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Fixed the parfor issue with non-consecutive channels
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,66 +1,67 @@ | ||
| function [signal, lineNoiseOut] = blasstLineNoise(signal, lineNoiseIn) | ||
| % Remove sharp spectral peaks from signal using Sleppian filters | ||
| % | ||
| % Usage: | ||
| % signal = cleanLineNoise(signal) | ||
| % [signal, lineNoiseOut] = hcleanLineNoise(signal, lineNoiseIn) | ||
| % | ||
| % Parameters: | ||
| % signal Structure with .data and .srate fields | ||
| % lineNoiseIn Input structure with fields described below | ||
| % | ||
| % Structure parameters (lineNoiseIn): | ||
| % fPassBand Frequency band used (default [0, Fs/2] = entire band) | ||
| % Fs Sampling frequency | ||
| % fScanBandWidth +/- bandwidth centered on each f0 to scan for significant | ||
| % lines (TM) | ||
| % lineFrequencies Line frequencies to be removed (default | ||
| % [60, 120, 180, 240, 300]) | ||
| % lineNoiseChannels Channels to remove line noise from (default | ||
| % size(data, 1)) | ||
| % maximumIterations Maximum times to iterate removal (default = 10) | ||
| % p Significance level cutoff (default = 0.01) | ||
| % pad FFT padding factor ( -1 corresponds to no padding, | ||
| % 0 corresponds to padding to next highest power of 2 | ||
| % etc.) (default is 0) | ||
| % pnts | ||
| % tapers Precomputed tapers from dpss | ||
| % taperBandWidth Taper bandwidth (default 2 Hz) | ||
| % taperWindowSize Taper sliding window length (default 4 sec) | ||
| % taperWindowStep Sliding window step size (default 4 sec = no overlap) | ||
| % tau Window overlap smoothing factor (default 100) | ||
| % | ||
| % This function is based on code originally written by Tim Mullen in a | ||
| % package called tmullen-cleanline which is based on the chronux_2 | ||
| % libraries. | ||
| % | ||
|
|
||
| lineNoiseOut = lineNoiseIn; | ||
| %% Remove line frequencies that are greater than Nyquist frequencies | ||
| tooLarge = lineNoiseOut.lineFrequencies >= lineNoiseOut.Fs/2; | ||
| if any(tooLarge) | ||
| warning('cleanLineNoise:LineFrequenciesTooLarge', ... | ||
| 'Eliminating frequencies greater than half the sampling rate'); | ||
| lineNoiseOut.lineFrequencies(tooLarge) = []; | ||
| lineNoiseOut.lineFrequencies = squeeze(lineNoiseOut.lineFrequencies); | ||
| end | ||
|
|
||
| %% Set up parameters for blassting the line noise | ||
| fRange = lineNoiseOut.fScanBandWidth; | ||
| frequencyRanges = repmat(fRange, length(lineNoiseOut.lineFrequencies)); | ||
| sRate = lineNoiseOut.Fs; | ||
| lineFrequencies = lineNoiseOut.lineFrequencies; | ||
| maxIterations = lineNoiseOut.maximumIterations; | ||
|
|
||
| %% Perform the calculation for each channel separately | ||
| data = double(signal.data); | ||
| chans = sort(lineNoiseOut.lineNoiseChannels); | ||
| parfor ch = chans | ||
| data(ch, :) = blasst(squeeze(data(ch, :)), lineFrequencies, ... | ||
| frequencyRanges, sRate, ... | ||
| 'MaximumIterations', maxIterations, ... | ||
| 'Verbose', 0); | ||
| end | ||
| signal.data = data; | ||
| clear data; | ||
|
|
||
| function [signal, lineNoiseOut] = blasstLineNoise(signal, lineNoiseIn) | ||
| % Remove sharp spectral peaks from signal using Sleppian filters | ||
| % | ||
| % Usage: | ||
| % signal = cleanLineNoise(signal) | ||
| % [signal, lineNoiseOut] = hcleanLineNoise(signal, lineNoiseIn) | ||
| % | ||
| % Parameters: | ||
| % signal Structure with .data and .srate fields | ||
| % lineNoiseIn Input structure with fields described below | ||
| % | ||
| % Structure parameters (lineNoiseIn): | ||
| % fPassBand Frequency band used (default [0, Fs/2] = entire band) | ||
| % Fs Sampling frequency | ||
| % fScanBandWidth +/- bandwidth centered on each f0 to scan for significant | ||
| % lines (TM) | ||
| % lineFrequencies Line frequencies to be removed (default | ||
| % [60, 120, 180, 240, 300]) | ||
| % lineNoiseChannels Channels to remove line noise from (default | ||
