Comments (14)
hi @cbin-cnl , did the problem of opening a file get solved on your end?
Do you get any specific error when trying to save a new file? If yes, can you copy the error track (printed in the terminal)?
from ecogvis.
Hi Luiz,
Yes I can open the file and add channels, but the gui crashes once I try to save. The error message is below:
Traceback (most recent call last): File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/ecogvis-1.0.1-py3.6.egg/ecogvis/ecogvis.py", line 530, in save_badchannel self.model.BadChannelSave() File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/ecogvis-1.0.1-py3.6.egg/ecogvis/functions/subFunctions.py", line 748, in BadChannelSave self.nwb.electrodes['bad'].data[indices] = aux File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/hdmf/common/table.py", line 504, in __getitem__ raise KeyError(key) KeyError: 'bad'
from ecogvis.
thanks for the report! I'll check it
from ecogvis.
@cbin-cnl it seems like you're not using the most updated code, could you please try installing the current repo version of EcogVIS in your working environment?
$ pip uninstall ecogvis
$ git clone https://github.com/catalystneuro/ecogVIS.git
$ cd ecogVIS
$ pip install .
I couldn't reproduce the error locally, this is probably because of some changes in ecogvis that were not published to pypi yet. If it's not urgent, you can also wait a couple of days max and I'll be releasing a new version, so you can upgrade through pip.
from ecogvis.
Hi Luiz, thanks for the quick response.
Unfortunately updating the code did not work, I still get the following error:
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/ecogvis/ecogvis.py", line 530, in save_badchannel
self.model.BadChannelSave()
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/ecogvis/functions/subFunctions.py", line 744, in BadChannelSave
self.nwb.electrodes['bad'].data[:] = aux
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/hdmf/common/table.py", line 504, in __getitem__
raise KeyError(key)
KeyError: 'bad'
To clarify, I can open the file fine, but cannot save the channels unless the NWB file already has a "bad" electrodes column.
Thanks again
from ecogvis.
of course, I can see it now
I'll put a fix for this in the current PR and let you know once it's merged!
from ecogvis.
Great thanks so much!
from ecogvis.
@cbin-cnl it took a bit, sorry, the merge is in place.
could you please confirm this solved the problem on your end?
from ecogvis.
Hi Luiz,
Unfortunately it still looks like there is a problem with adding a column to an existing Electrode table. I'm getting the following error:
self.model.BadChannelSave()
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/ecogvis-1.1.0-py3.6.egg/ecogvis/functions/subFunctions.py", line 765, in BadChannelSave
data=aux,
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/hdmf/utils.py", line 483, in func_call
return func(args[0], **parsed['args'])
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/pynwb/file.py", line 494, in add_electrode_column
call_docval_func(self.electrodes.add_column, kwargs)
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/hdmf/utils.py", line 364, in call_docval_func
return func(*fargs, **fkwargs)
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/hdmf/utils.py", line 483, in func_call
return func(args[0], **parsed['args'])
File "/home/cbin-user/tdt2nwb/ecogvis/lib/python3.6/site-packages/hdmf/common/table.py", line 462, in add_column
raise ValueError("column must have the same number of rows as 'id'")
ValueError: column must have the same number of rows as 'id'
Aborted (core dumped)
However, I think I can just ensure I have a "bad" channels column in my electrode table. Thank you.
from ecogvis.
I'll get this fix, thanks for reporting it
from ecogvis.
@cbin-cnl I managed to reproduce your error now
is it the case that your electricalseries is mapped to a subset of electrodes smaller than the total number of electrodes? Just to make sure we found the same problem
I'll fix it
from ecogvis.
Thanks Luiz, sorry just looking at this now. Thanks for making the change. Just wanted to check, the "save bad channels" button has been removed? Is the intention to just save a new NWB file with the bad channel annotation?
from ecogvis.
@cbin-cnl that's correct. Do you have the specific need of saving it in the same file?
from ecogvis.
Hi Luiz, no, that should be fine, just wanted to make sure that was the intention.
from ecogvis.
Related Issues (20)
- test_processing_data doesn't test preprocessing HOT 1
- add Hierarchical Behavioral Data view
- Remove misleading messages
- Spectral decomposition and high gamma duplicate code and processing
- Unnecessary package? HOT 1
- Packages missing from setup.py
- error when not selecting file HOT 1
- update survey to include nans HOT 2
- Running spectral decomposition twice crashes GUI HOT 1
- How to load HTK data? HOT 2
- feature request: write gridOrient file HOT 3
- Take out the check for 'speaker1' or 'speaker2' when opening the Audio Event Detection gui
- loading error HOT 1
- HierarchicalBehavioralTable is dropped by nwb_copy_file
- Save file name not the same as load file name
- Error after loading the processed file
- Upgrade to pynwb>=2.0.0
- Load different acquisitions
- Option to delete/remove/overwrite (CV Event) intervals HOT 2
- Notch filtering operates on the channels dimension rather than the time dimension HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ecogvis.