Mercurial > repos > stevecassidy > wrassp
changeset 1:dbcf9bc275e3 draft
planemo upload commit 063e049d569aeb45e1008cbf044f2dad850eca3d-dirty
| author | stevecassidy |
|---|---|
| date | Wed, 07 Dec 2016 19:10:51 -0500 |
| parents | 6d6dc275b107 |
| children | 6f4db0e89117 |
| files | g_cepstrum.R g_cepstrum.xml g_f0.R g_f0.xml g_forest.R g_forest.xml get_fm_at_midpoint.xml outputAssp.R r_wrapper.sh util.R |
| diffstat | 10 files changed, 352 insertions(+), 4 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/g_cepstrum.R Wed Dec 07 19:10:51 2016 -0500 @@ -0,0 +1,26 @@ + +library(wrassp) + +args = commandArgs(TRUE) +# args will be like +# ${wavfile} ${output} +# ${beginTime} ${endTime} +# ${windowShift} ${window} ${resolution} +# ${fftLength} + + +if (length(args) != 8) { + print("Wrong number of arguments!") + q("no", status=1) +} + +res = cepstrum(args[1], toFile=FALSE, + beginTime=as.numeric(args[3]), + endTime=as.numeric(args[4]), + windowShift=as.numeric(args[5]), + window=args[6], + resolution=as.numeric(args[7]), + fftLength=as.numeric(args[8]) + ) + +assp_to_tsv(res, args[2])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/g_cepstrum.xml Wed Dec 07 19:10:51 2016 -0500 @@ -0,0 +1,67 @@ +<tool id="g_cepstrum" name="Compute Cepstrum" version="0.01"> + <description>using wrassp</description> + + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="0.1.4">r-wrassp</requirement> + </requirements> + + <command interpreter="bash"> + r_wrapper.sh $__tool_directory__/g_cepstrum.R --args ${wavfile} ${output} + ${beginTime} ${endTime} ${windowShift} ${window} ${resolution} + ${fftLength} + </command> + + <inputs> + <param name="wavfile" type="data" format="wav" label="Audio File" help="Audio file in WAV format"/> + <param name="beginTime" type="integer" value="0" label="Start time for analysis (s)"/> + <param name="endTime" type="integer" value="0" label="End Time for analysis (s) 0 means end of signal"/> + <param name="windowShift" type="integer" value="5" label="Window Shift (ms)" help="set analysis window shift to dur ms"/> + <param name="resolution" type="integer" value="40" label="set FFT length to the smallest value which results in a frequency resolution of freq Hz or better"/> + + <param name="fftLength" type="integer" value="0" label="set FFT length to num points (overrules 'resolution' option)"/> + <param name="window" type="select"> + <option value="BLACKMAN" selected="true">Blackman</option> + <option value="RECTANGLE">rectangle</option> + <option value="PARABOLA">parabola/Riesz/Welch</option> + <option value="COS" >cosine</option> + <option value="HANN" >Hann/hanning/cosine^2</option> + <option value="COS_4" >cosine^4</option> + <option value="HAMMING" >Hamming</option> + <option value="BLACK_X" >exact Blackman</option> + <option value="BLACK_M3" >min. 3-term Blackman-Nuttal</option> + <option value="BLACK_M4" >min. 4-term Blackman-Nuttal</option> + <option value="NUTTAL_3" >3-term Nuttal (-18 dB/oct)</option> + <option value="NUTTAL_4" >4-term Nuttal (-18 dB/oct)</option> + <option value="KAISER2_0">Kaiser-Bessel (alpha = 2.0)</option> + <option value="KAISER3_0">Kaiser-Bessel (alpha = 3.0)</option> + <option value="KAISER4_0">Kaiser-Bessel (alpha = 4.0)</option> + </param> + </inputs> + + <outputs> + <data name="output" format="tabular" label="#echo $wavfile.element_identifier.replace('wav', 'cep') #" /> + </outputs> + + + <tests> + <test> + <param name="wavfile" value="1_1119_2_22_001-ch6-speaker16.wav"/> + <output name="output" file="1_1119_2_22_001-cepstrum.dat"/> + </test> + </tests> + + <help>Short-term cepstral analysis of the signal using the Fast Fourier Transform. The number of coefficients per output record will also equal the FFT length / 2 + 1 (i.e. be non-mirrored).