| Author: | Samuele Carcagno |
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pybdf is a Python library to read electroencephalographic recordings stored in the BIOSEMI 24-bit BDF format.
The latest release of pybdf can be downloaded from the python package index:
http://pypi.python.org/pypi/pybdf/
For developers: the source code of pybdf is hosted on github:
On all platforms, after having unpacked the archive you can install pybdf by running:
python setup.py install
Note that pybdf has been built and tested only on Linux with Python3. I don’t have enhough time to build and test binaries for Windows and Mac OS X, but if you try, please let me know how you get on with it.
To open a bdf file you need to create a bdfRecording object as follows:
bdfRec = bdfRecording('res1.bdf')
you can then query the properties of the recording stored in the BDF header using the appropriate functions, which are fully described here. Some examples are shown below.
Get the duration of the recording:
bdfRec.recordDuration
Get the sampling rate of each channel:
bdfRec.sampRate
Get the channel labels:
bdfRec.chanLabels
To read in the data use the following method:
rec = bdfRec.getData()
this returns a python dictionary with the following fields:
For example, to get the value of the first sample of the recording, in the first channel, you can type:
rec['data'][0,0]
the same sample value, but for the second channel, is stored in:
rec['data'][1,0]
The eventTable contains a list of the trigger codes for the experimental conditions:
rec['eventTable`]['code']
as well as a list of the sample numbers (or indexes) at which they started in the recording, and a list of their durations in seconds:
rec['eventTable']['idx']
rec['eventTable`]['dur']
The ActiveTwo actually stores one trigger code for each recording sample rather than a list of trigger onsets and durations as the eventTable does. The “raw” trigger channel with one trigger code for each recording sample can be retrieved by passing the argument trigChan = True to the getData() function:
rec = bdfRec.getData(trigChan=True)
the “raw” trigger channel will then be returned in rec[‘trigChan’]. Please, note that pybdf currently reads only the trigger inputs 1-8 and disregards the trigger inputs 9-16.
It is also possible to retrieve additional system codes (bits 16-23 of the status channel, see http://www.biosemi.com/faq/trigger_signals.htm), like CMS in/out-of range, battery low/OK. These are returned in rec[‘sysCodeChan’] when the sysCodeChan = True argument is passed to the getData() function. No particular effort has been made to decode these system codes.
Other usage examples are provided in the ‘examples’ directory inside the pybdf source archive.
Beware that pybdf does not check that you have sufficient RAM to read all the data in a bdf file. If you try to read a file that is too big for your hardware, you system may become slow or unresponsive. Initially try reading only a small amount of data, and check how much RAM that uses. You can read only a portion of the data by passing the beginning and end arguments to the getData() function. For example, to read the first 10 seconds of the recording, use:
rec = bdfRec.getData(beginning=0, end=10)
Please, report any bugs on github https://github.com/sam81/pybdf/issues
The filename or filepath of the BDF recording is currently limited to 256 characters. That should be sufficient for most purposes.
This module can be used to read the header and data from 24-bit Biosemi BDF files recorded with the ActiveTwo system.
Examples
>>> bdfRec = bdfRecording('res1.bdf') #create bdfRecording object
>>> bdfRec.recordDuration #how many seconds the recording lasts
>>> bdfRec.sampRate #sampling rate for each channel
>>> #read 10 seconds of data from the first two channels
>>> rec = bdfRec.getData(channels=[0, 1], beginning=0, end=10)
Class for dealing with BIOSEMI 24-bit BDF files. A bdfRecording object is created with the following syntax:
>>> bdfRec = bdfRecording('bdf_file.bdf')
This reads the BDF header, but not the data. You need to use the getData() method to read the data. The full documentation of the BDF file format can be found here: http://www.biosemi.com/faq/file_format.htm
Attributes
| idCode | str | Identification code |
| subjId | str | Local subject identification |
| recId | str | Local recording identification |
| startDate | str | Recording start date |
| startTime | str | Recording start time |
| nBytes | int | Number of bytes occupied by the bdf header |
| versionDataFormat | str | Version of data format |
| nDataRecords | int | Number of data records “-1” if unknown |
| recordDuration | float | Duration of a data record, in seconds |
| nChannels | int | Number of channels in data record |
| chanLabels | list of str | Channel labels |
| transducer | list of str | Transducer type |
| physDim | str | Physical dimension of channels |
| physMin | list of int | Physical minimum in units of physical dimension |
| physMax | list of int | Physical maximum in units of physical dimension |
| digMin | list of int | Digital minimum |
| digMax | list of int | Digital maximum |
| prefilt | list of str | Prefiltering |
| nSampRec | list of int | Number of samples in each data record |
| reserved | list of str | Reserved |
| scaleFactor | list of floats | Scaling factor for digital to physical dimension |
| sampRate | list of int | Recording sampling rate |
| statusChanIdx | int | Index of the status channel |
| nDataChannels | int | Number of data channels containing data (rather than trigger codes) |
| dataChanLabels | list of str | Labels of the channels containing data (rather than trigger codes) |
Methods
Read the data from a bdfRecording object
| Parameters : | beginning : int
end : int
channels : list of integers or strings
eventTable : boolean
trigChan : boolean
sysCodeChan : boolean
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| Returns : | rec : a dictionary with the following keys:
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Examples
>>> x = bdfRecording('res1.bdf')
>>> rec = x.getData(channels=[0, 2], beginning=0, end=10)