Installation on the microscope computer » History » Version 64
Anchi Cheng, 06/06/2012 08:26 PM
1 | 56 | Anchi Cheng | h1. Installation on the microscope computer for 2.2 |
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2 | 1 | Amber Herold | |
3 | 54 | Anchi Cheng | [[Installation on the microscope compute 2.1]] |
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5 | 11 | Anchi Cheng | Only processing-side of Leginon system is needed |
6 | 1 | Amber Herold | |
7 | 21 | Anchi Cheng | h1. Package requirement |
8 | 1 | Amber Herold | |
9 | 21 | Anchi Cheng | h2. Python and Support Packages (Note that python 2.5 must be used): |
10 | 1 | Amber Herold | |
11 | 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: |
12 | 11 | Anchi Cheng | |
13 | 38 | Anchi Cheng | |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/|| |
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15 | |wxPython 2.5.2.8 or newer| "http://www.wxpython.org":http://www.wxpython.org|| |
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16 | 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| |
17 | 38 | Anchi Cheng | |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|| |
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19 | |SciPy 0.5.1 or newer| "http://www.scipy.org":http://www.scipy.org|| |
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20 | 1 | Amber Herold | |
21 | 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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23 | 21 | Anchi Cheng | h2. SVN client used for check out from our repository |
24 | 12 | Anchi Cheng | |
25 | 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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26 | |||
27 | |_.Name:|_.Download site:| |
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28 | 11 | Anchi Cheng | |Tortoise SVN client| "http://tortoisesvn.tigris.org":http://tortoisesvn.tigris.org| |
29 | |||
30 | 1 | Amber Herold | |
31 | 21 | Anchi Cheng | h2. Required supporting programs for the CCD camera from camera makers |
32 | 1 | Amber Herold | |
33 | 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: |
34 | 1 | Amber Herold | |
35 | |_.Camera Make:|_.File:| |
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36 | | Gatan|TecnaiCCD.dll| |
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37 | | Tietz|CAMC4.exe*| |
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38 | 63 | Anchi Cheng | | DirectElectronDE12|DirectElectronAPI.exe| |
39 | 1 | Amber Herold | |
40 | 21 | Anchi Cheng | h2. Supporting programs for film exposure |
41 | 11 | Anchi Cheng | |
42 | 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. |
43 | 11 | Anchi Cheng | |
44 | |_.Name:|_.File:| |
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45 | 1 | Amber Herold | | exposure adaptor|adaexp.exe| |
46 | |||
47 | 21 | Anchi Cheng | h2. Packages required from NRAMM |
48 | 11 | Anchi Cheng | |
49 | 25 | Jim Pulokas | h3. These are the sub-packages of myami that you will install with the python installer. |
50 | 11 | Anchi Cheng | |
51 | 1 | Amber Herold | |_.Name:|_.Purpose:| |
52 | 11 | Anchi Cheng | | leginon|modular TEM image acquisition| |
53 | | pyami|general functions| |
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54 | | sinedon|Leginon/database interaction| |
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55 | | pyscope|microscope control and monitoring| |
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56 | | imageviewer|image viewing for tomography| |
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57 | |||
58 | 47 | Anchi Cheng | *For FEI Eagle Camera or Gatan Camera that uses TIA, comarray package needs to be install with python |
59 | 46 | Jim Pulokas | *[[Special Instructions for FEI Eagle Camera]] |
60 | 1 | Amber Herold | |
61 | 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. |
62 | 11 | Anchi Cheng | |
63 | 43 | Anchi Cheng | h3. These are the Leginon v2.0 python 2.5 compiled packages installed through python installer on Windows. Leginon v2.1 uses the same files. |
64 | 1 | Amber Herold | |
65 | 17 | Anchi Cheng | |_.Downloadfile Name|_.Purpose:| |
66 | |numextension-2.0.0.win32-py2.5.exe|c extension for numerical processing| |
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67 | 45 | Jim Pulokas | |comarray-2.0.0.win32-py2.5.exe|com module output conversion to array| |
68 | 17 | Anchi Cheng | |libCV-0.2.win32-py2.5.exe|small c library of algorithm from computer vision field| |
69 | 11 | Anchi Cheng | |
70 | 21 | Anchi Cheng | h1. Installation |
71 | 11 | Anchi Cheng | |
72 | 60 | Anchi Cheng | h2. Register TecnaiCCD.dll, CAMC4.exe (For Tietz camera), and adaexp.exe (For film exposure) |
73 | 1 | Amber Herold | |
74 | 59 | Jim Pulokas | * From the command prompt, run the following commands. You may need to enter the full path of the exe or dll: |
75 | 58 | Jim Pulokas | <pre>adaexp.exe /regserver |
76 | CAMC4.exe /regserver |
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77 | 59 | Jim Pulokas | REGSVR32 TecnaiCCD.dll</pre> |
78 | 18 | Anchi Cheng | |
79 | 26 | Jim Pulokas | h2. Install Python and supporting packages with their installers |
80 | 11 | Anchi Cheng | |
81 | 26 | Jim Pulokas | Excute the installer files and follow the instructions. |