</help> + + <citations> + <citation type='bibtex'> + @Manual{, + title = {wrassp: an R wrapper to the ASSP Library}, + author = {Lasse Bombien and Raphael Winkelmann and Michel + Scheffers}, + year = {2016}, + note = {R package version 0.1.4}, + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/g_f0.R Wed Dec 07 19:10:51 2016 -0500 @@ -0,0 +1,25 @@ + +library(wrassp) + +args = commandArgs(TRUE) +# args will be like +# ${wavfile} ${output} +# ${beginTime} ${endTime} ${windowShift} ${gender} ${maxF} ${minF} ${minAmp} ${maxZCR} + + + +if (length(args) != 10) { + print("Wrong number of arguments!") + q("no", status=1) +} + +res = ksvF0(args[1], toFile=FALSE, beginTime=as.numeric(args[3]), endTime=as.numeric(args[4]), + windowShift=as.numeric(args[5]), + gender=args[6], + maxF=as.numeric(args[7]), + minF=as.numeric(args[8]), + minAmp=as.numeric(args[9]), + maxZCR=as.numeric(args[10]) + ) + +assp_to_tsv(res, args[2])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/g_f0.xml Wed Dec 07 19:10:51 2016 -0500 @@ -0,0 +1,57 @@ +<tool id="g_f0" name="Get Pitch" version="0.01"> + <description>using wrassp ksvF0 pitch tracker</description> + + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="0.1.4">r-wrassp</requirement> + </requirements> + + <command interpreter="bash"> + r_wrapper.sh $__tool_directory__/g_f0.R --args ${wavfile} ${output} + ${beginTime} ${endTime} ${windowShift} ${gender} ${maxF} ${minF} ${minAmp} ${maxZCR} + </command> + + + <inputs> + <param name="wavfile" type="data" format="wav" label="Audio File" help="Audio file in WAV format"/> + <param name="beginTime" type="integer" value="0" label="Start time for analysis (s)"/> + <param name="endTime" type="integer" value="0" label="End Time for analysis (s) 0 means end of signal"/> + <param name="windowShift" type="integer" value="5" label="Window Shift (ms)" help="set analysis window shift to dur ms"/> + <param name="gender" type="select" label="Speaker Gender"> + <option value="m" selected="true">Male</option> + <option value="f">Female</option> + <option value="u">Unknown</option> + </param> + <param name="maxF" type="integer" value="500" label="Maximum F0 Frequency (Hz)"/> + <param name="minF" type="integer" value="50" label="Minimum F0 Frequency (Hz)"/> + <param name="minAmp" type="integer" value="100" label="Amplitude threshold for voiced samples"/> + <param name="maxZCR" type="integer" value="3000" label="Maximum zero crossing rate in Hz (for voicing detection)"/> + </inputs> + + <outputs> + <data name="output" format="tabular" label="#echo $wavfile.element_identifier.replace('wav', 'f0') #" /> + </outputs> + + + <tests> + <test> + <param name="wavfile" value="1_1119_2_22_001-ch6-speaker16.wav"/> + <output name="output" file="1_1119_2_22_001-F0.dat"/> + </test> + </tests> + + <help>F0 analysis of the signal using the K. Schaefer-Vincent periodicity detection algortithm. + </help> + + <citations> + <citation type='bibtex'> + @Manual{, + title = {wrassp: an R wrapper to the ASSP Library}, + author = {Lasse Bombien and Raphael Winkelmann and Michel + Scheffers}, + year = {2016}, + note = {R package version 0.1.4}, + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/g_forest.R Wed Dec 07 19:10:51 2016 -0500 @@ -0,0 +1,29 @@ + +library(wrassp) + +args = commandArgs(TRUE) +# args will be like +# ${wavfile} ${output} +# ${beginTime} ${endTime} ${windowShift} ${windowSize} ${effectiveLength} +# ${nominalF1} ${gender} ${estimate} ${order} ${incrOrder} ${numFormants} +# ${window} ${preEmphasis} + + +if (length(args) != 15) { + print("Wrong number of arguments!") + q("no", status=1) +} + +res = forest(args[1], toFile=FALSE, beginTime=as.numeric(args[3]), endTime=as.numeric(args[4]), + windowShift=as.numeric(args[5]), + windowSize=as.numeric(args[6]), + effectiveLength=as.integer(args[7]), + nominalF1=as.numeric(args[8]), + gender=args[9], + estimate=as.integer(args[10]), + order=as.numeric(args[11]), incrOrder=as.numeric(args[12]), + numFormants=as.numeric(args[13]), window=args[14], + preemphasis=as.numeric(args[15]) + ) + +assp_to_tsv(res, args[2])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/g_forest.xml