Current lut?

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Current lut?

Gabriel Landini
Hi,
I wonder if there is a way to retrieve what is the name of (the last?) LUT
applied to an image.
I appreciate that LUTs can be changed on the fly  without loading one from a
file and therefore might not be a robust way of knowing what is being
displayed.

Cheers

Gabriel

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Re: Current lut?

CARL Philippe (LBP)
Dear Gabriel,
Some more expert people may probably deny what I will be writing below.
But from my point of view, a LUT is just some kind of "sunglasses" that you can wear in order to look at your data (i.e. your picture) ; these data staying the same whatever sunglasses you try on.
Thus I don't really see a reason why the name of last used LUT on a given picture should be saved.
My best regards,
Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 42 89

----- Mail original -----
De: "Gabriel Landini" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Mardi 23 Juin 2020 13:00:09
Objet: Current lut?

Hi,
I wonder if there is a way to retrieve what is the name of (the last?) LUT
applied to an image.
I appreciate that LUTs can be changed on the fly  without loading one from a
file and therefore might not be a robust way of knowing what is being
displayed.

Cheers

Gabriel

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Re: Current lut?

Jeremy Adler
Dear Philippe,
As you say the LUT simply changes how an image appears on the screen when it is reopened,
But the LUT is saved with the image, so its name is useful - if I want to display another image using the same LUT.

Or if the image came from another computer, possibly with a different list of LUTs, what its name was and therefore which
name to use if I add the LUT to my computer.

Gabriel is not making an unreasonable request, and the name adds only a tiny amount of data to the image file.
At worst adding the name is harmless.


Jeremy Adler

===============================================
                    B i o V i s   P l a t f o r m of  Uppsala University
                   Light & EM microscopy / FlowCytometry & Cell Sorting / Image Analysis
===============================================
Jeremy Adler   PhD - Senior research engineer
Light, Confocal Microscopy, Image Analysis
E-mail: [hidden email]
070-1679349

Dag Hammarskjölds v 20
751 85 UPPSALA, SWEDEN
http://biovis.uu.se/
===============================================



-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of CARL Philippe (LBP)
Sent: Tuesday, June 23, 2020 1:16 PM
To: [hidden email]
Subject: Re: Current lut?

Dear Gabriel,
Some more expert people may probably deny what I will be writing below.
But from my point of view, a LUT is just some kind of "sunglasses" that you can wear in order to look at your data (i.e. your picture) ; these data staying the same whatever sunglasses you try on.
Thus I don't really see a reason why the name of last used LUT on a given picture should be saved.
My best regards,
Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies UMR 7021 CNRS - Université de Strasbourg Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 42 89

----- Mail original -----
De: "Gabriel Landini" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Mardi 23 Juin 2020 13:00:09
Objet: Current lut?

Hi,
I wonder if there is a way to retrieve what is the name of (the last?) LUT applied to an image.
I appreciate that LUTs can be changed on the fly  without loading one from a file and therefore might not be a robust way of knowing what is being displayed.

Cheers

Gabriel

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Re: Current lut?

Gabriel Landini
In reply to this post by CARL Philippe (LBP)
Hi,
Sure, sunglasses... I hope there is nothing wrong if I want to know what
sunglasses I am  wearing? :-) specially if they change the appearance of the
data I am looking at.

What prompted me to ask this is I programmed a LUT button that cycles thought
the many LUTs collected over the years.  If I find one I like and dif not keep
track of the name at the time of loading I do not know which one it is.

It might be useful in other instances: is it a linear greyscale or stretched
logarithmic greyscale LUT? They might look pretty close but to find out I have
to through Show LUT, compare it to another LUT, etc.

Also note that the "inverted LUT" is shown at the top of the frame but not
other LUTs. That alone would be useful, but to clarify, I am not requesting
this to be added. I am only asking if there is a way to know which one has
been applied last to a given image.

If there is no way of doing this, storing the LUT name might be one solution
(thanks Jeremy), and might bring other issues: load a LUT and then
programmatically (or via the LUT editor) change it. Would that require
resetting the stored name?
That issue happens with the current inverted LUT display, if you edit, the
window still says (inverting LUT) although it might not be so anymore).

Cheers

Gabriel

On Tuesday, 23 June 2020 12:15:47 BST [hidden email] wrote:
> Dear Gabriel,
> Some more expert people may probably deny what I will be writing below.
> But from my point of view, a LUT is just some kind of "sunglasses" that you
> can wear in order to look at your data (i.e. your picture) ; these data
> staying the same whatever sunglasses you try on. Thus I don't really see a
> reason why the name of last used LUT on a given picture should be saved. My
> best regards,
> Philippe
>

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Re: Current lut?

Herbie
Dear Gabriel,

the most convenient way to achieve what you want is the display of the
LUT-name as a subtitle-label, as with the inverted LUT. I think you can
easily write either some simple macro- or plugin-code to achieve this.

Another, less obvious way would be to set a checkmark in the LUT-menu
indicating the currently applied LUT. This appears more involved however.