| % size(data, 1)) | ||
| % maximumIterations Maximum times to iterate removal (default = 10) | ||
| % p Significance level cutoff (default = 0.01) | ||
| % pad FFT padding factor ( -1 corresponds to no padding, | ||
| % 0 corresponds to padding to next highest power of 2 | ||
| % etc.) (default is 0) | ||
| % pnts | ||
| % tapers Precomputed tapers from dpss | ||
| % taperBandWidth Taper bandwidth (default 2 Hz) | ||
| % taperWindowSize Taper sliding window length (default 4 sec) | ||
| % taperWindowStep Sliding window step size (default 4 sec = no overlap) | ||
| % tau Window overlap smoothing factor (default 100) | ||
| % | ||
| % This function is based on code originally written by Tim Mullen in a | ||
| % package called tmullen-cleanline which is based on the chronux_2 | ||
| % libraries. | ||
| % | ||
|
|
||
| lineNoiseOut = lineNoiseIn; | ||
| %% Remove line frequencies that are greater than Nyquist frequencies | ||
| tooLarge = lineNoiseOut.lineFrequencies >= lineNoiseOut.Fs/2; | ||
| if any(tooLarge) | ||
| warning('cleanLineNoise:LineFrequenciesTooLarge', ... | ||
| 'Eliminating frequencies greater than half the sampling rate'); | ||
| lineNoiseOut.lineFrequencies(tooLarge) = []; | ||
| lineNoiseOut.lineFrequencies = squeeze(lineNoiseOut.lineFrequencies); | ||
| end | ||
|
|
||
| %% Set up parameters for blassting the line noise | ||
| fRange = lineNoiseOut.fScanBandWidth; | ||
| frequencyRanges = repmat(fRange, length(lineNoiseOut.lineFrequencies)); | ||
| sRate = lineNoiseOut.Fs; | ||
| lineFrequencies = lineNoiseOut.lineFrequencies; | ||
| maxIterations = lineNoiseOut.maximumIterations; | ||
|
|
||
| %% Perform the calculation for each channel separately | ||
| signal.data = double(signal.data); | ||
| chans = lineNoiseOut.lineNoiseChannels; | ||
| data = signal.data(chans, :); | ||
| parfor ch = 1:size(data, 1) | ||
| data(ch, :) = blasst(squeeze(data(ch, :)), lineFrequencies, ... | ||
| frequencyRanges, sRate, ... | ||
| 'MaximumIterations', maxIterations, ... | ||
| 'Verbose', 0); | ||
| end | ||
| signal.data(chans, :) = data; | ||
| clear data; | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,62 +1,63 @@ | ||
| function [signal, lineNoiseOut] = cleanLineNoise(signal, lineNoiseIn) | ||
| % Remove sharp spectral peaks from signal using Sleppian filters | ||
| % | ||
| % Usage: | ||
| % signal = cleanLineNoise(signal) | ||
| % [signal, lineNoiseOut] = hcleanLineNoise(signal, lineNoiseIn) | ||
| % | ||
| % Parameters: | ||
| % signal Structure with .data and .srate fields | ||
| % lineNoiseIn Input structure with fields described below | ||
| % | ||
| % Structure parameters (lineNoiseIn): | ||
| % fPassBand Frequency band used (default [0, Fs/2] = entire band) | ||
| % Fs Sampling frequency | ||
| % fScanBandWidth +/- bandwidth centered on each f0 to scan for significant | ||
| % lines (TM) | ||
| % lineFrequencies Line frequencies to be removed (default | ||
| % [60, 120, 180, 240, 300]) | ||
| % lineNoiseChannels Channels to remove line noise from (default | ||
| % size(data, 1)) | ||
| % maximumIterations Maximum times to iterate removal (default = 10) | ||
| % p Significance level cutoff (default = 0.01) | ||
| % pad FFT padding factor ( -1 corresponds to no padding, | ||
| % 0 corresponds to padding to next highest power of 2 | ||
| % etc.) (default is 0) | ||
| % pnts | ||
| % tapers Precomputed tapers from dpss | ||
| % taperBandWidth Taper bandwidth (default 2 Hz) | ||
| % taperWindowSize Taper sliding window length (default 4 sec) | ||
| % taperWindowStep Sliding window step size (default 4 sec = no overlap) | ||
| % tau Window overlap smoothing factor (default 100) | ||
| % | ||
| % This function is based on code originally written by Tim Mullen in a | ||
| % package called tmullen-cleanline which is based on the chronux_2 | ||
| % libraries. | ||
| % | ||
|
|
||
| lineNoiseOut = lineNoiseIn; | ||
| %% Remove line frequencies that are greater than Nyquist frequencies | ||
