cluster.plot |
Plot data clusters |
detect.outline |
Detect otolith outline |
enrich.master.list |
Link information in the info.file to the coefficients obtained from the otolith images |
estimate.outline.reconstruction |
Estimate the outline reconstruction based on Fourier/wavelet compared to the outlines that have not been transformed |
FISH |
An example data file |
generateShapeCoefficients |
Get wavelet/Fourier coefficients and basic shape variables |
getFourier |
Get Fourier coefficients, filtered according to filter |
getMasterlist |
Get filtered master.list values |
getMeasurements |
Get simple shape variables, filtered according to filter |
getStdFourier |
Get standardized Fourier coefficients, filtered according to filter |
getStdMeasurements |
Get simple shape variables after standardization, filtered according to filter |
getStdWavelet |
Get standardized wavelet coefficients, filtered according to filter |
getWavelet |
Get wavelet coefficients, filtered according to filter |
outline.reconstruction.plot |
Plot outline reconstruction |
plotFourier |
Mean and standard deviation of the Fourier coefficients |
plotFourierShape |
Mean otolith shape based on Fourier reconstruction |
plotWavelet |
Mean and standard deviation of the wavelet coefficients |
plotWaveletShape |
Mean otolith shape based on wavelet reconstruction |
read.master.list |
Read updated master list |
remove.outline |
Remove otolith outline |
setFilter |
Set a filter to analyze the shape data |
shape |
An example shapeR instance including 160 images. |
shapeR |
shapeR |
shapeR-class |
shapeR |
show-method |
Show a shapeR object |
show.original.with.outline |
Show the extracted outline on top of the original image |
smoothout |
Contour smoothing |
stdCoefs |
Standardize coefficients |
write.image.with.outline |
Write outlines on top of the original images for quality checking |