Presently, the image info doesn't show the applied LUT (but of course it
could or you could use the new properties feature to show it).
Furthermore, the LUT-name is presently not included as tif-tag.

Kind regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 23.06.20 um 14:04 schrieb Gabriel Landini:

> Hi,
> Sure, sunglasses... I hope there is nothing wrong if I want to know what
> sunglasses I am  wearing? :-) specially if they change the appearance of the
> data I am looking at.
>
> What prompted me to ask this is I programmed a LUT button that cycles thought
> the many LUTs collected over the years.  If I find one I like and dif not keep
> track of the name at the time of loading I do not know which one it is.
>
> It might be useful in other instances: is it a linear greyscale or stretched
> logarithmic greyscale LUT? They might look pretty close but to find out I have
> to through Show LUT, compare it to another LUT, etc.
>
> Also note that the "inverted LUT" is shown at the top of the frame but not
> other LUTs. That alone would be useful, but to clarify, I am not requesting
> this to be added. I am only asking if there is a way to know which one has
> been applied last to a given image.
>
> If there is no way of doing this, storing the LUT name might be one solution
> (thanks Jeremy), and might bring other issues: load a LUT and then
> programmatically (or via the LUT editor) change it. Would that require
> resetting the stored name?
> That issue happens with the current inverted LUT display, if you edit, the
> window still says (inverting LUT) although it might not be so anymore).
>
> Cheers
>
> Gabriel
>
> On Tuesday, 23 June 2020 12:15:47 BST [hidden email] wrote:
>> Dear Gabriel,
>> Some more expert people may probably deny what I will be writing below.
>> But from my point of view, a LUT is just some kind of "sunglasses" that you
>> can wear in order to look at your data (i.e. your picture) ; these data
>> staying the same whatever sunglasses you try on. Thus I don't really see a
>> reason why the name of last used LUT on a given picture should be saved. My
>> best regards,
>> Philippe
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Current lut?

CARL Philippe (LBP)
Dear Herbie and Gabriel,
If I would like to save the used LUT data, I would rather store them within the picture meta data (maybe using the new info features Wayne implemented some weeks ago) than within the subtitle-label .
But as I understand the request of Gabriel (but since my last exchanges with Fred, who is drastically differentiating two sentences which are fully identical for me, I may probably have understanding issues in English) he would like to have these informations saved within the meta data as default.
Take care,
Philippe

----- Mail original -----
De: "l16" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Mardi 23 Juin 2020 14:33:40
Objet: Re: Current lut?

Dear Gabriel,

the most convenient way to achieve what you want is the display of the
LUT-name as a subtitle-label, as with the inverted LUT. I think you can
easily write either some simple macro- or plugin-code to achieve this.

Another, less obvious way would be to set a checkmark in the LUT-menu
indicating the currently applied LUT. This appears more involved however.

Presently, the image info doesn't show the applied LUT (but of course it
could or you could use the new properties feature to show it).
Furthermore, the LUT-name is presently not included as tif-tag.

Kind regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 23.06.20 um 14:04 schrieb Gabriel Landini:

> Hi,
> Sure, sunglasses... I hope there is nothing wrong if I want to know what
> sunglasses I am  wearing? :-) specially if they change the appearance of the
> data I am looking at.
>
> What prompted me to ask this is I programmed a LUT button that cycles thought
> the many LUTs collected over the years.  If I find one I like and dif not keep
> track of the name at the time of loading I do not know which one it is.
>
> It might be useful in other instances: is it a linear greyscale or stretched
> logarithmic greyscale LUT? They might look pretty close but to find out I have
> to through Show LUT, compare it to another LUT, etc.
>
> Also note that the "inverted LUT" is shown at the top of the frame but not
> other LUTs. That alone would be useful, but to clarify, I am not requesting
> this to be added. I am only asking if there is a way to know which one has
> been applied last to a given image.
>
> If there is no way of doing this, storing the LUT name might be one solution
> (thanks Jeremy), and might bring other issues: load a LUT and then
> programmatically (or via the LUT editor) change it. Would that require
> resetting the stored name?
> That issue happens with the current inverted LUT display, if you edit, the
> window still says (inverting LUT) although it might not be so anymore).
>
> Cheers
>
> Gabriel
>
> On Tuesday, 23 June 2020 12:15:47 BST [hidden email] wrote:
>> Dear Gabriel,
>> Some more expert people may probably deny what I will be writing below.
>> But from my point of view, a LUT is just some kind of "sunglasses" that you
>> can wear in order to look at your data (i.e. your picture) ; these data
>> staying the same whatever sunglasses you try on. Thus I don't really see a
>> reason why the name of last used LUT on a given picture should be saved. My
>> best regards,
>> Philippe
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Current lut?

Gabriel Landini
In reply to this post by Herbie
On Tuesday, 23 June 2020 13:33:40 BST [hidden email] wrote:
> the most convenient way to achieve what you want is the display of the
> LUT-name as a subtitle-label, as with the inverted LUT. I think you can
> easily write either some simple macro- or plugin-code to achieve this.

