I am trying to interface with an Ocean optics spectrometer using seabreeze (seabreeze) and pyseabreeze (pyseabreeze).
If I enter python from the command prompt (cmd) in windows and enter the following code line by line, it works. However, if I put it in a script (spec_test.py) and try running it from cmd.exe by using 'python spec_test.py', it will not work.
I have searched around a lot for similar problems but none seem to cover the issue I'm having. I am running Windows 7 64 bit, python 3.5.2 installed using anaconda. I also had to install pyusb and libusb to use pyseabreeze.
The code:
import seabreeze
seabreeze.use('pyseabreeze')
import seabreeze.spectrometers as sb
devs = sb.list_devices()
print(devs)
spec = sb.Spectrometer(devs[0])
print(spec.model)
and the error message I get:
[<SeaBreezeDevice USB2000PLUS:FLMS02379>]
Traceback (most recent call last):
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\seabreeze\pyseabreeze\interfaces\common.py", line 14, in decorated_func
return func(*args, **kwargs)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\seabreeze\pyseabreeze\interfaces\spectrometer.py", line 46, in open
self.open_device(device.handle)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\seabreeze\pyseabreeze\interfaces\communication.py", line 37, in open_device
device.set_configuration()
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\usb\core.py", line 869, in set_configuration
self._ctx.managed_set_configuration(self, configuration)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\usb\core.py", line 102, in wrapper
return f(self, *args, **kwargs)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\usb\core.py", line 148, in managed_set_configuration
self.backend.set_configuration(self.handle, cfg.bConfigurationValue)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\usb\backend\libusb0.py", line 493, in set_configuration
_check(_lib.usb_set_configuration(dev_handle, config_value))
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\usb\backend\libusb0.py", line 431, in _check
raise USBError(errmsg, ret)
usb.core.USBError: [Errno None] b'libusb0-dll:err [set_configuration] could not set config 1: win error: The parameter is incorrect.\r\n'
Traceback (most recent call last):
File "<ipython-input-9-ead886eb3666>", line 1, in <module>
runfile('C:/Users/Raman Lab/Python code/Spectrometers/spec_testing.py', wdir='C:/Users/Raman Lab/Python code/Spectrometers')
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 866, in runfile
execfile(filename, namespace)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/Raman Lab/Python code/Spectrometers/spec_testing.py", line 7, in <module>
spec = sb.Spectrometer(devs[0])
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\seabreeze\spectrometers.py", line 62, in __init__
self._open_device(device)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\seabreeze\spectrometers.py", line 90, in _open_device
lib.device_open(self._dev)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\seabreeze\pyseabreeze\wrapper.py", line 81, in device_open
return device.interface.open(device)
File "C:\Users\Raman Lab\AppData\Local\Continuum\Anaconda3\lib\site-packages\seabreeze\pyseabreeze\interfaces\common.py", line 23, in decorated_func
raise SeaBreezeError(msg)
SeaBreezeError: An error occured during opening.
Thanks for any help!
Edit:
For some reason I figured this out, thought it might help describe the issue. If I enter interactive python from cmd.exe and paste the code instead of typing it in manually, I get the same error. This makes me think (most likely I'm wrong) that it is somehow tied up with speed of imports. I tried adding a sleep for a few seconds in between lines 3 and 5, to simulate what happens when I am typing in the prompt, but that didn't help. I hope this was descriptive enough.
Your initial guess was not far off. I had exactly the same problem, however, on Windows 7 32bit with Python 2.7. The example code gchaks linked to was running fine.
When I tried executing the script several times in quick succession, the error message changed and pointed at a empty devices list. I added a delay of 2 seconds after
devs = sb.list_devices()
and that solved the problem. Your code was running just fine on a Linux machine btw.
Another hint: If your code should run once, but then you run into another error message, make sure you close the device connection or dis- and reconnect the spectrometer.
