Installation on the microscope computer » History » Version 36
Anchi Cheng, 02/02/2011 10:55 AM
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 | 21 | Anchi Cheng | h1. Package requirement |
6 | 1 | Amber Herold | |
7 | 21 | Anchi Cheng | h2. Python and Support Packages (Note that python 2.5 must be used): |
8 | 1 | Amber Herold | |
9 | 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: |
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. |
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21 | 21 | Anchi Cheng | h2. SVN client used for check out from our repository |
22 | 12 | Anchi Cheng | |
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 | 21 | Anchi Cheng | h2. Required supporting programs for the CCD camera from camera makers |
30 | 1 | Amber Herold | |
31 | 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: |
32 | 1 | Amber Herold | |
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 | 21 | Anchi Cheng | h2. Supporting programs for film exposure |
40 | 11 | Anchi Cheng | |
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 | 21 | Anchi Cheng | h2. Packages required from NRAMM |
47 | 11 | Anchi Cheng | |
48 | 25 | Jim Pulokas | h3. These are the sub-packages of myami that 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 | 25 | Jim Pulokas | *For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package needs to be install with python |
58 | 1 | Amber Herold | |
59 | |||
60 | 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. |
61 | 11 | Anchi Cheng | |
62 | 21 | Anchi Cheng | h3. These are the Leginon v2.0 python 2.5 compiled packages installed through python installer on Windows. |
63 | 1 | Amber Herold | |
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 | 21 | Anchi Cheng | h1. Installation |
70 | 11 | Anchi Cheng | |
71 | 21 | Anchi Cheng | h2. 1. Register TecnaiCCD.dll, CAMC4.exe, and adaexep.exe |
72 | 19 | Anchi Cheng | |
73 | 20 | Anchi Cheng | * For example, from the command prompt: |
74 | <pre>adaexp.exe /regserver</pre> |
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75 | 18 | Anchi Cheng | |
76 | 26 | Jim Pulokas | h2. Install Python and supporting packages with their installers |
77 | 11 | Anchi Cheng | |
78 | 26 | Jim Pulokas | Excute the installer files and follow the instructions. |
79 | 11 | Anchi Cheng | |
80 | 12 | Anchi Cheng | |
81 | 26 | Jim Pulokas | h2. 2. Install the Windows Installer Files from Leginon website http://emg.nysbc.org/projects/leginon/files |
82 | 1 | Amber Herold | |
83 | 26 | Jim Pulokas | Execute the installer files and follow the instructions. |
84 | 1 | Amber Herold | |
85 | 26 | Jim Pulokas | h2. 3. Check out SVN Source Files from the repository |
86 | 1 | Amber Herold | |
87 | 11 | Anchi Cheng | Use your mouse to do the following |
88 | * Create Leginon2.0 directory somewhere at your convenience |
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89 | 1 | Amber Herold | |
90 | * Change directory into Leginon2.0 |
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91 | |||
92 | * Right-click the mouse botton in this directory window and select Tortoise svn |
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93 | Checkout in the menu: |
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94 | !http://emg.nysbc.org/software/leginon/images/images/svnmenu.png! |
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95 | 11 | Anchi Cheng | |
96 | 1 | Amber Herold | |
97 | 23 | Anchi Cheng | * Set up svn checkout window like this to check out from http://emg.nysbc.org/svn/myami/branches/myami-2.0 to Leginon2.0 |
98 | 11 | Anchi Cheng | !http://emg.nysbc.org/software/leginon/images/images/svnco.png! |
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101 | 27 | Jim Pulokas | h2. 4. Install the packages you downloaded from NRAMM svn repository |
102 | 1 | Amber Herold | |
103 | 11 | Anchi Cheng | * Start a command line Window from Start Menu |
104 | 1 | Amber Herold | |
105 | 12 | Anchi Cheng | * Install the package in each folder with commands such as |
106 | <pre>cd Your_Download_Place\Leginon2.0\leginon |
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107 | c:\\python25\python.exe setup.py install</pre> |
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108 | 28 | Jim Pulokas | Then continue with the other packages, replacing leginon with the package name. |
