lowpassFilter: Lowpass filtering

In clampSeg: Idealisation of Patch Clamp Recordings

Description

Reexported from lowpassFilter. Creates lowpass filters.

Usage

lowpassFilter(type = c("bessel"), param, sr = 1, len = NULL, shift = 0.5)

Arguments

type	a string specifying the type of the filter, currently only Bessel filters are supported
param	a list specifying the parameters of the filter depending on type. For "bessel" the entries pole and cutoff have to be specified and no other named entries are allowed. pole has to be a single integer giving the number of poles (order). cutoff has to be a single positive numeric not larger than 1 giving the normalized cutoff frequency, i.e. the cutoff frequency (in the temporal domain) of the filter divided by the sampling rate
sr	a single numeric giving the sampling rate
len	a single integer giving the filter length of the truncated and digitised filter, see Value for more details. By default (NULL) it is chosen such that the autocorrelation function is below 1e-3 at len / sr and at all lager lags (len + i) / sr, with i a positive integer
shift	a single numeric between 0 and 1 giving a shift for the digitised filter, i.e. kernel and step are obtained by evaluating the corresponding functions at (0:len + shift) / sr

Value

An object of class lowpassFilter, i.e. a list that contains

"type", "param", "sr", "len"

the corresponding arguments

"kernfun"

the kernel function of the filter, obtained as the Laplace transform of the corresponding transfer function

"stepfun"

the step-response of the filter, i.e. the antiderivative of the filter kernel

"acfun"

the autocorrelation function, i.e. the convolution of the filter kernel with itself

"acAntiderivative"

the antiderivative of the autocorrelation function

"truncatedKernfun"

the kernel function of the at len / sr truncated filter, i.e. kernfun truncated and rescaled such that the new kernel still integrates to 1

"truncatedStepfun"

the step-response of the at len / sr truncated filter, i.e. the antiderivative of the kernel of the truncated filter

"truncatedAcfun"

the autocorrelation function of the at len / sr truncated filter, i.e. the convolution of the kernel of the truncated filter with itself

"truncatedAcAntiderivative"

the antiderivative of the autocorrelation function of the at len / sr truncated filter

"kern"

the digitised filter kernel normalised to one, i.e. kernfun((0:len + shift) / sr) / sum(kernfun((0:len + shift) / sr))

"step"

the digitised step-response of the filter, i.e. stepfun((0:len + shift) / sr)

"acf"

the discrete autocorrelation, i.e. acfun(0:len / sr)

"jump"

the last index of the left half of the filter, i.e. min(which(ret$step >= 0.5)) - 1L, it indicates how much a jump is shifted in time by a convolution of the signal with the digitised kernel of the lowpassfilter; if all values are below 0.5, len is returned with a warning

"number"

for developers; an integer indicating the type of the filter

"list"

for developers; a list containing precomputed quantities to recreate the filter in C++

Author(s)

This function is a modified and extended version of dfilter written by Thomas Hotz. New code is written by Florian Pein and Inder Tecuapetla-Gómez.

References

Pein, F., Bartsch, A., Steinem, C., Munk, A. (2020) Heterogeneous Idealization of Ion Channel Recordings - Open Channel Noise. arXiv:2008.02658.

Pein, F., Tecuapetla-Gómez, I., Schütte, O., Steinem, C., Munk, A. (2018) Fully-automatic multiresolution idealization for filtered ion channel recordings: flickering event detection. IEEE Trans. Nanobioscience, 17(3):300-320.

Pein, F. (2017) Heterogeneous Multiscale Change-Point Inference and its Application to Ion Channel Recordings. PhD thesis, Georg-August-Universität Göttingen. http://hdl.handle.net/11858/00-1735-0000-002E-E34A-7.

Hotz, T., Schütte, O., Sieling, H., Polupanow, T., Diederichsen, U., Steinem, C., and Munk, A. (2013) Idealizing ion channel recordings by a jump segmentation multiresolution filter. IEEE Trans. Nanobioscience, 12(4):376-386.

Examples

# the filter used for the gramicidin A recordings given by gramA
filter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 1e3 / 1e4),
                        sr = 1e4)

# filter kernel, truncated version
plot(filter$kernfun, xlim = c(0, 20 / filter$sr))
t <- seq(0, 20 / filter$sr, 0.01 / filter$sr)
# truncated version looks very similar
lines(t, filter$truncatedKernfun(t), col = "red")

# filter$len (== 11) is chosen such that filter$acf < 1e-3 for it and all larger lags
plot(filter$acfun, xlim = c(0, 20 / filter$sr), ylim = c(-0.003, 0.003))
abline(h = 0.001, lty = "22")
abline(h = -0.001, lty = "22")

abline(v = (filter$len - 1L) / filter$sr, col = "grey")
abline(v = filter$len / filter$sr, col = "red")

## zoom into a single jump of the idealisation
## we suggest to do this for every new measurement setup once 
## to control whether the correct filter is assumed
# idealisation by JULES (might take some time if not called somewhere before,
# please see its documentation for more details)
idealisation <- jules(gramA, filter = filter, startTime = 9, messages = 100)

## zoom into a single jump
plot(9 + seq(along = gramA) / filter$sr, gramA, pch = 16, col = "grey30",
     ylim = c(20, 50), xlim = c(9.6476, 9.6496), ylab = "Conductance in pS",
     xlab = "Time in s")

# idealisation
lines(idealisation, col = "red", lwd = 3)

# idealisation convolved with the filter
ind <- seq(9.647, 9.65, 1e-6)
convolvedSignal <- lowpassFilter::getConvolution(ind, idealisation, filter)
lines(ind, convolvedSignal, col = "blue", lwd = 3)

# idealisation with a wrong filter
# does not fit the recorded data points appropriately
wrongFilter <- lowpassFilter(type = "bessel",
                             param = list(pole = 6L, cutoff = 0.2),
                             sr = 1e4)
# the needed Monte-Carlo simulation depends on the number of observations and the filter
# hence a new simulation is required (if called for the first time)
idealisationWrong <- jules(gramA, filter = wrongFilter, startTime = 9, messages = 100)

# idealisation
lines(idealisationWrong, col = "orange", lwd = 3)

# idealisation convolved with the filter
ind <- seq(9.647, 9.65, 1e-6)
convolvedSignal <- lowpassFilter::getConvolution(ind, idealisationWrong, filter)
lines(ind, convolvedSignal, col = "darkgreen", lwd = 3)


# filter with sr == 1
filter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 1e3 / 1e4))

# filter kernel and its truncated version
plot(filter$kernfun, xlim = c(0, 20 / filter$sr))
t <- seq(0, 20 / filter$sr, 0.01 / filter$sr)
# truncated version, looks very similar
lines(t, filter$truncatedKernfun(t), col = "red")
# digitised filter
points((0:filter$len + 0.5) / filter$sr, filter$kern, col = "red", pch = 16)

# without a shift
filter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 1e3 / 1e4),
                        shift = 0)
# filter$kern starts with zero
points(0:filter$len / filter$sr, filter$kern, col = "blue", pch = 16)

# much shorter filter
filter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 1e3 / 1e4),
                        len = 4L)
points((0:filter$len + 0.5) / filter$sr, filter$kern, col = "darkgreen", pch = 16)

clampSeg documentation built on Jan. 28, 2022, 1:06 a.m.