Related
I was trying to install some module (i.e. pandas_profiling) in SQL Server so I can run the script directly from there. I was utilizing a Microsoft tool called 'sqlmlutils' to achieve this, but it returned an error specifically when I tried to install pandas_profiling (in fact another library called 'text-tools' was successfully installed. Here is the Python script to install the module to SQL Server:
import sqlmlutils
connection = sqlmlutils.ConnectionInfo(server="localhost", database="SQLAI")
sqlmlutils.SQLPackageManager(connection).install("pandas-profiling")
Here is the traceback:
Traceback (most recent call last):
File "<ipython-input-2-e8db1d445900>", line 1, in <module>
runfile('C:/Users/BusinessUser/Desktop/abc.py', wdir='C:/Users/BusinessUser/Desktop')
File "C:\Users\BusinessUser\Anaconda3\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 827, in runfile
execfile(filename, namespace)
File "C:\Users\BusinessUser\Anaconda3\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 110, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/BusinessUser/Desktop/abc.py", line 3, in <module>
sqlmlutils.SQLPackageManager(connection).install("pandas_profiling")
File "C:\Users\BusinessUser\Anaconda3\lib\site-packages\sqlmlutils\packagemanagement\sqlpackagemanager.py", line 74, in install
self._install_from_pypi(package, upgrade, version, install_dependencies, scope, out_file=out_file)
File "C:\Users\BusinessUser\Anaconda3\lib\site-packages\sqlmlutils\packagemanagement\sqlpackagemanager.py", line 151, in _install_from_pypi
self._install_from_file(target_package_file, scope, upgrade, out_file=out_file)
File "C:\Users\BusinessUser\Anaconda3\lib\site-packages\sqlmlutils\packagemanagement\sqlpackagemanager.py", line 171, in _install_from_file
required_installs = resolver.get_required_installs(target_package_requirements)
File "C:\Users\BusinessUser\Anaconda3\lib\site-packages\sqlmlutils\packagemanagement\dependencyresolver.py", line 34, in get_required_installs
self._server_packages, requirement.name, spec)
File "C:\Users\BusinessUser\Anaconda3\lib\site-packages\sqlmlutils\packagemanagement\dependencyresolver.py", line 60, in _check_if_installed_package_meets_spec
return getattr(operator, operator_map[op_str])(LooseVersion(installed_version), LooseVersion(req_version))
File "C:\Users\BusinessUser\Anaconda3\lib\distutils\version.py", line 46, in __eq__
c = self._cmp(other)
File "C:\Users\BusinessUser\Anaconda3\lib\distutils\version.py", line 337, in _cmp
if self.version < other.version:
TypeError: '<' not supported between instances of 'int' and 'str'
I just want to ask if anyone has ever gotten the same error. Any help is much appreciated!
me too.
My solution is to uninstall and install it again.
I've just installed pychecker on windows 7 Pro using "python setup.py install". When I run it on my script using the command:
c:\Python26\Scripts\pychecker -#100 finaltest17.py
I get the following error/traceback:
C:\Users\....\ToBeReleased>C:\Python26\python.exe C:\Python26\Lib\site-packages\pychecker\checker.py -#100 finaltest17.py
Processing module finaltest17 (finaltest17.py)...
Caught exception importing module finaltest17:
File "C:\Python26\Lib\site-packages\pychecker\pcmodules.py", line 533, in setupMainCode()
self.moduleName, self.moduleDir)
File "C:\Python26\Lib\site-packages\pychecker\pychecker\utils.py", line 184, in findModule()
handle, filename, smt = _q_find_module(p, path)
File "C:\Python26\Lib\site-packages\pychecker\pychecker\utils.py", line 162, in _q_find_module()
if not cfg().quixote:
File "C:\Python26\Lib\site-packages\pychecker\pychecker\utils.py", line 39, in cfg()
return _cfg[-1]
IndexError: list index out of range
Traceback (most recent call last):
File "C:\Python26\Lib\site-packages\pychecker\checker.py", line 364, in <module>
sys.exit(main(sys.argv))
File "C:\Python26\Lib\site-packages\pychecker\checker.py", line 337, in main
importWarnings = processFiles(files, _cfg, _print_processing)
File "C:\Python26\Lib\site-packages\pychecker\checker.py", line 270, in processFiles
loaded = pcmodule.load()
File "C:\Python26\Lib\site-packages\pychecker\pcmodules.py", line 477, in load
return utils.cfg().ignoreImportErrors
File "C:\Python26\Lib\site-packages\pychecker\pychecker\utils.py", line 39, in cfg
return _cfg[-1]
IndexError: list index out of range
If anyone could point me in the right direction that would be great.
Thanks
Stewart
Problem resolved.
I found the following support request on SourceForge which refers to a need to use short format (8.3) path and filenames in pychecker.bat and not long format as is allowed in newer versions of Windows.
https://sourceforge.net/p/pychecker/support-requests/7/#96cb
When I run the following code: http://dpaste.com/0210P09 everything works fine on my Linux distro.
However, in Windows7 (64bit) I cannot successfully save it in eps or svg.
This is the error that I get:
Traceback (most recent call last):
File "<ipython-input-1-b8da411d11b0>", line 1, in <module>
runfile('C:/Users/12151056/Documents/Python Scripts/MyPython/1Tplot_2.py', wdir='C:/Users/12151056/Documents/Python Scripts/MyPython')
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 685, in runfile
execfile(filename, namespace)
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 85, in execfile
exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace)
File "C:/Users/12151056/Documents/Python Scripts/MyPython/1Tplot_2.py", line 67, in <module>
plt.savefig('excel-6.eps')
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\matplotlib\pyplot.py", line 577, in savefig
res = fig.savefig(*args, **kwargs)
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\matplotlib\figure.py", line 1476, in savefig
self.canvas.print_figure(*args, **kwargs)
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\matplotlib\backend_bases.py", line 2211, in print_figure
**kwargs)
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\matplotlib\backends\backend_ps.py", line 1009, in print_eps
return self._print_ps(outfile, 'eps', *args, **kwargs)
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\matplotlib\backends\backend_ps.py", line 1033, in _print_ps
**kwargs)
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\matplotlib\backends\backend_ps.py", line 1398, in _print_figure_tex
rotated=psfrag_rotated)
File "C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-packages\matplotlib\backends\backend_ps.py", line 1556, in gs_distill
your image.\nHere is the full report generated by ghostscript:\n\n' + fh.read())
TypeError: Can't convert 'bytes' object to str implicitly
If i use text.usetex : False I have no problem at all.
