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dbridges / mea-tools

Tools for viewing, analyzing, and processing multi-electrode array data.
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Size limitation #6

Open Lswhiteh opened 6 years ago

Lswhiteh commented 6 years ago

Whenever using the Windows prepackaged version, anything above ~3 minutes worth of data (~400KB) returns an error in MEA Tools. I have tried both files from MC_Rack and Experimenter and the only commonality between the failures is the file size. I am attempting to process over half an hour's worth of recordings, so this would be nice if it could be fixed.

dbridges commented 6 years ago

I'm guessing you meant 400 MB? One of the limitations of MEA Viewer is that the data is loaded into memory, so I'd bet that you just ran out of memory. You could try closing other programs or increasing the amount of RAM (I'd suggest at least 8 - 16 GB). I've successfully opened multi-gigabyte files, so these seems to be a machine specific issue.

If you would like to troubleshoot further, please provide the full error message and the parameters of the recording (# electrodes, sample rate, etc).

Lswhiteh commented 6 years ago

I should have enough RAM, I'm running with 8 GB currently and only using about 20% before trying to run a ~1GB file. I'm posting the before and after of attempting to run, as well as a representative h5 file itself for this example. Recording was took with the 60 channel Multichannel Systems MEA setup (M2300 I believe?) , conversion attr in the HDF5 file is 61035.

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Lswhiteh commented 6 years ago

Solved it. In the pymea module there's a conversion going on (line 48 of pymea.py) which is attempting to use a negative exponent by 10, which numpy doesn't like. If you cast that as a float (10 as 10.0) it seems to work, and I was able to run on files I hadn't been able to before. Didn't think this was worth putting in a pull request for, but I'd be interested to see if this solves it in the GUI version as well.

colleen-j-brennan commented 4 years ago

Lswhiteh: What version of python were you running it on?

Lswhiteh commented 4 years ago

Oh boy, it's been quite a while, but it most likely would've been Python 3.6 on an Anaconda install. Hope that helps!