Re: Histogram Matching | python script attached, questions remain

Posted by Curtis Rueden-2 on Oct 08, 2019; 6:50pm
URL: http://imagej.273.s1.nabble.com/Histogram-Matching-python-script-attached-questions-remain-tp5022497p5022500.html

Hi Rainer,

> console: Failed to install '':
> java.nio.charset.UnsupportedCharsetException: cp0. What can I do about
> this char-error?

This is a bug in Jython on Windows:
https://bugs.jython.org/issue2222

See also:
https://forum.image.sc/t/script-editor-error-when-working-with-python-scripts/5893

If you launch ImageJ with:
  -Dpython.console.encoding=UTF-8
the error should be prevented. However, if I understand correctly, it does
not prevent the script from running successfully.

> I hoped calling it from a macro would work with ease.. but I do not
> know how or where to put the script.

Save your script somewhere like Fiji.app/scripts/Analyze/Match_Histogram.py.
Then you will have a menu entry Analyze > Match Histogram.
Launch the Macro Recorder, then run Match Histogram, and a macro line of
code will be generated.

See also:
https://imagej.net/Scripting#Adding_scripts_to_the_Plugins_menu

> Can someone point me to python examples of a script, which
> differentiates between image types?

You can check the type of the image using ImpImage1.getType() and compare
the result to ImagePlus.COLOR_RGB.

By the way: your script would be a lot shorter using script parameters:

--snip--
#@ ImagePlus (label="target image") ImpImage1
#@ ImagePlus (label="reference image") ImpImage2

import ij.IJ
from histogram2 import HistogramMatcher

ip1 = ImpImage1.getProcessor()
ip2 = ImpImage2.getProcessor()

hist1 = ip1.getHistogram()
hist2 = ip2.getHistogram()

matcher = HistogramMatcher()
newHist = matcher.matchHistograms(hist1, hist2)

ip1.applyTable(newHist)
ImpImage1.setProcessor(ip1)

ImpImage1.show()
ImpImage2.show()
--snap--

For details see https://imagej.net/Script_Parameters

Regards,
Curtis

--
Curtis Rueden
Software architect, LOCI/Eliceiri lab - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Have you tried the Image.sc Forum? https://forum.image.sc/



On Tue, Oct 8, 2019 at 6:55 AM Rainer M. Engel <[hidden email]> wrote:

> Hey everyone..
>
> I'm typically working with another software, where histogram matching is
> easy available. Recently I stumbled upon an thread on stack overflow on
> this topic with ImageJ
> https://stackoverflow.com/questions/25085871/match-histogram-imagej
>
> Since I wanted to create a "script plugin" which I can call from a
> macro, I finally chose python, because it was easier to find examples
> helping me out.
>
> I used these two images..
> "
> https://juliahartel.files.wordpress.com/2013/07/kornfeld-in-goldener-abendsonne.jpg
> "
> "
> https://naturfotografen-forum.de/data/o/142/713934/image::Frank_Steinmann_auwald_rheinaue_wald.jpg
> "
>
> Hoping the indentation is preserved!
> #PYTHON-CODE---------------------------------------------------
> from fiji.util.gui import GenericDialogPlus
> import ij.IJ
> from histogram2 import HistogramMatcher
>
>
> # Create an instance of GenericDialogPlus
> gui = GenericDialogPlus("histogram matching..")
>
> # Add possibility to choose some images already opened in Fiji
> gui.addImageChoice("target image","image1")
> gui.addImageChoice("reference image","image2")
>
> gui.showDialog()
>
> # Recover the inputs in order of "appearance"
> if gui.wasOKed():
>     ImpImage1 = gui.getNextImage() # This method directly returns the
> ImagePlus object
>     ImpImage2 = gui.getNextImage()
>
> ip1 = ImpImage1.getProcessor()
> ip2 = ImpImage2.getProcessor()
>
> hist1 = ip1.getHistogram()
> hist2 = ip2.getHistogram()
>
> matcher = HistogramMatcher()
> newHist = matcher.matchHistograms(hist1, hist2)
>
> ip1.applyTable(newHist)
> ImpImage1.setProcessor(ip1)
>
> ImpImage1.show()
> ImpImage2.show()
> #PYTHON-CODE---------------------------------------------------
>
>
> Questions:
> 1) This works interactively, but on first execution I get an error:
> [INFO] Reading available sites from https://imagej.net/
> console: Failed to install '':
> java.nio.charset.UnsupportedCharsetException: cp0.
> What can I do about this char-error?
>
>
> 2) I hoped calling it from a macro would work with ease.. but I do not
> know how or where to put the script.
>
> run("script:histogram-match.py", "target=[image
> Frank_Steinmann_auwald_rheinaue_wald.jpg]
> reference=kornfeld-in-goldener-abendsonne.jpg");
>
> With the above, I get an file.io error.
>
> <Error: java.io.FileNotFoundException:
>
> http://wsr.imagej.net/download/Examples/Python/script:G:ImageJ_hist-matchhistogram-match.py
> >
> in line 1:
>         var ; initializeSciJavaParameters ( ) ; run (
> "script:G:ImageJ_hist-matchhistogram-match.py" , "target=[image
> Frank_Ste...
>
>
> 3) Can someone point me to python examples of a script, which
> differentiates between image types? What the provided script needs is a
> fork for RGB images (Split Channels, working on them separately and
> merging them later on again). This creates very good results. One would
> only need to tiny smooth the correction curve, to reduce artefacts
> (especially if i.e. "kornfeld" is the target image). Currently I don't
> know if this is possible with "histogram2".
>
>
> Thank you very much, for any direction or help..
>
> Kind regards,
> Rainer
>
> --
> Rainer M. Engel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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