# on\_missing and time-frequency **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [October 1, 2014, 8:48am UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831 "2014-10-01T08:48:40Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 1, 2014, 8:48am UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/1 "2014-10-01T08:48:40Z")
Hello, 2 issues: 1. Using mne.Epochs with on\_missing='ignore' continues to return an error - and crashes the script. The error is returned irrespective of the argument I put in. It doesn't work in ipython or in spyder albeit others report it works in ipython but not in spyder. 2. I was giving a quick shot at TF analysis in sensor space using "tfr\_morlet" - although it runs fine, the returned power and itc are not in readable format or am I missing someting? e.g. "power.plot\_topo" is not recognized. This was run in spyder with updated mne-python. Any help appreciated! Best, -V ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 1, 2014, 10:58am UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/2 "2014-10-01T10:58:33Z")
Hi Virginie, 2014-10-01 10:48 GMT+02:00 Virginie van Wassenhove \< virginie.van.wassenhove at gmail.com\>: > Hello, > > 2 issues: > > 1. Using mne.Epochs with on\_missing='ignore' continues to return an error > - and crashes the script. thanks for reporting, we'll file a bug report and inquire. > The error is returned irrespective of the argument I put in. It doesn't > work in ipython or in spyder albeit others report it works in ipython but > not in spyder. > > 2. I was giving a quick shot at TF analysis in sensor space using > "tfr\_morlet" - although it runs fine, the returned power and itc are not in > readable format or am I missing someting? e.g. "power.plot\_topo" is not > recognized. This was run in spyder with updated mne-python. In which sense is the format not readable, how does this look like? What does it mean that "power.plot\_topo" is not recognized? -Denis > Any help appreciated! > > Best, > -V > > -- > Virginie van Wassenhove > Exec Dir NeuroSpin MEG > Group leader, Brain Dynamics > CEA.DSV.I2BM.NeuroSpin - INSERM Cognitive Neuroimaging Unit > B?t 145 Point Courrier 156 > Gif s/ Yvette F-91191 FRANCE > > +33(0)1.69.08.1667 > Virginie.van.Wassenhove at gmail.com > [https://sites.google.com/site/virginievanwassenhove/](https://sites.google.com/site/virginievanwassenhove/) > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20141001/f0fab1f9/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20141001/f0fab1f9/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 1, 2014, 11:06am UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/3 "2014-10-01T11:06:49Z")
One more thing. When you construct the Epochs with on\_missing='ignore' and you have a crash, how does the error message look like? Can you rule out that for some reason None of the events in your event\_id is found in the third column of `events`. In that case ignoring would not help. -D 2014-10-01 12:58 GMT+02:00 Denis-Alexander Engemann \< denis.engemann at gmail.com\>: > Hi Virginie, > > 2014-10-01 10:48 GMT+02:00 Virginie van Wassenhove \< > virginie.van.wassenhove at gmail.com\>: > > > Hello, > > > > 2 issues: > > > > 1. Using mne.Epochs with on\_missing='ignore' continues to return an error > > - and crashes the script. > > thanks for reporting, we'll file a bug report and inquire. > > > The error is returned irrespective of the argument I put in. It doesn't > > work in ipython or in spyder albeit others report it works in ipython but > > not in spyder. > > > > 2. I was giving a quick shot at TF analysis in sensor space using > > "tfr\_morlet" - although it runs fine, the returned power and itc are not in > > readable format or am I missing someting? e.g. "power.plot\_topo" is not > > recognized. This was run in spyder with updated mne-python. > > In which sense is the format not readable, how does this look like? > What does it mean that "power.plot\_topo" is not recognized? > > -Denis > > > Any help appreciated! > > > > Best, > > -V > > > > -- > > Virginie van Wassenhove > > Exec Dir NeuroSpin MEG > > Group leader, Brain Dynamics > > CEA.DSV.I2BM.NeuroSpin - INSERM Cognitive Neuroimaging Unit > > B?t 145 Point Courrier 156 > > Gif s/ Yvette F-91191 FRANCE > > > > +33(0)1.69.08.1667 > > Virginie.van.Wassenhove at gmail.com > > [https://sites.google.com/site/virginievanwassenhove/](https://sites.google.com/site/virginievanwassenhove/) > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Mne\_analysis mailing list > > Mne\_analysis at nmr.mgh.harvard.edu > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > The information in this e-mail is intended only for the person to whom it > > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > in error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20141001/422d3ba6/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20141001/422d3ba6/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 1, 2014, 12:01pm UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/4 "2014-10-01T12:01:02Z")