82 | 11 | Anchi Cheng | |
83 | 12 | Anchi Cheng | |
84 | 60 | Anchi Cheng | h2. Install the Windows Installer Files from Leginon website http://emg.nysbc.org/projects/leginon/files |
85 | 1 | Amber Herold | |
86 | 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. |
87 | 1 | Amber Herold | |
88 | 60 | Anchi Cheng | h2. Check out SVN Source Files from the repository |
89 | 1 | Amber Herold | |
90 | 11 | Anchi Cheng | Use your mouse to do the following |
91 | 48 | Anchi Cheng | * Create Leginon2.1 directory somewhere at your convenience |
92 | 1 | Amber Herold | |
93 | 48 | Anchi Cheng | * Change directory into Leginon2.1 |
94 | 1 | Amber Herold | |
95 | * Right-click the mouse botton in this directory window and select Tortoise svn |
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96 | Checkout in the menu: |
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97 | !http://emg.nysbc.org/software/leginon/images/images/svnmenu.png! |
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98 | 11 | Anchi Cheng | |
99 | 1 | Amber Herold | |
100 | 48 | Anchi Cheng | * Set up svn checkout window like this to check out from http://emg.nysbc.org/svn/myami/branches/myami-2.1 to Leginon2.1 |
101 | 11 | Anchi Cheng | !http://emg.nysbc.org/software/leginon/images/images/svnco.png! |
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103 | |||
104 | 60 | Anchi Cheng | h2. Install the packages you downloaded from NRAMM svn repository |
105 | 1 | Amber Herold | |
106 | 11 | Anchi Cheng | * Start a command line Window from Start Menu |
107 | 1 | Amber Herold | |
108 | 12 | Anchi Cheng | * Install the package in each folder with commands such as |
109 | 48 | Anchi Cheng | <pre>cd Your_Download_Place\Leginon2.1\leginon |
110 | 12 | Anchi Cheng | c:\\python25\python.exe setup.py install</pre> |
111 | 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. |
112 | 12 | Anchi Cheng | |
113 | 60 | Anchi Cheng | h2. Run updatecom.py |
114 | 1 | Amber Herold | |
115 | 33 | Jim Pulokas | From a command line window: |
116 | |||
117 | <pre>cd C:\python25\Lib\Site-Packages\pyScope |
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118 | C:\python25\python.exe updatecom.py</pre> |
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119 | |||
120 | The python window appears should say show the required type libraries it found: |
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121 | <pre> |
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122 | Generating .py files from type libraries... |
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123 | initializing TEM Scripting Error, cannot find typelib for "TEM Scripting" |
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124 | initializing Tecnai Scripting done. |
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125 | initializing TOM Moniker done. |
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126 | initializing Tecnai Low Dose Kit done. |
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127 | initializing Tecnai Exposure Adaptor done. |
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128 | |||
129 | initializing Tietz CCD Camera done. |
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130 | </pre> |
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131 | 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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132 | |||
133 | 1 | Amber Herold | You will only find Tecnai Exposure Adaptor (Scripting for film exposure) if you ask FEI for it. |
134 | |||
135 | 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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137 | 64 | Anchi Cheng | {{include(locate global config directory on Windows)}} |
138 | 60 | Anchi Cheng | |
139 | h2. Configure leginon.cfg: |
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141 | 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. |
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143 | 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) |
144 | 55 | Anchi Cheng | |
145 | 61 | Anchi Cheng | <pre> <Global configuration directory>\leginon.cfg</pre> |
146 | 11 | Anchi Cheng | |
147 | 55 | Anchi Cheng | Example: |
148 | 61 | Anchi Cheng | <pre> C:\Programs\myami\leginon.cfg</pre> |
149 | 11 | Anchi Cheng | |
150 | 1 | Amber Herold | |
151 | 40 | Anchi Cheng | * The skeleton (default) configuration file is available at: |
152 | 55 | Anchi Cheng | |
153 | 1 | Amber Herold | <pre> C:\Python25\Lib\site-packages\leginon\leginon.cfg.template</pre> |
154 | |||
155 | 33 | Jim Pulokas | |
156 | 60 | Anchi Cheng | h2. Configure sinedon.cfg: |
157 | 11 | Anchi Cheng | |
158 | 1 | Amber Herold | Follow instruction in [[Configure sinedon.cfg]] in the section for Linux installation but note the location of the configuration files follows. |
159 | |||
160 | 10 | Anchi Cheng | |
161 | 61 | Anchi Cheng | * (Recommanded on microscope computer) For all users, put sinedon.cfg in the *global configuration directory* such as |
162 | <pre>C:\Programs\myami\sinedon.cfg</pre> |
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163 | 1 | Amber Herold | |
164 | * the skeleton sinedon configuration file is |
