Problems with .h5 files

[Barbara Genocchi]

Hi,

I'm trying to analyze my mea data recorded with the Multi Channel Experimenter and then converted from .msrd to .h5 with Multi Channel DataManager.

However, I'm having troubles setting the parameters file.

can anyone suggest me how to set:

data_dtype =
data_header =

If I don't add them in the parameters file I get the following error:

(base) barbara@ubuntu:~/files$ spyking-circus 2019-04-04T10-23-0320190404-18154-2.h5
Traceback (most recent call last):
  File "/home/barbara/anaconda3/bin/spyking-circus", line 11, in <module>
    load_entry_point('spyking-circus==0.8.2', 'console_scripts', 'spyking-circus')()
  File "/home/barbara/anaconda3/lib/python3.7/site-packages/circus/scripts/launch.py", line 215, in main
    data_file    = params.get_data_file(source=True, has_been_created=False)
  File "/home/barbara/anaconda3/lib/python3.7/site-packages/circus/shared/parser.py", line 574, in get_data_file
    return self._create_data_file(data_file, is_empty, params, stream_mode)
  File "/home/barbara/anaconda3/lib/python3.7/site-packages/circus/shared/parser.py", line 503, in _create_data_file
    data              = __supported_data_files__[file_format](data_file, params, is_empty, stream_mode)
  File "/home/barbara/anaconda3/lib/python3.7/site-packages/circus/files/datafile.py", line 132, in __init__
    self._fill_from_header(self._read_from_header())
  File "/home/barbara/anaconda3/lib/python3.7/site-packages/circus/files/hdf5.py", line 49, in _read_from_header
    header['data_dtype']   = self.my_file.get(self.h5_key).dtype
AttributeError: 'Group' object has no attribute 'dtype'

Does anyone knows how to help me fix this problem?

Barbara

[Alice Falck]

Hey Barbara, 

Did someone help you or did you figure it out? I want to do the same and am also wonderung how to set the parameters.

Best, 

Alice

[Pierre Yger]

Dear Alice

I already answered to Barbara, see below and hope this helps

Best

Pierre

Ok, then you should be able to launch everything by adding

[data]

file_format    = hdf5                  # Can be raw_binary, openephys, hdf5, ... See >> spyking-circus help -i for more info
h5_key         = Data/Recording_0/AnalogStream/Stream_0/ChannelData
sampling_rate  = 20000 # Is it???

And then, you just need to provide the the probe layout, and it should works with the HDF5 file

Best

Pierre 

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