how do I use filtfilt on a GPU?
Hello,
I am trying to get filtfilt to run on a GPU and I’m unable to get the formatting right (I think).
Eventually, I’d like to calculate phase-amplitude coupling over a wide range of frequencies with a zero-phase filter.This ends up taking a very long time and the slowest step so far seems to be the bandpass filtering of my signals, so I’d like to run those on my GPU instead of the CPU. I’m basing my filter design on eegfilt.m from the EEGLab toolbox.
I’m trying to get my code to run with a small EEG snippet first. I’ve replaced the real signal with random numbers for this question, but I can share some real signal later if that helps.
I have tried two different ways of calling filtfilt with arrayfun and am receiving two different error messages:
Attempt1: I tried to use arrayfun in the way I’d normally use it (on a non-gpuArray). This gives ‘Use of functional workspace is not supported.’
In attempt 2: when I try to use arrayfun in a way that more closely resembles the GPU-related documentation, I get ‘Indexing is not supported’.
Is it possible to use filtfilt with a GPU array at all? Can someone please tell me what stupid thing I’m doing wrong?
srate = 1000;
locutoff = 10;
hicutoff = 12;
testbit = rand(12*srate,1) %testbit = EEG(1:12*srate);
%filter settings
minfac = 3; % this many (lo)cutoff-freq cycles in filter
min_filtorder = 15; % minimum filter length
filtorder = minfac*fix(srate/hicutoff);
if filtorder < min_filtorder
filtorder = min_filtorder;
end
filtwts = fir1(filtorder, [locutoff, hicutoff]./(srate/2));
% without GPU
filtsig1 = filtfilt(filtwts,1,testbit’);
%attempt 1 with GPU (does not work)
testbit = gpuArray(testbit’);
filtsig2 = arrayfun(@(x) filtfilt(filtwts,1,x),testbit);
%attempt 2 with GPU (also does not work)
testbit = gpuArray(testbit’);
filtsig2 = arrayfun(@filtfilt, filtwts,1,testbit);Hello,
I am trying to get filtfilt to run on a GPU and I’m unable to get the formatting right (I think).
Eventually, I’d like to calculate phase-amplitude coupling over a wide range of frequencies with a zero-phase filter.This ends up taking a very long time and the slowest step so far seems to be the bandpass filtering of my signals, so I’d like to run those on my GPU instead of the CPU. I’m basing my filter design on eegfilt.m from the EEGLab toolbox.
I’m trying to get my code to run with a small EEG snippet first. I’ve replaced the real signal with random numbers for this question, but I can share some real signal later if that helps.
I have tried two different ways of calling filtfilt with arrayfun and am receiving two different error messages:
Attempt1: I tried to use arrayfun in the way I’d normally use it (on a non-gpuArray). This gives ‘Use of functional workspace is not supported.’
In attempt 2: when I try to use arrayfun in a way that more closely resembles the GPU-related documentation, I get ‘Indexing is not supported’.
Is it possible to use filtfilt with a GPU array at all? Can someone please tell me what stupid thing I’m doing wrong?
srate = 1000;
locutoff = 10;
hicutoff = 12;
testbit = rand(12*srate,1) %testbit = EEG(1:12*srate);
%filter settings
minfac = 3; % this many (lo)cutoff-freq cycles in filter
min_filtorder = 15; % minimum filter length
filtorder = minfac*fix(srate/hicutoff);
if filtorder < min_filtorder
filtorder = min_filtorder;
end
filtwts = fir1(filtorder, [locutoff, hicutoff]./(srate/2));
% without GPU
filtsig1 = filtfilt(filtwts,1,testbit’);
%attempt 1 with GPU (does not work)
testbit = gpuArray(testbit’);
filtsig2 = arrayfun(@(x) filtfilt(filtwts,1,x),testbit);
%attempt 2 with GPU (also does not work)
testbit = gpuArray(testbit’);
filtsig2 = arrayfun(@filtfilt, filtwts,1,testbit); Hello,
I am trying to get filtfilt to run on a GPU and I’m unable to get the formatting right (I think).
Eventually, I’d like to calculate phase-amplitude coupling over a wide range of frequencies with a zero-phase filter.This ends up taking a very long time and the slowest step so far seems to be the bandpass filtering of my signals, so I’d like to run those on my GPU instead of the CPU. I’m basing my filter design on eegfilt.m from the EEGLab toolbox.
I’m trying to get my code to run with a small EEG snippet first. I’ve replaced the real signal with random numbers for this question, but I can share some real signal later if that helps.
I have tried two different ways of calling filtfilt with arrayfun and am receiving two different error messages:
Attempt1: I tried to use arrayfun in the way I’d normally use it (on a non-gpuArray). This gives ‘Use of functional workspace is not supported.’
In attempt 2: when I try to use arrayfun in a way that more closely resembles the GPU-related documentation, I get ‘Indexing is not supported’.
Is it possible to use filtfilt with a GPU array at all? Can someone please tell me what stupid thing I’m doing wrong?
srate = 1000;
locutoff = 10;
hicutoff = 12;
testbit = rand(12*srate,1) %testbit = EEG(1:12*srate);
%filter settings
minfac = 3; % this many (lo)cutoff-freq cycles in filter
min_filtorder = 15; % minimum filter length
filtorder = minfac*fix(srate/hicutoff);
if filtorder < min_filtorder
filtorder = min_filtorder;
end
filtwts = fir1(filtorder, [locutoff, hicutoff]./(srate/2));
% without GPU
filtsig1 = filtfilt(filtwts,1,testbit’);
%attempt 1 with GPU (does not work)
testbit = gpuArray(testbit’);
filtsig2 = arrayfun(@(x) filtfilt(filtwts,1,x),testbit);
%attempt 2 with GPU (also does not work)
testbit = gpuArray(testbit’);
filtsig2 = arrayfun(@filtfilt, filtwts,1,testbit); filtfilt, arrayfun, gpuarray, matlab2019b MATLAB Answers — New Questions
