trigger data in hdf5 files (converted with datamanager)

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trigger data in hdf5 files (converted with datamanager)

Post  benmcs on Fri Oct 31, 2014 1:58 am

Hello,

I am trying out using the mc datamanager to convert mcd to hdf5. it works fine, i can read the h5 files in matlab.

where do i find the timestamps from the triggerdetector in mc rack?

data.Recording{1,1} has the analog, frame, event, segment and timestamp streams but they all show as 0x0 cell. only analog stream contains data and i can plot the recorded signal with no problem.

i made sure to record the trigger stream in the recorder and i can see the trigger timestamps with mc datatool and export to txt.

benmcs

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Re: trigger data in hdf5 files (converted with datamanager)

Post  Hans MCS on Mon Nov 03, 2014 3:11 am

Hello benmcs

there might be a problem with the events. Could you send me a short example file so I can have a look here?

my email address is
loeffler
(at)
multichannelsystems.com

best regards
Hans

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Re: trigger data in hdf5 files (converted with datamanager)

Post  benmcs on Mon Nov 03, 2014 3:30 am

Hi Hans, I sent you an email a moment ago

thanks,

Ben

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Impossible to open exported .h5 file format from McsDataManager

Post  Chamaeleon on Thu Mar 10, 2016 2:51 am

Hi all,
after the recording I exported everything with the McsDataManager to the .h5 file format for the Matlab analysis.
I followed the procedure I found in "The McsHDF5 Matlab tools" document but I obtain the following error:


-----------------------

>> data = McsHDF5.McsData('2016-03-10T10-29-44_LFP_1b.h5');

Error using h5readc
The HDF5 library encountered an error and produced the following stack trace information:

   H5G_loc_find_cb      object 'ChannelDataTimeStamps' doesn't exist
   H5G_traverse_real    traversal operator failed
   H5G_traverse         internal path traversal failed
   H5G_loc_find         can't find object
   H5Dopen2             not found

Error in h5read (line 58)
[data,var_class] = h5readc(Filename,Dataset,start,count,stride);

Error in McsHDF5.McsAnalogStream (line 65)
               timestamps = h5read(filename, [strStruct.Name '/ChannelDataTimeStamps']);

Error in McsHDF5.McsRecording (line 80)
                           rec.AnalogStream{streams} = McsHDF5.McsAnalogStream(filename,
                           recStruct.Groups(gidx).Groups(streams));

Error in McsHDF5.McsData (line 153)
                   data.Recording{recs} = McsHDF5.McsRecording(filename, inf.Groups.Groups(recs));


-----------------------


the .h5 file is not corrupted (I can open and surf it with HDFView), if I export the experiment in the .nex file format and I use the matlab script provided by Neuroexplorer for the conversion it works as well.
I think I'm missing something.
Someone can help?

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Re: trigger data in hdf5 files (converted with datamanager)

Post  Armin MCS on Fri Mar 11, 2016 1:02 am

Hi

the HDF5 Matlab toolbox expects that each AnalogStream has a field "ChannelDataTimeStamps" which it seems to be unable to find in your case for some reason. In HDFView, you should see below each Stream in AnalogStream 3 structures: "ChannelData", "ChannelDataTimeStamps" and "InfoChannel". If one of them is missing, this is likely a problem of the HDF5 export, otherwise the import into Matlab is the culprit..... in any case, in order to check out what went wrong, it would be very helpful if you could send us the problematic file(s).

Could you please upload both the original file and the exported h5 file via this link? https://www.dropbox.com/request/47MPkbQpHhZN1mXss3jb

Thanks!
Armin

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Re: trigger data in hdf5 files (converted with datamanager)

Post  Chamaeleon on Sun Mar 13, 2016 11:20 pm

Hi, thanks for the reply.

This is the screenshot from HDFView of one of the file I can not read in Matlab.

http://i84.servimg.com/u/f84/19/43/91/00/captur11.png

Armin wrote:If one of them is missing, this is likely a problem of the HDF5 export, otherwise the import into Matlab is the culprit.....

Apparently there is something missing during the first export?
I put all the files in the dopbox link as suggested.

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Re: trigger data in hdf5 files (converted with datamanager)

Post  Armin MCS on Sun Mar 13, 2016 11:44 pm

Hi,

thanks for sending the files, I was able to replicate the problem here.

It seems that the Analog Input channels were deactivated which produced an empty stream in the exported file. This is perfectly valid of course but is not handled properly in the current version of the DataManager / HDF5 Matlab interface. We will release a new version of them soon where this bug is fixed.

As a simple workaround, you can export your data without the Analog Raw Data: In the Multi Channel DataManager, remove the check mark in the "A" column, then export the file to HDF5. This results in a valid file that can be loaded into Matlab.

Sorry for the inconvenience
Armin

Edit: Version 1.0.1 of the HDF5 Matlab interface which fixes this bug is now available from our web site or the Matlab File Exchange.

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Re: trigger data in hdf5 files (converted with datamanager)

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