def polarityReversal(timeData: TimeData,
reversal: Dict[str, bool],
inplace: bool = True) -> TimeData:
"""Multiply the data by -1 (polarity reversal)
Parameters
----------
timeData : TimeData
timeData to normalise
reversal : Dict[str, bool]
Keys are channels and values are boolean flags for reversing
inplace : bool, optional
Whether to manipulate the data inplace
Returns
-------
TimeData
Normalised time data
"""
if not inplace:
timeData = timeData.copy()
timeData.data = polarityReversalData(timeData.data, reversal)
timeData.addComment(
"Polarity reversal with parameters: {}".format(reversal))
return timeData
def interpolateToSecond(timeData: TimeData, inplace: bool = True) -> TimeData:
"""Interpolate data to be on the second
Some formats of time data (e.g. SPAM) do not start on the second with their sampling. This method interpolates so that sampling starts on the second and improves interoperability with other recording formats.
Parameters
----------
timeData : TimeData
Time data to interpolate onto the second
inplace : bool, optional
Whether to do the interpolation inplace or not. Default is True.
Returns
-------
TimeData
Time data interpolated to start on the second
"""
startTimeInterp, numSamplesInterp, dataInterp = interpolateToSecondData(
timeData.data, timeData.sampleFreq, timeData.startTime
)
if not inplace:
timeData = timeData.copy()
timeData.numSamples = numSamplesInterp
timeData.startTime = startTimeInterp
# calculate end timeEnd
timeData.stopTime = timeData.startTime + timedelta(
seconds=(1.0 / timeData.sampleFreq) * (timeData.numSamples - 1)
)
timeData.data = dataInterp
timeData.addComment(
"Time data interpolated to nearest second. New start time {}, new end time {}, new number of samples {} ".format(
timeData.startTime, timeData.stopTime, timeData.numSamples
)
)
return timeData
def resample(timeData: TimeData, resampFreq: float, inplace: bool = True) -> TimeData:
"""Resample time data
Parameters
----------
timeData : TimeData
timeData to filter
resampFreq : float
The frequency to resample to
inplace : bool, optional
Whether to manipulate the data inplace
Returns
-------
TimeData
Filtered time data
"""
origFreq = timeData.sampleFreq
if not inplace:
timeData = timeData.copy()
timeData.data = resampleData(timeData.data, timeData.sampleFreq, resampFreq)
# update the time info
timeData.sampleFreq = resampFreq
timeData.numSamples = timeData.data[timeData.chans[0]].size
timeData.stopTime = timeData.startTime + timedelta(
seconds=(1.0 / timeData.sampleFreq) * (timeData.numSamples - 1)
)
timeData.addComment(
"Time data resampled from {:.6f} Hz to {:.6f} Hz".format(origFreq, resampFreq)
)
return timeData
def bandPass(
timeData: TimeData, cutoffLow: float, cutoffHigh: float, inplace: bool = True
) -> TimeData:
"""Bandpass butterworth filter for time data
Parameters
----------
timeData : TimeData
timeData to filter
cutoff : float
Cutoff frequency in Hz
inplace : bool, optional
Whether to manipulate the data inplace
Returns
-------
TimeData
Filtered time data
"""
if not inplace:
timeData = timeData.copy()
timeData.data = bandPassData(
timeData.data, timeData.sampleFreq, cutoffLow, cutoffHigh
)
timeData.addComment(
"Band pass filter applied with cutoffs {} Hz and {} Hz".format(
cutoffLow, cutoffHigh
)
)
return timeData
def normalise(timeData: TimeData, inplace: bool = True) -> TimeData:
"""Normalise time data
Parameters
----------
timeData : TimeData
timeData to normalise
inplace : bool, optional
Whether to manipulate the data inplace
Returns
-------
TimeData
Normalised time data
"""
if not inplace:
timeData = timeData.copy()
timeData.data = normaliseData(timeData.data)
timeData.addComment("Data normalised")
return timeData
def scale(timeData: TimeData,
scalars: Dict[str, bool],
inplace: bool = True) -> TimeData:
"""Scale the data by an arbitrary amount
Parameters
----------
timeData : TimeData
timeData to normalise
scalars : Dict[str, float]
Keys are channels and values are boolean flags for reversing
inplace : bool, optional
Whether to manipulate the data inplace
Returns
-------
TimeData
Normalised time data
"""
if not inplace:
timeData = timeData.copy()
timeData.data = scaleData(timeData.data, scalars)
timeData.addComment("Time data scaled with scalars: {}".format(scalars))
return timeData
def notchFilter(timeData: TimeData, notch: float, inplace: bool = True) -> TimeData:
"""Bandpass butterworth filter for time data
Parameters
----------
timeData : TimeData
timeData to filter
notch : float
Frequency to notch filter in Hz
inplace : bool, optional
Whether to manipulate the data inplace
Returns
-------
TimeData
Filtered time data
"""
if not inplace:
timeData = timeData.copy()
timeData.data = notchFilterData(
timeData.data, timeData.sampleFreq, notch, notch / 5.0
)
timeData.addComment("Notch filter applied at {} Hz".format(notch))
return timeData
def calibrate(
self,
timeData: TimeData,
sensor: Dict[str, str],
serial: Dict[str, int],
chopper: Dict[str, bool],
) -> TimeData:
"""Calibrate time data
For each channel in timeData, searches for a matching calibration file based on sensor type, serial number and chopper. If a calibration file is found, the channel is calibrated using the data in the file. If useTheoretical is False and no file is found, the data is not calibrated
todo:
If no calibration file is found and the channel is a magnetic data channel, a theoretical function can be used
Parameters
----------
timeData : TimeData
TimeData object
sensor : Dict
Dictionary of sensor information with channels as the key and sensor as the value (sensor is a string)
serial :
Dictionary of serial information with channels as the key and sensor as the value (serial is a number)
chopper :
Dictionary of chopper information with channels as the key and sensor as the value (chopper is a bool)
Returns
-------
timeData : TimeData
Calibration TimeData object
"""
calIO = CalibrationIO()
# iterate over data
for chan in timeData.chans:
# output some info
self.printText("Calibrating channel {}".format(chan))
# try and find calibration file
calFile, calFormat = self.getCalFile(sensor[chan], serial[chan],
chopper[chan])
if calFile == "":
# no file found
if self.useTheoretical and isMagnetic(chan):
# use theoretical
calData = self.getTheoreticalCalData(sensor[chan])
timeData.data[chan] = self.calibrateChan(
timeData.data[chan], timeData.sampleFreq, calData)
timeData.addComment(
"Channel {} calibrated with theoretical calibration function"
.format(chan))
continue
else:
self.printText(
"No Calibration data found - channel will not be calibrated"
)
timeData.addComment(
"Channel {} not calibrated".format(chan))
continue # nothing to do
# else file found
# no need to separately apply static gain, already included in cal data
calIO.refresh(calFile,
calFormat,
chopper=chopper[chan],
extend=self.extend)
calData = calIO.read()
self.printText(
"Calibration file found for sensor {}, serial number {}, chopper {}: {}"
.format(sensor[chan], serial[chan], chopper[chan], calFile))
self.printText("Format: {}".format(calFormat))
self.printText(
"Static gain correction of {} applied to calibration data".
format(calData.staticGain))
# calibrate time data
timeData.data[chan] = self.calibrateChan(timeData.data[chan],
timeData.sampleFreq,
calData)
timeData.addComment(
"Channel {} calibrated with calibration data from file {}".
format(chan, calFile))
# return calibrated time data
return timeData