Yes, I know in advance that is in some conditions and in some runs, no events will be found which is the reason why I want to use the "ignore" option when that happens. Am I understanding this option incorrectly? What is the "on\_missing" referring to o.w.? the error message is : "ValueError: no desired events found." Thanks! V ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 1, 2014, 12:05pm UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/5 "2014-10-01T12:05:22Z")
> > 2. I was giving a quick shot at TF analysis in sensor space using > > "tfr\_morlet" - although it runs fine, the returned power and itc are not in > > readable format or am I missing someting? e.g. "power.plot\_topo" is not > > recognized. This was run in spyder with updated mne-python. > > In which sense is the format not readable, how does this look like? What does it mean that "power.plot\_topo" is not recognized? > I had to close that console, lost the 2 hours computations and I can't tell you the exact "format" value it was reporting when calling the apparently non-existent "power" variable despite having computed it for 2 hours. I'll try that again and be more specific. Is it possible that "power.\_getdata()" need to be used to actually load the results of tfr\_morlet in a spyder console? for "power.pot\_topo", I need to recompute and I'll tell you. Later, thanks! V ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 1, 2014, 12:18pm UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/6 "2014-10-01T12:18:42Z")
Hi Virginie 1. this is in fact an issue with the documentation, not a bug. The 'ignore' option will avoid crashes if one or many events are missing but at least one remains. If all events are missing nothing will be ignored, currently the constructor needs at east one event. We might want to rethink the semantics. Out of curiosity, what are you doing with epochs for which you know in advance that events and ids don't match? In other words, would there be a use case for the behavior you expected from 'ignore'? If it's just to avoid crashes when no event is found, I would manually check that and skip computations if nothing is found. For example (in a loop that iterates over datasets or subjects): if not np.any(np.in1d(event\_ids.values(), events[:, 2])):     continue 2. the second issue sounds mysterious to me, I don't `smell` what might be going on there. 2014-10-01 14:05 GMT+02:00 Virginie van Wassenhove \< virginie.van.wassenhove at gmail.com\>: > > > 2. I was giving a quick shot at TF analysis in sensor space using > > > "tfr\_morlet" - although it runs fine, the returned power and itc are not in > > > readable format or am I missing someting? e.g. "power.plot\_topo" is not > > > recognized. This was run in spyder with updated mne-python. > > > > In which sense is the format not readable, how does this look like? > > What does it mean that "power.plot\_topo" is not recognized? > > > > > I had to close that console, lost the 2 hours computations and I can't > tell you the exact "format" value it was reporting when calling the > apparently non-existent "power" variable despite having computed it for 2 > hours. I'll try that again and be more specific. So you imply that power = tfr\_morlet completed (after 2 hours?) but that `power` was not found? > Is it possible that "power.\_getdata()" need to be used to actually load > the results of tfr\_morlet in a spyder console? This should not be necessay, this one is private and should be ignored for regular usage. -Denis > for "power.pot\_topo", I need to recompute and I'll tell you. > > Later, thanks! > V > > > -Denis > > > > > Any help appreciated! > > > > > > Best, > > > -V > > > > > > -- > > > Virginie van Wassenhove > > > Exec Dir NeuroSpin MEG > > > Group leader, Brain Dynamics > > > CEA.DSV.I2BM.NeuroSpin - INSERM Cognitive Neuroimaging Unit > > > B?t 145 Point Courrier 156 > > > Gif s/ Yvette F-91191 FRANCE > > > > > > +33(0)1.69.08.1667 > > > Virginie.van.Wassenhove at gmail.com > > > [https://sites.google.com/site/virginievanwassenhove/](https://sites.google.com/site/virginievanwassenhove/) > > > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > > Mne\_analysis mailing list > > > Mne\_analysis at nmr.mgh.harvard.edu > > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > > > The information in this e-mail is intended only for the person to whom > > > it is > > > addressed. If you believe this e-mail was sent to you in error and the > > > e-mail > > > contains patient information, please contact the Partners Compliance > > > HelpLine at > > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > > in error > > > but does not contain patient information, please contact the sender and > > > properly > > > dispose of the e-mail. > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Mne\_analysis mailing list > > Mne\_analysis at nmr.mgh.harvard.edu > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > The information in this e-mail is intended only for the person to whom it > > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > in error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > -- > Virginie van Wassenhove > Exec Dir NeuroSpin MEG > Group leader, Brain Dynamics > CEA.DSV.I2BM.NeuroSpin - INSERM Cognitive Neuroimaging Unit > B?t 145 Point Courrier 156 > Gif s/ Yvette F-91191 FRANCE > > +33(0)1.69.08.1667 > Virginie.van.Wassenhove at gmail.com > [https://sites.google.com/site/virginievanwassenhove/](https://sites.google.com/site/virginievanwassenhove/) > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20141001/b27f8f93/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20141001/b27f8f93/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 2, 2014, 7:11am UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/7 "2014-10-02T07:11:06Z")
