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JEOL setup » History » Revision 9

Revision 8 (Neil Voss, 03/02/2012 12:05 PM) → Revision 9/10 (Neil Voss, 03/02/2012 12:17 PM)

h1. JEOL setup 

 h2. more info 

 http://cryoem.nysbc.org/CemRobotics.html 

 h2. instruments.cfg 

 <pre> 
 [TEM] 
 class: jeol1230.jeol1230 
 </pre> 

 h2. Testing pyscope instrument script functions 

 On the instrument host of the instrument, a TEM host that uses Tecnai class, for example, you can launch python command line window and try to create an instance of the instrument and then call a function such as getMagnifications in that like this: 

 <pre> 
 import pyscope.registry 
 s = pyscope.registry.getClass('jeol1230')() 
 s.getMagnifications() 
 </pre> 

 h2. Potential problems 

 h3. import serial 

 <pre> 
 >>> import pyscope.registry 
 Traceback (most recent call last): 
   File "<stdin>", line 1, in <module> 
   File "c:\Python25\Lib\site-packages\pyscope\registry.py", line 9, in <module> 
     import config 
   File "c:\Python25\Lib\site-packages\pyscope\config.py", line 39, in <module> 
     mod = imp.load_module(fullmodname, *args) 
   File "c:\Python25\Lib\site-packages\pyscope\jeol1230.py", line 8, in <module> 
     from pyscope import jeol1230lib 
   File "c:\Python25\Lib\site-packages\pyscope\jeol1230lib.py", line 8, in <module> 
     import serial 
 ImportError: No module named serial 
 >>> 
 </pre> 

 you need to install "Python Serial Port Extensions" http://pypi.python.org/pypi/pyserial 

 h3. defocus.cfg 

 <pre> 
 C:\Python25>c:\Python25\python.exe 
 Python 2.5.4 (r254:67916, Dec 23 2008, 15:10:54) [MSC v.1310 32 bit (Intel)] on win32 
 Type "help", "copyright", "credits" or "license" for more information. 
 >>> import pyscope.registry 
 >>> s = pyscope.registry.getClass('jeol1230')() 
 Traceback (most recent call last): 
   File "<stdin>", line 1, in <module> 
   File "c:\Python25\Lib\site-packages\pyscope\jeol1230.py", line 27, in __init__ 
     self.jeol1230lib = jeol1230lib.jeol1230lib() 
   File "c:\Python25\Lib\site-packages\pyscope\jeol1230lib.py", line 25, in __init__ 
     self.zeroDefocus = self.readZeroDefocus() 
   File "c:\Python25\Lib\site-packages\pyscope\jeol1230lib.py", line 35, in readZeroDefocus 
     infile = open(self.defocusFile,"r") 
 IOError: [Errno 2] No such file or directory: 'C:\\Python25\\Lib\\site-packages\\pyScope\\defocus.cfg' 
 >>> 
 </pre> 

 create an empty file called defocus.cfg 

 h3. serial port permissions 

 <pre> 
 >>> import pyscope.registry 
 >>> s = pyscope.registry.getClass('jeol1230')() 
 Traceback (most recent call last): 
   File "<stdin>", line 1, in <module> 
   File "c:\python25\Lib\site-packages\pyscope\jeol1230.py", line 27, in __init__ 
     self.jeol1230lib = jeol1230lib.jeol1230lib() 
   File "c:\python25\Lib\site-packages\pyscope\jeol1230lib.py", line 25, in __init__ 
     self.zeroDefocus = self.readZeroDefocus() 
   File "c:\python25\Lib\site-packages\pyscope\jeol1230lib.py", line 37, in readZeroDefocus 
     line = lines[0] 
 IndexError: list index out of range 
 >>> 
 </pre>