reading channel display color

[Leoncio Vergara]

Hi, I have a very simple question. Is there a macro instruction to read the display color for a channel in image J? I can read the min and max display values for the gray values, I can also setup the color for a given channel, but if I want to et the information from an open image and transfer it to another one, I cant find the solution. I would appreciate if anybody could point me in the right direction.

Thank you

Leo Vergara

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi Leoncio,

the color information is in the LUT (color lookup table) of each channel.
In a macro, you can read the LUT with
   getLut(reds, greens, blues)
and set it with
   setLut(reds, greens, blues)

You have to transfer the LUT for each channel.

Michael
________________________________________________________________
On 27.10.20 16:52, Leoncio Vergara wrote:
> Hi, I have a very simple question. Is there a macro instruction to read the display color for a channel in image J? I can read the min and max display values for the gray values, I can also setup the color for a given channel, but if I want to et the information from an open image and transfer it to another one, I cant find the solution. I would appreciate if anybody could point me in the right direction.
>
> Thank you
>
> Leo Vergara
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Robert Smith]

Hello Leo,
If you are skilled in math, simply match the ranges of the two images. Maximum to maximum, and minimum to minimum.  You can do this with Process>Math.
Bob


________________________________
From: Leoncio Vergara <[hidden email]>
Sent: Tuesday, October 27, 2020 11:52 AM
To: [hidden email] <[hidden email]>
Subject: reading channel display color

Hi, I have a very simple question. Is there a macro instruction to read the display color for a channel in image J? I can read the min and max display values for the gray values, I can also setup the color for a given channel, but if I want to et the information from an open image and transfer it to another one, I cant find the solution. I would appreciate if anybody could point me in the right direction.

Thank you

Leo Vergara
.
--
ImageJ mailing list: https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&amp;data=04%7C01%7C%7C74655f4294364a36645b08d87a90d427%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637394109730408717%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=zBzoab9vgE7z5albw39isFMmZFGopR5BxHJNaBVkDlk%3D&amp;reserved=0

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Krs5]

Dear Leo,

The macro code below detect the colour of a channel.

run("Neuron (5 channels)");
Stack.getDimensions(width, height, channels, slices, frames);
color=newArray(channels+1);
for (i=1; i<=channels; i++){
if (channels>1) Stack.setChannel(i);
getLut(reds, greens, blues);
if ((reds[i]==i)&&(greens[i]==0)&&(blues[i]==0)) color[i] = "red";
if ((reds[i]==0)&&(greens[i]==i)&&(blues[i]==0)) color[i] = "green";
if ((reds[i]==0)&&(greens[i]==0)&&(blues[i]==i)) color[i] = "blue";
if ((reds[i]==0)&&(greens[i]==i)&&(blues[i]==i)) color[i] = "cyan";
if ((reds[i]==i)&&(greens[i]==0)&&(blues[i]==i)) color[i] = "magenta";
if ((reds[i]==i)&&(greens[i]==1)&&(blues[i]==0)) color[i] = "yellow";
if ((reds[i]==i)&&(greens[i]==i)&&(blues[i]==i)) color[i] = "gray";
print (color[i]);
}

You can then use this information to set the LUT for a channel.

Hope this helps

Best wishes

Kees


Dr Ir K.R. Straatman
Advanced Imaging Facility

University of Leicester
www.le.ac.uk/advanced-imaging-facility<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.le.ac.uk%2Fadvanced-imaging-facility&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C59b63365222d4a2d72dc08d7a0dad4b6%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637154734055515186&sdata=821yl9l42Hs2RuVMTZexifQ2LAz%2FsheYZrJPxzgIxkE%3D&reserved=0>


________________________________
From: Leoncio Vergara
Sent: 27 October 2020 15:52
Subject: reading channel display color

Hi, I have a very simple question. Is there a macro instruction to read the display color for a channel in image J? I can read the min and max display values for the gray values, I can also setup the color for a given channel, but if I want to et the information from an open image and transfer it to another one, I cant find the solution. I would appreciate if anybody could point me in the right direction.

