http://imagej.273.s1.nabble.com/FFT-and-Inverse-FFT-problem-for-an-Electron-Microscope-Image-tp5013915p5013969.html
probably JTransform in the future) support 16 bit FFT. (if anyone knows
scaling problems. The same logic should eventually be easy to implement
> Thank you very much for that. I will try this code later when I am near my
> computer.
> Just one query please ? How does it work where I would like my final
> image to be 16 bits please ? Thank you for taking the time to do this.
>
> Sent from my iPad
>
> > On 10 Aug 2015, at 13:30, Brian Northan <
[hidden email]> wrote:
> >
> > If anyone is interested in an example of ops fft, below is a jython
> script
> > example that shows how to use the ops fft interface (it also uses
> > parameterized scripting and calls pieces of imglib2 using jython). It is
> > based on this imglib tutorial
> >
> >
>
https://github.com/imglib/imglib2-tutorials/blob/master/src/main/java/Example6c.java> >
> > If one copies and pastes the code at the bottom of this message into the
> > script editor of the latest Fiji release it should run and produce the
> same
> > result as the java tutorial. The images (DrosophillaWing.tif and
> > WingTemplate.tif) are available in the imglib2-tutorials repository.
> >
> >
https://github.com/imglib/imglib2-tutorials> >
> > Keep in mind the ops fft interfaces are fairly new and still in beta.
> > Feedback (and contributions) are very welcome - Brian
> >
> > # @DisplayService display
> > # @OpService ops
> > # @net.imagej.Dataset image
> > # @net.imagej.Dataset template
> >
> > '''
> > This example is an 'ops' version of:
> >
> >
>
http://fiji.sc/ImgLib2_Examples#Example_6c_-_Complex_numbers_and_Fourier_transforms> >
> > for which the code and images can be found
> >
> >
https://github.com/imglib/imglib2-tutorials> >
> > '''
> > from net.imglib2.img.display.imagej import ImageJFunctions;
> > from net.imglib2.type.numeric.complex import ComplexFloatType;
> > from net.imglib2.outofbounds import OutOfBoundsMirrorExpWindowingFactory;
> >
> > from net.imglib2.converter import ComplexImaginaryFloatConverter;
> > from net.imglib2.converter import ComplexPhaseFloatConverter;
> > from net.imglib2.converter import ComplexRealFloatConverter;
> >
> > from jarray import array
> >
> > # perform fft of the template
> >
> > # basic fft call with no parameters
> > #templateFFT=ops.fft(template.getImgPlus())
> >
> > # alternatively to pass an outofbounds factory we have to pass every
> > parameter. We want:
> > # output='None', input=template, borderSize=10 by 10, fast='True',
> > outOfBoundsFactor=OutOfBoundsMirrorExpWindowingFactory
> > templateFFT=ops.fft(None, template.getImgPlus(), array([10, 10], 'l'),
> > True, OutOfBoundsMirrorExpWindowingFactory(0.25));
> >
> > # display fft (by default in generalized log power spectrum)
> > ImageJFunctions.show(templateFFT).setTitle("fft power spectrum");
> >
> > # display fft phase spectrum
> > ImageJFunctions.show( templateFFT,ComplexPhaseFloatConverter()
> ).setTitle(
> > "fft phase spectrum" );
> >
> > # display fft real values
> > ImageJFunctions.show( templateFFT,ComplexRealFloatConverter() ).setTitle(
> > "fft real values" );
> >
> > # display fft imaginary values
> > ImageJFunctions.show( templateFFT, ComplexImaginaryFloatConverter()
> > ).setTitle( "fft imaginary values" );
> >
> > # complex invert the fft of the template
> > c = ComplexFloatType();
> > for t in templateFFT:
> > c.set(t);
> > t.complexConjugate();
> > c.mul(t);
> > t.div(c);
> >
> > # create Img memory for inverse FFT and compute inverse
> > templateInverse=ops.createImg(array([template.dimension(0),
> > template.dimension(1)], 'l'))
> >
> > ops.ifft(templateInverse, templateFFT)
> > display.createDisplay("template inverse", templateInverse)
> >
> > # convolve templateInverse with image
> > final=ops.convolve(image, templateInverse);
> > display.createDisplay("final", final)
> >
> >> On Fri, Aug 7, 2015 at 4:40 PM, Curtis Rueden <
[hidden email]>
> wrote:
> >>
> >> Hi everyone,
> >>
> >> Regarding FFT and IFFT operations, I just wanted to mention that ImageJ
> Ops
> >> (distributed as part of ImageJ2!) does have these operations [1, 2, 3,
> 4,
> >> 5], driven by the powerful ImgLib2 library [6]. And very soon to be
> using
> >> JTransforms [7] as mentioned by Dimiter (currently it uses Mines JTK [8,
> >> 9]).
