Get a nicer LUT on Cellpose output

[NicoKiaru]

Setting a LUT to an ImagePlus without using IJ.runis nightmarish.
IJ.run works, but it interferes with the macro recording and thus can't be used.

Here's the few things I tried but didn't work:

            new LUT()
            /*LutLoader ll = new LutLoader();
            ll.run("3-3-2 RGB.lut");
            //IndexColorModel lut = LutLoader.getLut("3-3-2 RGB");
            LutLoader.getLut("3-3-2 RGB.lut")
            //LUT lut = LutLoader.getLut("3-3-2 RGB");*/
            //new LutLoader("3-3-2 RGB").

            /*String IJ_LUT_FOLDER = IJ.getDirectory("luts");

            File lutFile = lutFiles.get(b);

            LUT currentLUT = LutLoader.openLut(lutFile.getAbsolutePath());


            Map<String, URL> luts = lutservice.findLUTs();

            if (luts.containsKey("3-3-2 RGB.lut")) {
                ColorTable lut = lutservice.loadLUT(luts.get("3-3-2 RGB.lut"));



                /*lutservice.applyLUT();

                DefaultLUTService dls;*/

                /*luts.get("3-3-2 RGB.lut")
                //String path = java.net.URLDecoder.decode(luts.get("3-3-2 RGB.lut").toString(), StandardCharsets.UTF_8.name()); // Because 3-3-2 RGB has a space
                lut = LutLoader.openLut(luts.get("3-3-2 RGB.lut"));
                cellpose_imp.setLut(lut);*/
            // }

            //add a LUT
            //IJ.run(cellpose_imp, "3-3-2 RGB", "");

So until we find a solution that is simple, the output is going to be in grayscale.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-wrapper-s-for-cellpose-and-omnipose-new-version-big-decisions/94735/33

[NicoKiaru]

issue was duplicated in #40

[NicoKiaru]

See @tferr's solution in

in https://forum.image.sc/t/fiji-wrapper-s-for-cellpose-and-omnipose-new-version-big-decisions/94735/36

[haesleinhuepf]

Hi @NicoKiaru ,

I just saw the discussion on image.sc. If you're still worroied about the macro recording, you can turn of the recorder for a moment and then reactivate it like this:

https://github.com/clij/clij/blob/caad98e4703911cd0b78b2bf751473141b2bb5cc/src/main/java/net/haesleinhuepf/clij/macro/AbstractCLIJPlugin.java#L495-L500

Cheers,
Robert

[NicoKiaru]

Hey, thanks Robert! Indeed that's something I rediscovered yesterday 😓 in a different context. And I had to do even worse for concatenator.

But I did not realize I could also do it for the LUT, thanks! This looks like an easy solution indeed.