Thank you

Leo Vergara

--
ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&amp;data=04%7C01%7Ckrs5%40leicester.ac.uk%7C7230667c35a945820ee908d87a90d3fb%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637394109748541556%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=gBcVJZ1MZK46cphvDCoCHg%2BAYAVLIeJZH7SMjYNY2uk%3D&amp;reserved=0

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Gabriel Landini]

Hi Kees,
Nice script. Can I contribute a suggestion?
You could test if the LUT is incrementally linear for the R G B components of
the LUT through the 256 levels, in case some other LUT has been applied or
inverted.
For example when using a different lut the modification below would detect it
(just uncomment line 2 to test).
There might be more elegant ways to test if the LUT linearly increases to 255.
The suggestion below checks that increments are all 1 between levels and that
the highest LUT value is 255.

run("Neuron (5 channels)");
//run("Ice"); //uncomment to test a different LUT
Stack.getDimensions(width, height, channels, slices, frames);
color=newArray(channels+1);
for (i=1; i<=channels; i++){
  if (channels>1) Stack.setChannel(i);
  getLut(reds, greens, blues);
  chr= chg= chb=-1;
  for (j=0;j<255;j++) {
   if (reds[j+1]-reds[j]!=1) chr=0;
   if (greens[j+1]-greens[j]!=1) chg=0;
   if (blues[j+1]-blues[j]!=1) chb=0;
  }
  if (reds[255]!=255) chr=0;
  if (greens[255]!=255) chg=0;
  if (blues[255]!=255) chb=0;
  //print (chr, chg, chb);

 color[i]="unrecognised LUT";
  if (chr==-1 && chg ==0 && chb==0) color[i] = "red";
  if (chr==0 && chg ==-1 && chb==0)  color[i] = "green";
  if  (chr==0 && chg ==0 && chb==-1) color[i] = "blue";
  if  (chr==0 && chg ==-1 && chb==-1) color[i] = "cyan";
  if  (chr==-1 && chg ==0 && chb==-1)  color[i] = "magenta";
  if  (chr==-1 && chg ==-1 && chb==0) color[i] = "yellow";
  if  (chr==-1 && chg ==-1 && chb==-1) color[i] = "gray";
  print (color[i]);
}

Cheers

Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jeremy Adler]

Hi Gabriel,

For added masochism you could compare the values of the LUT with the LUTs available in ImageJ - and find the LUT's actual name.
Except that the LUT might not be present and the name (e.g. glasbey) might not give dominant colour.

Jeremy Adler





-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Gabriel Landini
Sent: Wednesday, October 28, 2020 12:18 PM
To: [hidden email]
Subject: Re: reading channel display color

Hi Kees,
Nice script. Can I contribute a suggestion?
You could test if the LUT is incrementally linear for the R G B components of the LUT through the 256 levels, in case some other LUT has been applied or inverted.
For example when using a different lut the modification below would detect it (just uncomment line 2 to test).
There might be more elegant ways to test if the LUT linearly increases to 255.
The suggestion below checks that increments are all 1 between levels and that the highest LUT value is 255.

run("Neuron (5 channels)");
//run("Ice"); //uncomment to test a different LUT Stack.getDimensions(width, height, channels, slices, frames); color=newArray(channels+1); for (i=1; i<=channels; i++){
  if (channels>1) Stack.setChannel(i);
  getLut(reds, greens, blues);
  chr= chg= chb=-1;
  for (j=0;j<255;j++) {
   if (reds[j+1]-reds[j]!=1) chr=0;
   if (greens[j+1]-greens[j]!=1) chg=0;
   if (blues[j+1]-blues[j]!=1) chb=0;
  }
  if (reds[255]!=255) chr=0;
  if (greens[255]!=255) chg=0;
  if (blues[255]!=255) chb=0;
  //print (chr, chg, chb);

 color[i]="unrecognised LUT";
  if (chr==-1 && chg ==0 && chb==0) color[i] = "red";
  if (chr==0 && chg ==-1 && chb==0)  color[i] = "green";
  if  (chr==0 && chg ==0 && chb==-1) color[i] = "blue";
  if  (chr==0 && chg ==-1 && chb==-1) color[i] = "cyan";
  if  (chr==-1 && chg ==0 && chb==-1)  color[i] = "magenta";
  if  (chr==-1 && chg ==-1 && chb==0) color[i] = "yellow";
  if  (chr==-1 && chg ==-1 && chb==-1) color[i] = "gray";
  print (color[i]);
}

Cheers

Gabriel

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html








När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html