109 | 12 | Anchi Cheng | |
110 | 33 | Jim Pulokas | h2. 5. Run updatecom.py |
111 | 1 | Amber Herold | |
112 | 33 | Jim Pulokas | From a command line window: |
113 | |||
114 | <pre>cd C:\python25\Lib\Site-Packages\pyScope |
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115 | C:\python25\python.exe updatecom.py</pre> |
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116 | |||
117 | The python window appears should say show the required type libraries it found: |
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118 | <pre> |
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119 | Generating .py files from type libraries... |
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120 | initializing TEM Scripting Error, cannot find typelib for "TEM Scripting" |
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121 | initializing Tecnai Scripting done. |
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122 | initializing TOM Moniker done. |
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123 | initializing Tecnai Low Dose Kit done. |
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124 | initializing Tecnai Exposure Adaptor done. |
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125 | |||
126 | initializing Tietz CCD Camera done. |
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127 | </pre> |
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128 | 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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129 | |||
130 | 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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131 | |||
132 | h2. 6. Configure leginon.cfg: |
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133 | |||
134 | 1 | Amber Herold | 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. |
135 | |||
136 | 11 | Anchi Cheng | * Configurations for all users |
137 | 1 | Amber Herold | |
138 | 11 | Anchi Cheng | <pre> <Python directory>\Lib\site-packages\Leginon\config\leginon.cfg</pre> |
139 | 1 | Amber Herold | |
140 | 11 | Anchi Cheng | Example: |
141 | <pre> C:\Python25\Lib\site-packages\Leginon\config\leginon.cfg</pre> |
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142 | 1 | Amber Herold | |
143 | 11 | Anchi Cheng | |
144 | 1 | Amber Herold | * Configurations for individual users |
145 | 11 | Anchi Cheng | |
146 | <pre> <Home directory>\leginon.cfg</pre> |
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147 | 1 | Amber Herold | |
148 | Example: |
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149 | 11 | Anchi Cheng | <pre> C:\Documents and Settings\Leginon User\leginon.cfg </pre> |
150 | 1 | Amber Herold | |
151 | 11 | Anchi Cheng | |
152 | 1 | Amber Herold | * A skeleton (default) configuration file is available: |
153 | |||
154 | 21 | Anchi Cheng | <pre> C:\Python25\Lib\site-packages\Leginon\config\default.cfg</pre> |
155 | 1 | Amber Herold | |
156 | |||
157 | 33 | Jim Pulokas | h2. 7. Configure sinedon.cfg: |
158 | 11 | Anchi Cheng | |
159 | Follow instruction in [[Configure sinedon.cfg]] in the section for Linux installation but note the location of the configuration files follows. |
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160 | 1 | Amber Herold | |
161 | 10 | Anchi Cheng | |
162 | * For all users, put sinedon.cfg with the installed package as |
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163 | 21 | Anchi Cheng | <pre>C:\Python25\Lib\site-packages\sinedon\sinedon.cfg</pre> |
164 | 10 | Anchi Cheng | |
165 | |||
166 | 1 | Amber Herold | * Your home directory on Windows: |
167 | 10 | Anchi Cheng | <pre>C:\Documents and Settings\your_name></pre> |
168 | |||
169 | |||
170 | 1 | Amber Herold | * the skeleton sinedon configuration file is |
171 | 10 | Anchi Cheng | <pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre> |
172 | 1 | Amber Herold | |
173 | 33 | Jim Pulokas | h2. 8. Configure instruments.cfg: |
174 | 1 | Amber Herold | |
175 | * A template for instruments.cfg is in the installed pyscope directory as "instruments.cfg.template". Copy it to "instruments.cfg". |
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176 | |||
177 | * Remove the Sim Tem and Sim Cam modules in the configuration. |
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178 | |||