Wed Dec 07 19:10:51 2016 -0500 @@ -0,0 +1,87 @@ +<tool id="g_forest" name="Get Formants" version="0.01"> + <description>using wrassp formant tracker</description> + + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="0.1.4">r-wrassp</requirement> + </requirements> + + <command interpreter="bash"> + r_wrapper.sh $__tool_directory__/g_forest.R --args ${wavfile} ${output} + ${beginTime} ${endTime} ${windowShift} ${windowSize} ${effectiveLength} + ${nominalF1} ${gender} ${estimate} ${order} ${incrOrder} ${numFormants} + ${window} ${preemphasis} + </command> + + + <inputs> + <param name="wavfile" type="data" format="wav" label="Audio File" help="Audio file in WAV format"/> + <param name="beginTime" type="integer" value="0" label="Start time for analysis (s)"/> + <param name="endTime" type="integer" value="0" label="End Time for analysis (s) 0 means end of signal"/> + <param name="windowShift" type="integer" value="5" label="Window Shift (ms)" help="set analysis window shift to dur ms"/> + <param name="windowSize" type="integer" value="20" label="Window Size (ms)" help="set analysis window size to dur ms"/> + <param name="effectiveLength" type="select" label="make window size effective rather than exact"> + <option value="1" selected="true">Yes</option> + <option value="0">No</option> + </param> + <param name="nominalF1" type="integer" value="500" label="Nominal F1 Frequency (Hz)"/> + <param name="gender" type="select" label="Speaker Gender"> + <option value="m" selected="true">Male</option> + <option value="f">Female</option> + <option value="u">Unknown</option> + </param> + <param name="estimate" type="select" label="Insert rough frequency estimates of missing formants (default: frequency set to zero)"> + <option value="1">Yes</option> + <option value="0" selected="true">No</option> + </param> + <param name="order" type="integer" value="0" label="analysis order (default 0 means automatic)"/> + <param name="incrOrder" type="integer" value="0" label="increment/decrement analysis order"/> + <param name="numFormants" type="integer" value="4" label="Number of formants"/> + <param name="window" type="select"> + <option value="BLACKMAN" selected="true">Blackman</option> + <option value="RECTANGLE">rectangle</option> + <option value="PARABOLA">parabola/Riesz/Welch</option> + <option value="COS" >cosine</option> + <option value="HANN" >Hann/hanning/cosine^2</option> + <option value="COS_4" >cosine^4</option> + <option value="HAMMING" >Hamming</option> + <option value="BLACK_X" >exact Blackman</option> + <option value="BLACK_M3" >min. 3-term Blackman-Nuttal</option> + <option value="BLACK_M4" >min. 4-term Blackman-Nuttal</option> + <option value="NUTTAL_3" >3-term Nuttal (-18 dB/oct)</option> + <option value="NUTTAL_4" >4-term Nuttal (-18 dB/oct)</option> + <option value="KAISER2_0">Kaiser-Bessel (alpha = 2.0)</option> + <option value="KAISER3_0">Kaiser-Bessel (alpha = 3.0)</option> + <option value="KAISER4_0">Kaiser-Bessel (alpha = 4.0)</option> + </param> + <param name="preemphasis" type="float" value="-0.8" min="-1" max="0" label="Pre-emphasis"/> + </inputs> + + <outputs> + <data name="output" format="tabular" label="#echo $wavfile.element_identifier.replace('wav', 'fm') #" /> + </outputs> + + + <tests> + <test> + <param name="wavfile" value="1_1119_2_22_001-ch6-speaker16.wav"/> + <output name="output" file="1_1119_2_22_001-formants.dat"/> + </test> + </tests> + + <help>Calculate the formant tracks for segments of an audio file. + Raw resonance frequency and bandwidth values are obtained by root-solving of the Linear Prediction polynomial from the autocorrelation method and the Split-Levinson-Algorithm (SLA). Resonances are then classified as formants using the so-called Pisarenko frequencies (by-product of the SLA) and a formant frequeny range table derived from the nominal F1 frequency. The latter may have to be increased by about 12% for female voices (see NominalF1 and Gender options). + </help> + + <citations> + <citation type='bibtex'> + @Manual{, + title = {wrassp: an R wrapper to the ASSP Library}, + author = {Lasse Bombien and Raphael Winkelmann and Michel + Scheffers}, + year = {2016}, + note = {R package version 0.1.4}, + } + </citation> + </citations> +</tool>
