I am making a finger plethysmograph(FP) using an LED and a receiver. The sensor produces an analog pulse waveform that is filtered, amplified and fed into a microcontroller input with a range of 3.3-0V. This signal is converted into its digital form.
Smapling rate is 8MHz, Processor frequency is 26MHz, Precision is 10 or 8 bit.
I am having problems coming up with a robust method for peak detection. I want to be able to detect heart pulses from the finger plethysmograph. I have managed to produce an accurate measurement of heart rate using a threshold method. However, the FP is extremely sensitive to movement and the offset of the signal can change based on movement. However, the peaks of the signal will still show up but with varying voltage offset.
Therefore, I am proposing a peak detection method that uses the slope to detect peaks. In example, if a peak is produced, the slope before and after the maximum point will be positive and negative respectively.
How feasible do you think this method is? Is there an easier way to perform peak detection using a microcontroller?
You can still introduce detection of false peaks when the device is moved. This will be present whether you are timing average peak duration or applying an FFT (fast Fourier Transform).
With an FFT you should be able to ignore peaks outside the range of frequencies you are considering (ie those < 30 bpm and > 300 bpm, say).
As Kenny suggests, 8MHz might overwhelm a 26MHz chip. Any particular reason for such a high sampling rate?
Like some of the comments, I would also recommend lowering your sample rate since you only care about pulse (i.e. heart rate) for now. So, assuming you're going to be looking at resting heart rate, you'll be in the sub-1Hz to 2Hz range (60 BPM = 1Hz), depending on subject health, age, etc.
In order to isolate the frequency range of interest, I would also recommend a simple, low-order digital filter. If you have access to Matlab, you can play around with Digital Filter Design using its Filter Design and Analysis Tool (Introduction to the FDATool). As you'll find out, Digital Filtering (wiki) is not computationally expensive since it is a matter of multiplication and addition.
To answer the detection part of your question, YES, it is certainly feasible to implement peak detection on the plethysmograph waveform within a microcontroller. Taking your example, a slope-based peak detection algorithm would operate on your waveform data, searching for changes in slope, essentially where the slope waveform crosses zero.
Here are a few other things to consider about your application:
Calculating slope can have a "spread" (i.e. do you find the slope between adjacent samples, or samples which are a few samples apart?)
What if your peak detection algorithm locates peaks that are too close together, or too far apart, in a physiological sense?
A Pulse Oximeter (wiki) often utilizes LEDs which emit Red and Infrared light. How does the frequency of the LED affect the plethysmograph? (HINT: It may not be significant, but I believe you'll find one wavelength to yield greater amplitudes in your frequency range of interest.)
Of course you'll find a variety of potential algorithms if you do a literature search but I think slope-based detection is great for its simplicity. Hope it helps.
If you can detect the period using zero crossing, even at 10x oversampling of 10 Hz, you can use a line fit of the quick-n-dirty-edge to find the exact period, and then subtract the new wave's samples in that period with the previous, and get a DC offset. The period measurement will have the precision of your sample rate. Doing operations on the time and amplitude-normalized data will be much easier.
This idea is computationally light compared to FFT, which still needs additional data processing.
Related
I read the very interesting and informative article on image noise located here:
http://www.cambridgeincolour.com/tutorials/image-noise-2.htm
One of the key points is noise frequency which can be high or low. I was curious as to how this would be calculated?
I came across another article in which the developer achieved low frequency iage noise by sampling the surrounding pixels and then performing an average. But this requires a separate calculation pass after all the noise has been calculated.
Is this how it's traditionally done or is there a different way to calculate image noise frequency?
Thanks
Look up Perlin noise.
"Salt and pepper noise" is white or black pixels scattered at random over the source. It's a fairly common sort of noise, but not useful for much visually. It has the highest frequency that the image sampling supports.
Perlin noise consists of noise of several frequencies, or "octaves" superimposed on each other. It is useful, with various parameters it looks like wood, or clouds, or swirling lava. It can also be used a bit more subtly to give slightly rugged effects to non-smooth surfaces.
The frequency is simply the distance in pixels at which existence of noise at one pixel bears no relation to the noise at the other pixel (for non-repeating noise) or the "repeat length" for repeating noise.
I need to detect an accelerometer event when user hits the device on table/floor.