179 | 33 | Jim Pulokas | * Add the modules for your microscope and camera. 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. For example, if your microscope uses Tecnai Scripting Interface and you have a Gatan camera that you interface through DigitalMicrograph: |
180 | 1 | Amber Herold | |
181 | <pre>[tem] |
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182 | class: tecnai.Tecnai |
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183 | [camera] |
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184 | class: gatan.Gatan</pre> |
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185 | |||
186 | The file contains other examples of microscope and camera drivers that we distribute from NRAMM. |
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187 | |||
188 | 29 | Jim Pulokas | h2. 9. Additional setup on Tietz cameras |
189 | 1 | Amber Herold | |
190 | 29 | Jim Pulokas | Register the Tietz ping callback function. From a command line window: |
191 | 1 | Amber Herold | |
192 | 29 | Jim Pulokas | <pre>cd C:\python25\Lib\Site-Packages\pyScope |
193 | C:\python25\python.exe tietzping.py</pre> |
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194 | 1 | Amber Herold | |
195 | 30 | Jim Pulokas | h2. 10. For strange dimension cameras |
196 | 1 | Amber Herold | |
197 | 36 | Anchi Cheng | {{include(strange dimension cameras)}} |
198 | 1 | Amber Herold | |
199 | 30 | Jim Pulokas | h2. 11. Create Leginon and Leginon Client shortcut in Start menu menu under Leginon |
200 | 1 | Amber Herold | |
201 | |||
202 | This instruction applies to Windows XP. |
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203 | 11 | Anchi Cheng | |
204 | 1 | Amber Herold | |
205 | * Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new |
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206 | folder named Leginon. |
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207 | 11 | Anchi Cheng | |
208 | |||
209 | 1 | Amber Herold | * In another window, go to |
210 | <pre>C:\Python25\Lib\site-packages\leginon</pre> |
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211 | 11 | Anchi Cheng | |
212 | |||
213 | * Create a shortcut from start-leginon.py as Leginon and a shortcut from launcher.py as Leginon Client. |
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214 | |||
215 | 1 | Amber Herold | |
216 | 11 | Anchi Cheng | * Move the two shortcuts into |
217 | <pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre> |
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218 | |||
219 | |||
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221 | 30 | Jim Pulokas | h2. 12. Mapping Drives (Optional): |
222 | 11 | Anchi Cheng | |
223 | 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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224 | |||
225 | * Start, My Computer |
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226 | |||
227 | |||
228 | * Tools menu, Map network drive |
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229 | |||
230 | |||
231 | * Use an unmapped drive such as Z: |
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232 | |||
233 | 12 | Anchi Cheng | Enter shared path in Windows format as |
234 | 11 | Anchi Cheng | <pre>\\your_smbserver\your_share_point</pre> |
235 | |||
236 | |||
237 | 12 | Anchi Cheng | * Add the drive and the Linux path to leginon.cfg on the Windows machine as |
238 | 11 | Anchi Cheng | <pre>[Drive Mapping] |
239 | Z:/your_data_path</pre> |
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240 | |||
241 | |||
242 | 12 | Anchi Cheng | * Add image path to leginon.cfg on the Windows machine in Linux format as |
243 | 11 | Anchi Cheng | <pre>[Images] |
244 | path:/your_data_path/leginon</pre> |
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245 | |||
246 | |||
247 | h2. Additional Software (Optional): |
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248 | 3 | Amber Herold | |
249 | 12 | Anchi Cheng | TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room just to open the column valves. |
250 | 1 | Amber Herold | |
251 | 3 | Amber Herold | |
252 | 1 | Amber Herold | ______ |
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254 | 15 | Anchi Cheng | [[Web Server Installation|< Web Server Installation]] | [[Steps involved in the installation| Steps needed for Installation Using Database Administration Tools >]] |
255 | 1 | Amber Herold | |
256 | |||
257 | ______ |