neo and .abf

[Maja K]

Hello,

I am using neo to read my .abf data files - it works without any problem if the data is saved in the gap free mode, but if it is saved in oscilloscope mode the block has no segments and therefore I cannot extract the data.

I am using commands:

    reader = neo.io.AxonIO(filename=fname)
    block = reader.read_block()

block.segments is empty
reader.read() gives the same results.

Is there another way I can access this data?

All the best and thank you in advance for your help,
Maja

[Samuel Garcia]

Hi,
I am the author of AxonIO.

Could you send the file via http ?

If the file is small enough (<10Mo), would you be agree if I put this
file on server with public read but private write.
neo.test() download them for testing.


Samuel


Le 12/09/2012 16:02, Maja K a �crit :

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[P Mullen]

Hi Samuel,

I think I am experiencing a similar problem to Maja. The problem is empty segments in the block of my abf file (contains sweeps of ephys recordings).  I was wondering if you had solved Maja's issue already, any help is greatly appreciated :) I'm using python 3 with anaconda and installed neo via pip

 

This is my code:

 

import neo

r= neo.io.AxonIO(filename="test2.abf")
bl= r.read_block(lazy=False, cascade=True)
print(bl)
print(bl.segments)
print(bl.channel_indexes)
print(neo.io.AxonIO.readable_objects)

 

 

Which produces:

 

<neo.core.block.Block object at 0x0000000005855A20>

[]

[]

[<class 'neo.core.block.Block'>]

 

I’ve tried saving the abf file as floating point, integer and as older abf versions but problem persists,

 

Thanks,

 

PIerce

[Samuel Garcia]

Hi,
I am not able to find  patch or issue on github about that.

Can you open issue on github and send me teh file please ?


Samuel

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