Device is having a STM32 low-power microcontroller at 8 MHz and an LIS3DH accelerometer.
The accelerometer is operating in +- 2G range. Sample numbers are signed 16-bit integers.
I have collected accelerometer data for such an event by reading from the accelerometer at 50 Hz. I have attached the graph of x, y and z samples. The "hit" event is clearly visible in the graphs, red dots on the time axis show the point when the event occurred. But I have no idea how to detect such event in code.
The DC offset changes for 3 axes according to orientation of device.
Again, sampled at 100 Hz, the graph is for the X axis only and shows 2 hit events. Such spikes will happen simultaneously on all 3 axes, but amplitude and direction may vary. The time scale is zoomed in, compared to the other graphs. Sampling at 100 Hz is not possible in the actual application code.
The device orientation change and movements in hand of user causes a lot of signal variation. Below is a graph for the Y axis with hand movement, orientation change and hit event. Such changes will happen across all axes.
As suggested by Martin James, you should measure the differences in accelerations between the current and last tick. You need to do this on each axis, because from your data, some of the hits don't affect every axis. One might suppose that you could use the total acceleration by using the sum of squares, but I don't think this will work.
To measure the difference, you will need to keep the last reading in a variable. You might need the previous two readings, depending on how fast the sampling rate is; if the rate is too high, then the differences may always be small. You should also keep a count of ticks since the last hit.
Then, when taking the current reading, compare the current readings with the previous readings. If the difference is above a threshold on any axis, mark it as a hit and reset the time_since_hit_count -- unless a hit happened recently. You want to avoid counting the same hit many times as the acceleration changes during a single hit. Your data suggests a threshold of around 5000.
If the difference is not above the threshold on any axis, increment the time_since_hit_count and replace the stored readings with the current ones.
(If you are storing the previous two hits, compare against each, and move the stored values appropriately.)
From your data, some hits take 3 ticks to occur, so you could discount hits if the time_since_hit_count is less than 5, say. That's 100 ms per hit. Depending on the application, that might be okay. A drum stick could bounce faster than that, but a finger probably not.
You'll probably have to experiment with the acc threshold and the hit count threshold as you collect data.
I have a 2 column vector with times and speeds of a subset of data, like so:
5 40
10 37
15 34
20 39
And so on. I want to get the fourier transform of speeds to get a frequency. How would I go about doing this with a fast fourier transform (fft)?
If my vector name is sampleData, I have tried
fft(sampleData);
but that gives me a vector of real and imaginary numbers. To be able to get sensible data to plot, how would I go about doing this?
Fourier Transform will yield a complex vector, when you fft you get a vector of frequencies, each has a spectral phase. These phases can be extremely important! (they contain most of the information of the time-domain signal, you won't see interference effects without them etc...). If you want to plot the power spectrum, you can
plot(abs(fft(sampleData)));
To complete the story, you'll probably need to fftshift, and also produce a frequency vector. Here's a more elaborate code:
% Assuming 'time' is the 1st col, and 'sampleData' is the 2nd col:
N=length(sampleData);
f=window(#hamming,N)';
dt=mean(diff(time));
df=1/(N*dt); % the frequency resolution (df=1/max_T)
if mod(N,2)==0
f_vec= df*((1:N)-1-N/2); % frequency vector for EVEN length vector
else
f_vec= df*((1:N)-0.5-N/2);
end
fft_data= fftshift(fft(fftshift(sampleData.*f))) ;
plot(f_vec,abs(fft_data))
I would recommend that you back up and think about what you are trying to accomplish, and whether an FFT is an appropriate tool for your situation. You say that you "want to ... get a frequency", but what exactly do you mean by that? Do you know that this data has exactly one frequency component, and want to know what the frequency is? Do you want to know both the frequency and phase of the component? Do you just want to get a rough idea of how many discrete frequency components are present? Are you interested in the spectrum of the noise in your measurement? There are many questions you can ask about "frequencies" in a data set, and whether or not an FFT and/or power spectrum is the best approach to getting an answer depends on the question.
In a comment above you asked "Is there some way to correlate the power spectrum to the time values?" This strikes me as a confused question, but also makes me think that maybe the question you are really trying to answer is "I have a signal whose frequency varies with time, and I want to get an estimate of the frequency vs time". I'm sure I've seen a question along those lines within the past few months here on SO, so I would search for that.
