jpgill86
commented
5 years ago Hi @pplenck, thanks for trying ephyviewer!
It sounds like you are having success with launching ephyviewer and loading your data into it, and the problem only arises when you close the window.
I don't use Spyder, and I haven't experienced this issue before with ephyviewer in the contexts I use it (standalone, neurotic, Jupyter notebooks). If I had more time, I'd try it in Spyder, but today I don't.
However, what you describe reminds me of something I reported for tridesclous in Jupyter notebooks (tridesclous/tridesclous#117). In that report I described how, after closing a tridesclous GUI window, control of the kernel was not returned to the notebook, and I was forced to restart the kernel.
That issue has not been completely solved, and since there are some similarities between tridesclous's and ephyviewer's use of Qt for GUI creation, I wonder if they might be linked.
In that other report, I suggested that a particular matplotlib backend might be the cause of the tridesclous hangup. ephyviewer doesn't have an analogous matplotlib backend setting, but maybe Spyder is automatically setting it to something that causes problems in that context?
It's a shot in the dark, but you could try running this at the very top of your script, before import matplotlib.pyplot as plt:
import matplotlib
matplotlib.use('Qt5agg') # I'm assuming you are using Qt5If that doesn't help, maybe a different backend would work.
Let me know if that makes any difference!
As for your other question:
source = InMemoryAnalogSignalSource(data, SF, T1) # why use a source by the way?
I presume you mean, "Why not use the RawIO reader directly as the TraceViewer's source?"
Firstly, you should check out AnalogSignalFromNeoRawIOSource and its cousins in neosource.py. I'm realizing now that they are not represented by the example for using Neo with ephyviewer, which showcases only some of ephyviewer's Neo integrations (non-raw objects, specifically). We'll have to remedy that (#73).
Secondly, to answer your question. ephyviewer doesn't strictly depend on Neo. I think @samuelgarcia designed it to be as lightweight as possible with few dependencies. The "InMemory" sources are intended for lightweight numpy arrays, to handle the simplest cases. If you are already using Neo, you probably want to try the sources provided in neosource.py.
pplenck
samuelgarcia
munrokrulle
Hi Guys thanks for this cool library, I am trying to use it throroughly and make my own viewer with it but it does not want to close properly when I run it and close the main window. I use Spyder and the commandline seems to try to "save_all_setting" and gets stuck there. here is my code:
import matplotlib.pyplot as plt from scipy import signal import numpy as np import ephyviewer from ephyviewer import mkQApp, MainViewer, TraceViewer, TimeFreqViewer from ephyviewer import InMemoryAnalogSignalSource
FilePth=(r"D:\SALOME\gad_cre_vir_hr2P8_Bis20190204\2019-02-04_18-16-17\Klusta") FileNm=r'2019-02-04_18-16-17.dat'
get to the folder
os.chdir(str(FilePth))
SF=30000
reader=RawBinarySignalRawIO (filename=FileNm, dtype=u'int16', sampling_rate=SF, nb_channel=32) reader.parse_header() print (reader) T1=0; Tend=200;
data=reader.get_analogsignal_chunk(i_start = T1, i_stop = Tend*SF) T=np.linspace(T1, Tend, len(data)) app = ephyviewer.mkQApp()
create a window
win = ephyviewer.MainViewer(debug=True, show_auto_scale = True)
source = InMemoryAnalogSignalSource(data, SF, T1) # why use a source by the way?
view1 = TraceViewer(source=source, name='trace')
Parameters can be set in script
view1.params['scale_mode'] = 'same_for_all' view1.params['display_labels'] = True
view1.params['color'] = '#FFFEED'
view1.auto_scale()
win.add_view(view1) win.show()
launch the app
app.exec_()