> >>
> >> So for anyone considering reinventing this wheel: please consider
> >> contributing to Ops rather that starting a new and instantly obsolete
> >> plugin. ;-)
> >>
> >> Regards,
> >> Curtis
> >>
> >> [1]
> >>
> >>
>
https://github.com/imagej/imagej-ops/tree/imagej-ops-0.16.0/src/main/java/net/imagej/ops/filter/fft> >> [2]
> >>
> >>
>
https://github.com/imagej/imagej-ops/tree/imagej-ops-0.16.0/src/main/java/net/imagej/ops/filter/fftSize> >> [3]
> >>
> >>
>
https://github.com/imagej/imagej-ops/tree/imagej-ops-0.16.0/src/main/java/net/imagej/ops/filter/ifft> >> [4]
> >>
> >>
>
https://github.com/imagej/imagej-ops/blob/imagej-ops-0.16.0/src/main/java/net/imagej/ops/filter/FilterNamespace.java#L569-L702> >> [5]
> >>
> >>
>
https://github.com/imagej/imagej-ops/blob/imagej-ops-0.16.0/src/main/java/net/imagej/ops/filter/FilterNamespace.java#L879-L910> >> [6]
https://github.com/imglib/imglib2-algorithm-fft> >> [7]
https://github.com/imglib/imglib2-algorithm-fft/pull/3> >> [8]
https://github.com/imglib/imglib2/issues/61> >> [9]
https://github.com/imglib/imglib2/issues/38> >>
> >>
> >> On Fri, Aug 7, 2015 at 9:05 AM, Rosenberg, Mark F <
> >>
[hidden email]> wrote:
> >>
> >>> Dear Dimiter
> >>> Thank you for your feedback and suggestions too.
> >>> Best Regards,
> >>> Mark
> >>>> On 7 Aug 2015, at 11:12, Dimiter Prodanov <
[hidden email]>
> wrote:
> >>>>
> >>>> Dear all,
> >>>>
> >>>> Handing of FFTs (and complex numbers) is a definite weakness of
> ImageJ.
> >>>> Actually ImageJ implements only the Discrete Hartley transform in
> order
> >>> to
> >>>> avoid as much as possible use of complex numbers.
> >>>> May be this was a reasonable design choice 15 years ago when ImageJ
> was
> >>>> hardly more than an applet displaying an image but now I think it will
> >>> make
> >>>> much sense to reconsider this.
> >>>>
> >>>> To put it simply without canonical state of the art FFT/IFFT routine
> >>>> ImageJ is not suitable for serious work in linear filtering/signal
> >>>> processing.
> >>>>
> >>>> It will be nice to expose FFTs using for example JTransforms library
> >>>>
https://sites.google.com/site/piotrwendykier/software/jtransforms> >>>>
> >>>> I think that the licenses are compatible.
> >>>>
> >>>> best regards,
> >>>>
> >>>> Dimiter Prodanov
> >>>>
> >>>> --
> >>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >>>
> >>> --
> >>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >>>
> >>
> >> --
> >> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >>
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>