Posted by
bnorthan on
Mar 21, 2014; 12:02pm
URL: http://imagej.273.s1.nabble.com/Rephrased-FFT-Question-tp5007000p5007030.html
Dedicated Java code is for sure the way to go. In this case FFTJ is
already dedicated Java code. The problem was the overhead in calling the
plugin. Since the script was written in Python it is actually possible to
import and access java directly.
The first (inefficient) implementation of the Macro
IJ.run("FFTJ Script", "real=TimeProfile imaginary=<none> complex344=[Single
> Precision] fft=forward fourier=[At (0,0,0)] show_power_spectrum")
> spectrum_plus=IJ.getImage()
> spectrum_pix=spectrum_plus.getProcessor().getPixels()
>
This actually can be easily reworked by using the java interfaces directly
transformer= SinglePrecFFT3D(timeprofile.getStack(), None)
> transformer.fft()
> spectrum_plus=transformer.toImagePlus(ComplexValueType.POWER_SPECTRUM,
> FourierDomainOrigin.AT_ZERO );
> spectrum_pix=spectrum_plus.getProcessor().getPixels()
>
I updated the "macro" (perhaps it should be called a script) and it should
be much faster now
https://github.com/bnorthan/RogueImageJPlugins/blob/master/FFTJ_scriptable/macros/Time_Macro.pyThe source code for FFTJ is provided with the plugin
http://rsb.info.nih.gov/ij/plugins/fftj.htmlBy inspecting it one can see which java interfaces are available and play
with the different ways of presenting the output (real and complex parts,
phase spectrum, power spectrum, etc.)
On Fri, Mar 21, 2014 at 6:31 AM, Doube, Michael <
[hidden email]> wrote:
> On 21/03/14 10:22, Herbie wrote:
> > Dedicated Java-code
> > could considerably speed-up the processing.
>
> +1 to that: macros are very slow at doing pixel-by-pixel calculations.
> Experience shows that you will get some orders of magnitude speed-up by
> implementing your algorithm in Java rather than macro. (and some orders of
> magnitude more if it's amenable to being shifted onto the GPU)
>
>
>
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