profitBenchmarkConv: Benchmark convolution of an image with a point spread...

Description Usage Arguments Details Value Notes Author(s) See Also Examples

View source: R/profitBenchmarkConv.R

Description

This function will benchmark convolution of an image with a point spread function (PSF), returning results as well as a list of data stored by profitSetupData for optimising calls to profitConvolvePSF.

Usage

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profitBenchmarkConv(image=NULL, psf=NULL, calcregion=NULL, nbench=10,
  methods = c("Bruteconv","FFTconv","FFTWconv"), imagedim=NULL, psfdim=NULL, 
  refftpsf=FALSE, fftwplan=NULL,  maxfftwplaneffort=0)

Arguments

image

A matrix containing the image to benchmark convolution for. It should already be padded by half of the PSF width on either side to ensure that the convolved model can be cropped to the same size as the data. If no image is supplied, the user must supply imagedim.

psf

A matrix containing the PSF image to convolve the model image with. If no PSF is supplied, the user must supply psfdim.

calcregion

A logical matrix specifying regions of the image to avoid computing convolution for. See profitBruteConv and profitConvolvePSF for more details.

nbench

Integer; the number of times to benchmark each method. Repeated convolutions can vary in running time for all kinds of reasons, so nbench >= 10 is recommended.

methods

List of strings specifying which methods to test. Valid methods are Bruteconv", "FFTconv", and "FFTWconv". FFTconv is rarely fastest.

imagedim

Vector of dimensions of the image to create, if image is not provided.

psfdim

Vector of dimensions of the PSF to create, if psf is not provided.

refftpsf

Logical specifying whether to re-do the PSF FFT every iteration, which would be necessary if one is fitting the PSF.

fftwplan

A pre-computed plan for FFTW to decompose the FFT, as returned by "fftwplan" (can this be linked?). It must have been computed for a transform of an image with the same dimensions as the product of all image and PSF dimensions.

maxfftwplaneffort

The maximum effort level to compute the FFTW plan. FFTW plans can take a very long time to set up, so consider carefully before increasing beyond 0 - particularly if your padded image only has a few large prime factors.

Details

This function does two important things. Firstly it determines which of three different convolution options will work fastest given the provided combination of iamge and psf. In situations where the psf has much smaller dimensions than image this will pretty much always be Brute force convolution, but when the psf becomes comparable in size to the image then one of the two FFT routines will often be faster. In the provided example all three are similar speed.

The second important output of this function is preparing all the structures needed for FFT convolution if using profitConvolvePSF and selecting wither FFT or FFTW. The Examples show a clear example of how you use this output fft list in practice.

Value

List; complex structure containing:

result

A character string summarizing the benchmark results.

times

A vector of average time in ms for each method.

best

A list containing:

name

The name of the fastest method.

time

The average time in ms for the fastest method.

method

A character string containing the name of the best method (one of Bruteconv, FFTconv, FFTWconv), which defaults to best[['name']]. method can be directly parsed into profitConvolvePSF options.

fft

A list of useful items for FFT. fft can be directly parsed into profitConvolvePSF options., including:

fftwplan

The FFTW plan.

paddim

The dimensions of the zero-padded image, usually twice the input image dimensions and necessary to avoid periodicity artefacts.

padimagex

The x coordinates to place the original image in; by default the bottom-left corner of the padded image.

padimagey

The y coordinates to place the original image in; by default the bottom-left corner of the padded image.

cropx

The x coordinates of the convolved image within the padded output image; usually in the centre.

cropy

The y coordinates of the convolved image within the padded output image; usually in the centre.

fft

A list of useful items relating to the PSF, including:

r

The R FFT of the PSF.

w

The FFTW of the PSF. Should be nearly identical to r.

x

The x coordinates to place the PSF in; by default the centre of the bottom-left quadrant of the padded image.

y

The y coordinates to place the PSF in; by default the centre of the bottom-left quadrant of the padded image.

Notes

profitBruteConv is usually the fastest method, except for very large image/PSF combinations. Similarly, FFTW is almost always faster than R's built-in FFT.

Author(s)

Dan Taranu & Aaron Robotham

See Also

profitBruteConv, profitConvolvePSF, profitMakeModel, profitSetupData

Examples

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## Not run: 
model = list(
	sersic = list(
		xcen   = c(180, 60),
		ycen   = c(90, 10),
		mag = c(15, 13),
		re  = c(14, 5),
		nser  = c(3, 10),
		ang  = c(46, 80),
		axrat  = c(0.4, 0.6),
		box = c(0.5,-0.5)
	)
)

model.image=profitMakeModel(model=model, dim=c(200,200))$z

psf=profitMakeGaussianPSF()

#Do some benchmarking:

temp=profitBenchmarkConv(model.image, psf=psf, nbench=1)

#Check the best:

temp$best

#And we can use all three:

magimage(profitConvolvePSF(model.image, psf, options=list(method='Bruteconv')))
magimage(profitConvolvePSF(model.image, psf, options=list(method='FFTconv', fft=temp$fft)))
magimage(profitConvolvePSF(model.image, psf, options=list(method='FFTWconv', fft=temp$fft)))

#Some benchmarking for different size PSFs:

profitBenchmarkConv(imagedim=c(200,200), psfdim=c(11,11), nbench=1)
profitBenchmarkConv(imagedim=c(200,200), psfdim=c(21,21), nbench=1)
profitBenchmarkConv(imagedim=c(200,200), psfdim=c(31,31), nbench=1)

#Note they are all very similar in speed when psfdim=21. The time for FFT and FFTW
#pretty much scales with the number of pixels in the image (regardless of PSF).

#Because of how they scale, there are some rough rules-of-thumb you can use:

#Brute force is usually faster when psfdim<=21:

profitBenchmarkConv(imagedim=c(200,200), psfdim=c(15,15), nbench=1)

#FFT is usually faster when imagedim<400 & psfdim>21 & psfdim<100:

profitBenchmarkConv(imagedim=c(200,200), psfdim=c(51,51), nbench=1)

#FFTW is usually faster when imagedim>400 & psfdim>21

profitBenchmarkConv(imagedim=c(400,400), psfdim=c(25,25), nbench=1)

## End(Not run)

ProFit documentation built on July 23, 2019, 9:04 a.m.