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165 | 10 | Anchi Cheng | <pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre> |
166 | 1 | Amber Herold | |
167 | h2. Configure instruments.cfg: |
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168 | |||
169 | 61 | Anchi Cheng | * A template for instruments.cfg is in the installed pyscope directory as "instruments.cfg.template". Copy it to |
170 | <pre>C:\Programs\myami\instruments.cfg</pre> |
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171 | 60 | Anchi Cheng | |
172 | 1 | Amber Herold | * Remove the Sim Tem and Sim Cam modules in the configuration. |
173 | |||
174 | 61 | Anchi Cheng | * Add the modules for your microscope and camera. |
175 | ** If you have Direct Electron camera DE12, your camera module.class is de.DE12 |
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176 | ** If your microscope uses Tecnai Scripting Interface, youe scope module.class is tecnai.Tecnai |
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177 | ** If you have a Gatan camera that you interface through DigitalMicrograph, your camera module.class is gatan.Gatan |
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178 | 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. |
179 | |||
180 | 55 | Anchi Cheng | {{include(instruments.cfg for 2.2)}} |
181 | 1 | Amber Herold | |
182 | The file contains other examples of microscope and camera drivers that we distribute from NRAMM. |
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183 | |||
184 | 60 | Anchi Cheng | h2. Additional setup on Tietz cameras |
185 | 1 | Amber Herold | |
186 | 42 | Anchi Cheng | Register the Tietz ping callback function. From a command line window: |
187 | 29 | Jim Pulokas | |
188 | 1 | Amber Herold | <pre>cd C:\python25\Lib\Site-Packages\pyscope |
189 | C:\python25\python.exe tietzping.py</pre> |
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190 | 57 | Jim Pulokas | |
191 | 1 | Amber Herold | Troubleshooting Tietz cameras: |
192 | 57 | Jim Pulokas | |
193 | 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. |
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194 | |||
195 | 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. |
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197 | 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. |
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199 | 60 | Anchi Cheng | h2. For strange dimension cameras |
200 | 1 | Amber Herold | |
201 | 36 | Anchi Cheng | {{include(strange dimension cameras)}} |
202 | 1 | Amber Herold | |
203 | 60 | Anchi Cheng | h2. Create Leginon Admin and Leginon Client shortcut in Start menu menu under Leginon |
204 | 1 | Amber Herold | |
205 | |||
206 | 11 | Anchi Cheng | This instruction applies to Windows XP. |
207 | 1 | Amber Herold | |
208 | |||
209 | * Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new |
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210 | 11 | Anchi Cheng | folder named Leginon. |
211 | |||
212 | 1 | Amber Herold | |
213 | * In another window, go to |
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214 | <pre>C:\Python25\Lib\site-packages\leginon</pre> |
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215 | 11 | Anchi Cheng | |
216 | |||
217 | 51 | Neil Voss | * Create a shortcut from start-leginon.py as "Leginon Admin" and a shortcut from launcher.py as "Leginon Client". |
218 | 11 | Anchi Cheng | |
219 | 1 | Amber Herold | |
220 | 11 | Anchi Cheng | * Move the two shortcuts into |
221 | <pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre> |
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225 | 60 | Anchi Cheng | h2. Mapping Drives (Optional): |
226 | 11 | Anchi Cheng | |
227 | 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/. |
228 | 11 | Anchi Cheng | |
229 | * Start, My Computer |
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230 | |||
231 | |||
232 | * Tools menu, Map network drive |
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233 | |||
234 | |||
235 | * Use an unmapped drive such as Z: |
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236 | |||
237 | 12 | Anchi Cheng | Enter shared path in Windows format as |
238 | 11 | Anchi Cheng | <pre>\\your_smbserver\your_share_point</pre> |
239 | |||
240 | |||
241 | 12 | Anchi Cheng | * Add the drive and the Linux path to leginon.cfg on the Windows machine as |
242 | 11 | Anchi Cheng | <pre>[Drive Mapping] |
243 | Z:/your_data_path</pre> |
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244 | |||
245 | |||
246 | 12 | Anchi Cheng | * Add image path to leginon.cfg on the Windows machine in Linux format as |
247 | 11 | Anchi Cheng | <pre>[Images] |
248 | path:/your_data_path/leginon</pre> |
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249 | |||
250 | |||
251 | h2. Additional Software (Optional): |
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252 | 3 | Amber Herold | |
253 | 12 | Anchi Cheng | TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room just to open the column valves. |
254 | 1 | Amber Herold | |
255 | 3 | Amber Herold | |
256 | 1 | Amber Herold | ______ |
257 | |||
258 | 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 >]] |
259 | 1 | Amber Herold | |
260 | |||
261 | ______ |