> 1. this is in fact an issue with the documentation, not a bug. The > 'ignore' option will avoid crashes if one or many events are missing but at > least one remains. If all events are missing nothing will be ignored, > currently the constructor needs at east one event. We might want to rethink > the semantics. Out of curiosity, what are you doing with epochs for which > you know in advance that events and ids don't match? In other words, would > there be a use case for the behavior you expected from 'ignore'? If it's > just to avoid crashes when no event is found, I would manually check that > and skip computations if nothing is found. For example (in a loop that > iterates over datasets or subjects): > > if not np.any(np.in1d(event\_ids.values(), events[:, 2])): >     continue The reason is purely pragmatic for batch processing (all runs of all participants; in some runs there may be some conditions missing due to the nature of the task) > 2. the second issue sounds mysterious to me, I don't `smell` what might be > going on there. I might have found the bug. -V ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 2, 2014, 8:46am UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/8 "2014-10-02T08:46:37Z")
> The reason is purely pragmatic for batch processing (all runs of all > participants; in some runs there may be some conditions missing due to the > nature of the task) either we have it crash at epochs creation or it will crash later. I think you should detect it and address the problem on your side when running your batch script. ALex ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 2, 2014, 12:52pm UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/9 "2014-10-02T12:52:16Z")
Ok thanks. You may want to clarify the "no\_missing" option on the wiki. Cheers, V ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 2, 2014, 1:20pm UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/10 "2014-10-02T13:20:03Z")
ok bug fixed, tfr\_morlet works great along with the superb figure suite tools! very nifty! -V quick test outcome on 1 participant: some lovely parietal alpha and low gamma 40 min with n\_jobs= 4, 2s epoch, decimfactor=3 (333 Hz) [image: Inline image 1] ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 2, 2014, 4:30pm UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/11 "2014-10-02T16:30:21Z")
nice to hear it works how would you phrase the doc? It is currently:     on\_missing : str         What to do if an event id is not found in the recording.         Valid keys are 'error' | 'warning' | 'ignore'         Default is 'error'. If on\_missing is 'warning' it will proceed but         warn, if 'ignore' it will proceed silently. Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20141002/e38ecb57/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20141002/e38ecb57/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 2, 2014, 8:42pm UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/12 "2014-10-02T20:42:38Z")
simply specify that "if no event id are found in the data, an error will be automatically generated irrespective of the str" however, i am still unclear about what "no\_missing" means: how would mne.epochs know in advance whether an event should be there or not (hence that it is missing)? -V ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 3, 2014, 8:59am UTC](https://mne.discourse.group/t/on-missing-and-time-frequency/831/13 "2014-10-03T08:59:18Z")
Thanks Virginie, I opened a PR, which is based on your suggestion. 2014-10-02 22:42 GMT+02:00 Virginie van Wassenhove \< virginie.van.wassenhove at gmail.com\>: > simply specify that "if no event id are found in the data, an error will > be automatically generated irrespective of the str" > > however, i am still unclear about what "no\_missing" means: how would > mne.epochs know in advance whether an event should be there or not (hence > that it is missing)? The mismatch is produced as follows: You pass an event\_id that will be a dict in most cases, e.g. {'left': 1, 'right':2}. Second you pass events at which to segment the continuous recordings. For simplicity let's assume we only have two of them. np.array([[1, 0, 14], [1, 0, 2]]) In this case the event id 'left' is not found in the events (not in the data) and 'on\_missing' becomes relevant. For the sourcecode see: > If no event id is found at all and 'on\_missing' is set to 'ignore' it will crash here: > -Denis > -V > > > nice to hear it works > > > > how would you phrase the doc? It is currently: > > > >      on\_missing : str > >         What to do if an event id is not found in the recording. > >         Valid keys are 'error' | 'warning' | 'ignore' > >         Default is 'error'. If on\_missing is 'warning' it will proceed but > >         warn, if 'ignore' it will proceed silently. > > > > Alex > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20141003/ea291354/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20141003/ea291354/attachment.html)