I have livetex full and Ghostscript installed.
Any suggestions to try and solve it?
There are two problems here. The first and minor one is that in
C:\Users\12151056\AppData\Local\Continuum\Anaconda3\lib\site-package\matplotlib\backends\backend_ps.py", line 1556
you should change
fh.read()
to
fh.read().decode()
This is a Python 2/3 bug, that occurs while handling the fact that something with Ghostscript went wrong.
The main problem is that matplotlib cannot find Ghostscript because it is not in the path environmental variable. You can check that by opening a command prompt and trying the command gswin32c or gs. If these commands are not found you have to add the path of these Ghostscript executables to the path environmental variable. In my case it was:
C:\Program Files (x86)\gs\gs8.54\bin
but it depends on your installation path.
I have an IPython notebook that I was running as multi-threaded and have changed over to try and run on multiple processors. There is a substantial amount of code that I won't quote here unless someone thinks it would be helpful to look at a specific portion of it. The gist of it is that I'm trying to wrap a load balancer around PyOpenCL so I need to feed multiple independent queues-- partly to solve a specific problem (particle simulation) and partly as a learning exercise.
At no point am I intentionally opening any files, yet it's crashing with this error:
Traceback (most recent call last):
File "//anaconda/lib/python3.4/site-packages/IPython/core/interactiveshell.py", line 3035, in run_code
File "<ipython-input-23-d29c87aba720>", line 1, in <module>
co.convergeStep(mags[3])
File "<ipython-input-17-0eac43f0bbbf>", line 62, in convergeStep
evt=self.nlb.qTask(evtList,(b,k),b.forces,k,out=b.forceAccum,out2=k.forceAccum,sum=True)
File "<ipython-input-13-0f26b8ae660e>", line 36, in qTask
t=StagingThread(waitlist,c,self.pool)
File "<ipython-input-10-549b980aea87>", line 7, in __init__
self.killme=mp.Event()
File "//anaconda/lib/python3.4/multiprocessing/context.py", line 91, in Event
File "//anaconda/lib/python3.4/multiprocessing/synchronize.py", line 336, in __init__
File "//anaconda/lib/python3.4/multiprocessing/context.py", line 76, in Condition
File "//anaconda/lib/python3.4/multiprocessing/synchronize.py", line 215, in __init__
File "//anaconda/lib/python3.4/multiprocessing/context.py", line 81, in Semaphore
File "//anaconda/lib/python3.4/multiprocessing/synchronize.py", line 127, in __init__
File "//anaconda/lib/python3.4/multiprocessing/synchronize.py", line 60, in
__init__ OSError: [Errno 24] Too many open files
Is there something opening files in the background that I'm not considering?
It looks like I have 11 processes spawned at the time of failure. I'm running under OS X 10.10.3, Python 3.4.3, IPython 3.1. I am not using multiprocessing.Pool (at least not intentionally). It looks like the failure is happening in Event? There are other exceptions that occur while handling this one, but they're mostly too many files errors and then some traceback failures and other things that look like they're a result of one of the above...
I am calling an R script file from python using pyrserve. I have rserve running. At arbitrary points in the R script, pyrserve gives an error and quits:
Traceback (most recent call last):
File "scriptV2.py", line 272, in <module>
rConn.eval("source(file.PropensityFlow)")
File "/Users/dipayanmaiti/Py3.3venv/lib/python3.3/site-packages/pyRserve/rconn.py", line 47, in decoCheckIfClosed
return func(self, *args, **kw)
File "/Users/dipayanmaiti/Py3.3venv/lib/python3.3/site-packages/pyRserve/rconn.py", line 119, in eval
return rparse(src, atomicArray=atomicArray)
File "/Users/dipayanmaiti/Py3.3venv/lib/python3.3/site-packages/pyRserve/rparser.py", line 539, in rparse
return rparser.parse()
File "/Users/dipayanmaiti/Py3.3venv/lib/python3.3/site-packages/pyRserve/rparser.py", line 349, in parse
self.lexer.readHeader()
File "/Users/dipayanmaiti/Py3.3venv/lib/python3.3/site-packages/pyRserve/rparser.py", line 94, in readHeader
self.responseCode = struct.unpack(b'<i', self.read(3) + b'\x00')[0]
File "/Users/dipayanmaiti/Py3.3venv/lib/python3.3/site-packages/pyRserve/rparser.py", line 149, in read
raise EndOfDataError()
pyRserve.rparser.EndOfDataError
I have set rserv.conf to the following:
maxinbuf 20000000
maxsendbuf 0
Does anybody know why this happens? This looks like some buffer problem, because the R script runs by itself.
It is a late answer, but in such situations it is useful to run Rserve in debug mode so its output can be monitored in a separate shell.
R CMD Rserve.dbg
In some rare cases I've seen Rserve printing warnings to the console, and when this happened the command sent thru pyRserve didn't return any value from Rserve - which led to the 'EndOfDataError' above.