JEOL setup » History » Version 9
Neil Voss, 03/02/2012 12:17 PM
| 1 | 1 | Neil Voss | h1. JEOL setup |
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| 3 | 8 | Neil Voss | h2. more info |
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| 5 | http://cryoem.nysbc.org/CemRobotics.html |
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| 7 | 2 | Neil Voss | h2. instruments.cfg |
| 8 | 1 | Neil Voss | |
| 9 | <pre> |
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| 10 | [TEM] |
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| 11 | class: jeol1230.jeol1230 |
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| 12 | 2 | Neil Voss | </pre> |
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| 14 | h2. Testing pyscope instrument script functions |
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| 16 | 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: |
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| 18 | <pre> |
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| 19 | import pyscope.registry |
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| 20 | 6 | Neil Voss | s = pyscope.registry.getClass('jeol1230')() |
| 21 | 2 | Neil Voss | s.getMagnifications() |
| 22 | 1 | Neil Voss | </pre> |
| 23 | 3 | Neil Voss | |
| 24 | 4 | Neil Voss | h2. Potential problems |
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| 26 | 7 | Neil Voss | h3. import serial |
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| 28 | 3 | Neil Voss | <pre> |
| 29 | >>> import pyscope.registry |
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| 30 | Traceback (most recent call last): |
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| 31 | File "<stdin>", line 1, in <module> |
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| 32 | File "c:\Python25\Lib\site-packages\pyscope\registry.py", line 9, in <module> |
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| 33 | import config |
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| 34 | File "c:\Python25\Lib\site-packages\pyscope\config.py", line 39, in <module> |
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| 35 | mod = imp.load_module(fullmodname, *args) |
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| 36 | File "c:\Python25\Lib\site-packages\pyscope\jeol1230.py", line 8, in <module> |
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| 37 | from pyscope import jeol1230lib |
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| 38 | File "c:\Python25\Lib\site-packages\pyscope\jeol1230lib.py", line 8, in <module> |
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| 39 | import serial |
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| 40 | ImportError: No module named serial |
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| 41 | >>> |
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| 42 | </pre> |
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| 43 | 4 | Neil Voss | |
| 44 | 5 | Neil Voss | you need to install "Python Serial Port Extensions" http://pypi.python.org/pypi/pyserial |
| 45 | 7 | Neil Voss | |
| 46 | h3. defocus.cfg |
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| 47 | |||
| 48 | <pre> |
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| 49 | >>> import pyscope.registry |
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| 50 | >>> s = pyscope.registry.getClass('jeol1230')() |
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| 51 | Traceback (most recent call last): |
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| 52 | File "<stdin>", line 1, in <module> |
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| 53 | File "c:\Python25\Lib\site-packages\pyscope\jeol1230.py", line 27, in __init__ |
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| 54 | self.jeol1230lib = jeol1230lib.jeol1230lib() |
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| 55 | File "c:\Python25\Lib\site-packages\pyscope\jeol1230lib.py", line 25, in __init__ |
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| 56 | self.zeroDefocus = self.readZeroDefocus() |
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| 57 | 1 | Neil Voss | File "c:\Python25\Lib\site-packages\pyscope\jeol1230lib.py", line 35, in readZeroDefocus |
| 58 | infile = open(self.defocusFile,"r") |
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| 59 | IOError: [Errno 2] No such file or directory: 'C:\\Python25\\Lib\\site-packages\\pyScope\\defocus.cfg' |
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| 60 | 9 | Neil Voss | >>> |
| 61 | </pre> |
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| 62 | |||
| 63 | create an empty file called defocus.cfg |
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| 64 | |||
| 65 | h3. serial port permissions |
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| 66 | |||
| 67 | <pre> |
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| 68 | >>> import pyscope.registry |
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| 69 | >>> s = pyscope.registry.getClass('jeol1230')() |
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| 70 | Traceback (most recent call last): |
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| 71 | File "<stdin>", line 1, in <module> |
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| 72 | File "c:\python25\Lib\site-packages\pyscope\jeol1230.py", line 27, in __init__ |
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| 73 | self.jeol1230lib = jeol1230lib.jeol1230lib() |
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| 74 | File "c:\python25\Lib\site-packages\pyscope\jeol1230lib.py", line 25, in __init__ |
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| 75 | self.zeroDefocus = self.readZeroDefocus() |
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| 76 | File "c:\python25\Lib\site-packages\pyscope\jeol1230lib.py", line 37, in readZeroDefocus |
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| 77 | line = lines[0] |
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| 78 | IndexError: list index out of range |
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| 79 | 7 | Neil Voss | >>> |
| 80 | </pre> |