</pre> |
124 | |||
125 | 1 | Amber Herold | Example: |
126 | <pre> C:\Documents and Settings\Leginon User\leginon.cfg </pre> |
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127 | 10 | Anchi Cheng | |
128 | 11 | Anchi Cheng | |
129 | 1 | Amber Herold | * A skeleton (default) configuration file is available: |
130 | 11 | Anchi Cheng | |
131 | 1 | Amber Herold | <pre> C:\Python25\Lib\site-packages\Leginon\config\default.cfg</pre> |
132 | |||
133 | 11 | Anchi Cheng | |
134 | h2. Configure sinedon.cfg: |
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135 | 1 | Amber Herold | |
136 | 12 | Anchi Cheng | Follow instruction in [[Configure sinedon.cfg]] in the section for Linux installation but note the location of the configuration files follows. |
137 | 11 | Anchi Cheng | |
138 | |||
139 | 1 | Amber Herold | * For all users, put sinedon.cfg with the installed package as |
140 | <pre>C:\Python25\Lib\site-packages\sinedon\sinedon.cfg</pre> |
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141 | 11 | Anchi Cheng | |
142 | |||
143 | 1 | Amber Herold | * Your home directory on Windows: |
144 | <pre>C:\Documents and Settings\your_name></pre> |
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145 | 11 | Anchi Cheng | |
146 | |||
147 | 1 | Amber Herold | * the skeleton sinedon configuration file is |
148 | <pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre> |
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149 | |||
150 | h2. Modify instruments.cfg: |
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151 | |||
152 | 16 | Anchi Cheng | * The file is in the installed pyscope directory |
153 | |||
154 | * Remove the Sim Tem and Sim Cam modules in the configuration. |
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155 | |||
156 | * Add the modules for your microscope and camera. For example, if your microscope uses Tecnai Scripting Interface and you have a Gatan camera that you interface through DigitalMicrograph: |
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157 | 1 | Amber Herold | |
158 | <pre>[tem] |
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159 | 10 | Anchi Cheng | class: tecnai.Tecnai |
160 | [camera] |
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161 | class: gatan.Gatan</pre> |
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162 | 1 | Amber Herold | |
163 | 10 | Anchi Cheng | The file contains other examples of microscope and camera drivers that we distribute from NRAMM. |
164 | |||
165 | h2. Run updatecom.py |
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166 | |||
167 | From a command line window: |
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168 | 1 | Amber Herold | |
169 | 10 | Anchi Cheng | <pre>cd C:\python25\Lib\Site-Packages\pyScope |
170 | C:\python25\python.exe updatecom.py</pre> |
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171 | |||
172 | The python window appears should say show the required type libraries it found: |
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173 | 1 | Amber Herold | <pre> |
174 | Generating .py files from type libraries... |
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175 | initializing TEM Scripting Error, cannot find typelib for "TEM Scripting" |
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176 | initializing Tecnai Scripting done. |
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177 | initializing TOM Moniker done. |
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178 | initializing Tecnai Low Dose Kit done. |
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179 | initializing Tecnai Exposure Adaptor done. |
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180 | |||
181 | initializing Tietz CCD Camera done. |
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182 | </pre> |
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183 | 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". |
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184 | |||
185 | 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 |
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186 | |||
187 | |||
188 | h2. Additional setup on Tietz PXL camera (optional) |
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189 | |||
190 | |||
191 | 12 | Anchi Cheng | The actual Tietz PXL camera dimension is slightly larger than 2048 x 2048. If you'd like to take the images using the maximum of 2048 x 2048 pixels, you may modify the function that get camera dimension in tietz.py of pyScope package. |
192 | 1 | Amber Herold | |
193 | |||
194 | * Go to C:\Python25\Lib\site-packages\pyScope\ |
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195 | |||
196 | |||
197 | * Edit tietz.py with a plain text editor |
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198 | |||
199 | |||
200 | * Find the lines: |
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201 | |||
202 | <pre> def getCameraSize(self): |
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203 | # {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}} |
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204 | x = self._getParameterValue('cpTotalDimensionX') |
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205 | y = self._getParameterValue('cpTotalDimensionY') |
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206 | return {'x': x, 'y': y} |
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207 | </pre> |
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208 | |||
209 | * Change the last line to: |
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210 | |||
211 | 11 | Anchi Cheng | <pre> return {'x': 2048, 'y': 2048}</pre> |
212 | 1 | Amber Herold | |
213 | 11 | Anchi Cheng | h2. Create Leginon and Leginon Client shortcut in Start menu menu under Leginon |
214 | 1 | Amber Herold | |
215 | |||
216 | This instruction applies to Windows XP. |
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217 | 11 | Anchi Cheng | |
218 | 1 | Amber Herold | |
219 | * Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new |
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220 | folder named Leginon. |
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221 | 11 | Anchi Cheng | |
222 | |||
223 | 1 | Amber Herold | * In another window, go to |
224 | <pre>C:\Python25\Lib\site-packages\leginon</pre> |
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225 | 11 | Anchi Cheng | |
226 | |||
227 | * Create a shortcut from start-leginon.py as Leginon and a shortcut from launcher.py as Leginon Client. |
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228 | |||
229 | 1 | Amber Herold | |
230 | 11 | Anchi Cheng | * Move the two shortcuts into |
231 | <pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre> |
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232 | |||
233 | |||
234 | |||
235 | h2. Mapping Drives: |
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236 | |||
237 | 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/. |
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238 | |||
239 | * Start, My Computer |
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240 | |||
241 | |||
242 | * Tools menu, Map network drive |
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243 | |||
244 | |||
245 | * Use an unmapped drive such as Z: |
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246 | |||
247 | 12 | Anchi Cheng | Enter shared path in Windows format as |
248 | 11 | Anchi Cheng | <pre>\\your_smbserver\your_share_point</pre> |
249 | |||
250 | |||
251 | 12 | Anchi Cheng | * Add the drive and the Linux path to leginon.cfg on the Windows machine as |
252 | 11 | Anchi Cheng | <pre>[Drive Mapping] |
253 | Z:/your_data_path</pre> |
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254 | |||
255 | |||
256 | 12 | Anchi Cheng | * Add image path to leginon.cfg on the Windows machine in Linux format as |
257 | 11 | Anchi Cheng | <pre>[Images] |
258 | path:/your_data_path/leginon</pre> |
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259 | |||
260 | |||
261 | h2. Additional Software (Optional): |
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262 | 3 | Amber Herold | |
263 | 12 | Anchi Cheng | TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room just to open the column valves. |
264 | 1 | Amber Herold | |
265 | 3 | Amber Herold | |
266 | 1 | Amber Herold | ______ |
267 | |||
268 | 15 | Anchi Cheng | [[Web Server Installation|< Web Server Installation]] | [[Steps involved in the installation| Steps needed for Installation Using Database Administration Tools >]] |
269 | 1 | Amber Herold | |
270 | |||
271 | ______ |