I would like to know how noise can be removed from data (say, radio data that is an array of rows and columns with each data point representing intensity of the radiation in the given frequency and time).The array can contain radio bursts. But many fixed frequency radio noise also exists(RFI=radio frequency intereference).How to remove such noise and bring out only the burst.
I don't mean to be rude, but this question isn't clear at all. Please sharpen it up.
The normal way to remove noise is first to define it exactly and then filter it out. Usually this is done in the frequency domain. For example, if you know the normalized power spectrum P(f) of the noise, build a filter with response
e/(e + P(f))
where e<1 is an attenuation factor.
You can implement the filter digitally using FFT or a convolution kernel.
When you don't know the spectrum of the noise or when it's white, then just use the inverse of the signal band.
What is a simple way to see if my low-pass filter is working? I'm in the process of designing a low-pass filter and would like to run tests on it in a relatively straight forward manner.
Presently I open up a WAV file and stick all the samples in a array of ints. I then run the array through the low-pass filter to create a new array. What would an easy way to check if the low-pass filter worked?
All of this is done in C.
You can use a broadband signal such as white noise to measure the frequency response:
generate white noise input signal
pass white noise signal through filter
take FFT of output from filter
compute log magnitude of FFT
plot log magnitude
Rather than coding this all up you can just dump the output from the filter to a text file and then do the analysis in e.g. MATLAB or Octave (hint: use periodogram).
Depends on what you want to test. I'm not a DSP expert, but I know there are different things one could measure about your filter (if that's what you mean by testing).
If the filter is linear then all information of the filter can be found in the impulse response. Read about it here: http://en.wikipedia.org/wiki/Linear_filter
E.g. if you take the Fourier transform of the impulse response, you'll get the frequency response. The frequency response easily tells you if the low-pass filter is worth it's name.
Maybe I underestimate your knowledge about DSP, but I recommend you to read the book on this website: http://www.dspguide.com. It's a very accessible book without difficult math. It's available as a real book, but you can also read it online for free.
EDIT: After reading it I'm convinced that every programmer that ever touches an ADC should definitely have read this book first. I discovered that I did a lot of things the difficult way in past projects that I could have done a thousand times better when I had a little bit more knowledge about DSP. Most of the times an unexperienced programmer is doing DSP without knowing it.
Create two monotone signals, one of a low frequency and one of a high frequency. Then run your filter on the two. If it works, then the low frequency signal should be unmodified whereas the high frequency signal will be filtered out.
Like Bart above mentioned.
If it's LTI system, I would insert impulse and record the samples and perform FFT using matlab and plot magnitude.
You ask why?
In time domain, you have to convolute the input x(t) with the impulse response d(t) to get the transfer function which is tedious.
y(t) = x(t) * d(t)
In frequency domain, convolution becomes simple multiplication.
y(s) = x(s) x d(s)
So, transfer function is y(s)/x(s) = d(s).
That's the reason you take FFT of impulse response to see the behavior of the filter.
You should be able to programmatically generate tones (sine waves) of various frequencies, stuff them into the input array, and then compare the signal energy by summing the squared values of the arrays (and dividing by the length, though that's mathematically not necessary here because the signals should be the same length). The ratio of the output energy to the input energy gives you the filter gain. If your LPF is working correctly, the gain should be close to 1 for low frequencies, close to 0.5 at the bandwidth frequency, and close to zero for high frequencies.
A note: There are various (but essentially the same in spirit) definitions of "bandwidth" and "gain". The method I've suggested should be relatively insensitive to the transient response of the filter because it's essentially averaging the intensity of the signal, though you could improve it by ignoring the first T samples of the input, where T is related to the filter bandwidth. Either way, make sure that the signals are long compared to the inverse of the filter bandwidth.
When I check a digital filter, I compute the magnitude response graph for the filter and plot it. I then generate a linear sweeping sine wave in code or using Audacity, and pass the sweeping sine wave through the filter (taking into account that things might get louder, so the sine wave is quiet enough not to clip) . A visual check is usually enough to assert that the filter is doing what I think it should. If you don't know how to compute the magnitude response I suspect there are tools out there that will compute it for you.
Depending on how certain you want to be, you don't even have to do that. You can just process the linear sweep and see that it attenuated the higher frequencies.