--- a/get_fm_at_midpoint.xml Mon Aug 15 23:48:20 2016 -0400 +++ b/get_fm_at_midpoint.xml Wed Dec 07 19:10:51 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="get_fm_at_midpoint" name="Get Formants at segment midpoint" version="0.01" force_history_refresh="True"> +<tool id="get_fm_at_midpoint" name="Get Formants at segment midpoint" version="0.01"> <description>using wrassp formant tracker</description> <requirements>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/outputAssp.R Wed Dec 07 19:10:51 2016 -0500 @@ -0,0 +1,37 @@ +assp_to_est <- function(assp, outfile) { + + # convert to a dataframe + result <- data.frame(assp[1]) + for(idx in seq(2,length(attr(assp,'names')))) { + result <- cbind(result, assp[idx]) + } + # add a column of timestamps + start <- attr(assp, 'startTime') + rate <- attr(assp, 'sampleRate') + sampletime <- seq(start, by=1/rate, length.out=nrow(result)) + # and a column of 1s for some reason + #one <- rep(1, nrow(result)) + result <- cbind(sampletime, result) + + # write header + #write("EST_File Track", file=outfile) + #write("DataType ascii", file=outfile, append=T) + #write("BreaksPresent true", file=outfile, append=T) + #write(paste("NumFrames", nrow(result)), file=outfile, append=T) + + #count <- 0 # count overall number of columns + #vcount <- 1 # count variables in assp obj + #for(name in attr(assp,'names')) { + # for (coln in seq(ncol(data.frame(assp[vcount])))) { + # colname = paste(name, coln, sep="_") + # write(c(paste("Channel_", count, " ", colname, sep="")), file=outfile, append=T) + # count <- count+1 + # } + # vcount <- vcount+1 + #} + #write(paste("NumChannels", count), file=outfile, append=T) + #write("EST_Header_End", file=outfile, append=T) + + + write.table(result, file=outfile, sep="\t", quote=F, row.names=F, col.names=T, append=F) +} \ No newline at end of file
--- a/r_wrapper.sh Mon Aug 15 23:48:20 2016 -0400 +++ b/r_wrapper.sh Wed Dec 07 19:10:51 2016 -0500 @@ -1,6 +1,6 @@ #!/bin/sh -### Run R providing the R script in $1 as standard input and passing +### Run R providing the R script in $1 as standard input and passing ### the remaining arguments on the command line # Function that writes a message to stderr and exits @@ -11,7 +11,9 @@ } # Ensure R executable is found -which R > /dev/null || fail "'R' is required by this tool but was not found on path" +which R > /dev/null || fail "'R' is required by this tool but was not found on path" + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" # Extract first argument infile=$1; shift @@ -20,4 +22,5 @@ test -f $infile || fail "R input file '$infile' does not exist" # Invoke R passing file named by first argument to stdin -R --vanilla --slave $* < $infile +# add in the util.R file too containing common functions +cat $DIR/util.R $infile | R --vanilla --slave $*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/util.R Wed Dec 07 19:10:51 2016 -0500 @@ -0,0 +1,17 @@ +assp_to_tsv <- function(assp, outfile) { + + # convert to a dataframe, need to add one column at a time + result <- data.frame(assp[1]) + if (length(attr(assp,'names'))>1) { + for(idx in seq(2,length(attr(assp,'names')))) { + result <- cbind(result, assp[idx]) + } + } + # add a column of timestamps + start <- attr(assp, 'startTime') + rate <- attr(assp, 'sampleRate') + time <- seq(start, by=1/rate, length.out=nrow(result)) + result <- cbind(time, result) + + write.table(result, file=outfile, sep="\t", quote=F, row.names=F, col.names=T, append=F) +}