| tooLarge = lineNoiseOut.lineFrequencies >= lineNoiseOut.Fs/2; | ||
| if any(tooLarge) | ||
| warning('cleanLineNoise:LineFrequenciesTooLarge', ... | ||
| 'Eliminating frequencies greater than half the sampling rate'); | ||
| lineNoiseOut.lineFrequencies(tooLarge) = []; | ||
| lineNoiseOut.lineFrequencies = squeeze(lineNoiseOut.lineFrequencies); | ||
| end | ||
|
|
||
| %% Set up multi-taper parameters | ||
| hbw = lineNoiseOut.taperBandWidth/2; % half-bandwidth | ||
| lineNoiseOut.taperTemplate = [hbw, lineNoiseOut.taperWindowSize, 1]; | ||
| Nwin = round(lineNoiseOut.Fs*lineNoiseOut.taperWindowSize); % number of samples in window | ||
| lineNoiseOut.tapers = checkTapers(lineNoiseOut.taperTemplate, Nwin, lineNoiseOut.Fs); | ||
|
|
||
| %% Perform the calculation for each channel separately | ||
| data = double(signal.data); | ||
| chans = sort(lineNoiseOut.lineNoiseChannels); | ||
| parfor ch = chans | ||
| data(ch, :) = removeLinesMovingWindow(squeeze(data(ch, :)), lineNoiseOut); | ||
| end | ||
| signal.data = data; | ||
| clear data; | ||
|
|
||
| function [signal, lineNoiseOut] = cleanLineNoise(signal, lineNoiseIn) | ||
| % Remove sharp spectral peaks from signal using Sleppian filters | ||
| % | ||
| % Usage: | ||
| % signal = cleanLineNoise(signal) | ||
| % [signal, lineNoiseOut] = hcleanLineNoise(signal, lineNoiseIn) | ||
| % | ||
| % Parameters: | ||
| % signal Structure with .data and .srate fields | ||
| % lineNoiseIn Input structure with fields described below | ||
| % | ||
| % Structure parameters (lineNoiseIn): | ||
| % fPassBand Frequency band used (default [0, Fs/2] = entire band) | ||
| % Fs Sampling frequency | ||
| % fScanBandWidth +/- bandwidth centered on each f0 to scan for significant | ||
| % lines (TM) | ||
| % lineFrequencies Line frequencies to be removed (default | ||
| % [60, 120, 180, 240, 300]) | ||
| % lineNoiseChannels Channels to remove line noise from (default | ||
| % size(data, 1)) | ||
| % maximumIterations Maximum times to iterate removal (default = 10) | ||
| % p Significance level cutoff (default = 0.01) | ||
| % pad FFT padding factor ( -1 corresponds to no padding, | ||
| % 0 corresponds to padding to next highest power of 2 | ||
| % etc.) (default is 0) | ||
| % pnts | ||
| % tapers Precomputed tapers from dpss | ||
| % taperBandWidth Taper bandwidth (default 2 Hz) | ||
| % taperWindowSize Taper sliding window length (default 4 sec) | ||
| % taperWindowStep Sliding window step size (default 4 sec = no overlap) | ||
| % tau Window overlap smoothing factor (default 100) | ||
| % | ||
| % This function is based on code originally written by Tim Mullen in a | ||
| % package called tmullen-cleanline which is based on the chronux_2 | ||
| % libraries. | ||
| % | ||
|
|
||
| lineNoiseOut = lineNoiseIn; | ||
| %% Remove line frequencies that are greater than Nyquist frequencies | ||
| tooLarge = lineNoiseOut.lineFrequencies >= lineNoiseOut.Fs/2; | ||
| if any(tooLarge) | ||
| warning('cleanLineNoise:LineFrequenciesTooLarge', ... | ||
| 'Eliminating frequencies greater than half the sampling rate'); | ||
| lineNoiseOut.lineFrequencies(tooLarge) = []; | ||
| lineNoiseOut.lineFrequencies = squeeze(lineNoiseOut.lineFrequencies); | ||
| end | ||
|
|
||
| %% Set up multi-taper parameters | ||
| hbw = lineNoiseOut.taperBandWidth/2; % half-bandwidth | ||
| lineNoiseOut.taperTemplate = [hbw, lineNoiseOut.taperWindowSize, 1]; | ||
| Nwin = round(lineNoiseOut.Fs*lineNoiseOut.taperWindowSize); % number of samples in window | ||
| lineNoiseOut.tapers = checkTapers(lineNoiseOut.taperTemplate, Nwin, lineNoiseOut.Fs); | ||
|
|
||
| %% Perform the calculation for each channel separately | ||
| signal.data = double(signal.data); | ||
| chans = lineNoiseOut.lineNoiseChannels; | ||
| data = signal.data(chans, :); | ||
| parfor ch = 1:size(data, 1) | ||
| data(ch, :) = removeLinesMovingWindow(squeeze(data(ch, :)), lineNoiseOut); | ||
| end | ||
| signal.data(chans, :) = data; | ||
| clear data; | ||
|
|