JEOL setup¶

more info¶

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

instruments.cfg¶

[TEM]
class: jeol1230.jeol1230

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:

import pyscope.registry
s = pyscope.registry.getClass('jeol1230')()
s.getMagnifications()

Potential problems¶

import serial¶

>>> 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
>>>

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

defocus.cfg¶

>>> 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'
>>>

create an empty file called defocus.cfg

serial port permissions¶

>>> 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
>>> s = pyscope.registry.getClass('jeol1230')()
close connection to JEOL1230 through COM1 port
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 18, in __init__
    self.ser = serial.Serial(port='COM1', baudrate=9600, bytesize=8, parity='N', stopbits=1, xonxoff = 0, timeout=10, rt
scts=0)
  File "serial\serialwin32.py", line 31, in __init__
    SerialBase.__init__(self, *args, **kwargs)
  File "serial\serialutil.py", line 261, in __init__
    self.open()
  File "serial\serialwin32.py", line 59, in open
    raise SerialException("could not open port %s: %s" % (self.portstr, ctypes.WinError()))
serial.serialutil.SerialException: could not open port COM1: [Error 5] Access is denied.
>>>