Hi Herbie,
Yes that would work, if the LUT is stored in the TIFF header, it
could store the name as well but the problem of how that name gets updated
remains.

So I am guessing that the answer to my question is  "no" (we cannot retrieve
the name).

There is always brute: generate a dictionary of the LUTs in the LUT folder and
try to match the current image LUT with an entry in the dictionary.

Cheers

Gabriel

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Re: Current lut?

Herbie
In reply to this post by CARL Philippe (LBP)
Dear Philippe,

there is not much difference with showing the LUT-name as a
subtitle-label and with storing it as a property and with storing it in
the tif-header. In fact all three are essentially the same...

1. In general, if you store some (text)data, or more generally
*meta-data*, with the image, you need to write it to the (tif)image-header.

2. If you set a LUT, it is mentioned in the image info (currently not
the name) and of course the data is in the image and in the image-header.

3. If you write to the subtitle, it is stored in the image-header:
"
*setMetadata("Label", string)*
Sets string as the label of the current image or stack slice. The first
60 characters, or up to the first newline, of the label are displayed as
part of the image subtitle. The labels are saved as part of the TIFF header.
"

4. If you write a property, I'm sure it is also stored in the
image-header. Where else (see 1.)?

Meta-data is meta-data -- no?
The difference consists in how and where it is displayed.

Kind regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::
Am 23.06.20 um 15:05 schrieb CARL Philippe (LBP):

> Dear Herbie and Gabriel,
> If I would like to save the used LUT data, I would rather store them within the picture meta data (maybe using the new info features Wayne implemented some weeks ago) than within the subtitle-label .
> But as I understand the request of Gabriel (but since my last exchanges with Fred, who is drastically differentiating two sentences which are fully identical for me, I may probably have understanding issues in English) he would like to have these informations saved within the meta data as default.
> Take care,
> Philippe
>
> ----- Mail original -----
> De: "l16" <[hidden email]>
> À: "imagej" <[hidden email]>
> Envoyé: Mardi 23 Juin 2020 14:33:40
> Objet: Re: Current lut?
>
> Dear Gabriel,
>
> the most convenient way to achieve what you want is the display of the
> LUT-name as a subtitle-label, as with the inverted LUT. I think you can
> easily write either some simple macro- or plugin-code to achieve this.
>
> Another, less obvious way would be to set a checkmark in the LUT-menu
> indicating the currently applied LUT. This appears more involved however.
>
> Presently, the image info doesn't show the applied LUT (but of course it
> could or you could use the new properties feature to show it).
> Furthermore, the LUT-name is presently not included as tif-tag.
>
> Kind regards
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::::
> Am 23.06.20 um 14:04 schrieb Gabriel Landini:
>> Hi,
>> Sure, sunglasses... I hope there is nothing wrong if I want to know what
>> sunglasses I am  wearing? :-) specially if they change the appearance of the
>> data I am looking at.
>>
>> What prompted me to ask this is I programmed a LUT button that cycles thought
>> the many LUTs collected over the years.  If I find one I like and dif not keep
>> track of the name at the time of loading I do not know which one it is.
>>
>> It might be useful in other instances: is it a linear greyscale or stretched
>> logarithmic greyscale LUT? They might look pretty close but to find out I have
>> to through Show LUT, compare it to another LUT, etc.
>>
>> Also note that the "inverted LUT" is shown at the top of the frame but not
>> other LUTs. That alone would be useful, but to clarify, I am not requesting
>> this to be added. I am only asking if there is a way to know which one has
>> been applied last to a given image.
>>
>> If there is no way of doing this, storing the LUT name might be one solution
>> (thanks Jeremy), and might bring other issues: load a LUT and then
>> programmatically (or via the LUT editor) change it. Would that require
>> resetting the stored name?
>> That issue happens with the current inverted LUT display, if you edit, the
>> window still says (inverting LUT) although it might not be so anymore).
>>
>> Cheers
>>
>> Gabriel
>>
>> On Tuesday, 23 June 2020 12:15:47 BST [hidden email] wrote:
>>> Dear Gabriel,
>>> Some more expert people may probably deny what I will be writing below.
>>> But from my point of view, a LUT is just some kind of "sunglasses" that you
>>> can wear in order to look at your data (i.e. your picture) ; these data
>>> staying the same whatever sunglasses you try on. Thus I don't really see a
>>> reason why the name of last used LUT on a given picture should be saved. My
>>> best regards,
>>> Philippe
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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>

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Re: Current lut?

Herbie
In reply to this post by Gabriel Landini
Dear Gabriel,

I'm not perfectly sure where you see a problem.

"if the LUT is stored in the TIFF header"

Do you mean the values or the LUT-name?

If you write the LUT-name to the subtitle (so that is immediately
visible) it is of course stored in the TIFF header when you save the image.

The values are 8bit-color and there is a TIFF-tag that tells this fact.
BITS_PER_SAMPLE = 8
PHOTOMETRIC_INTERPRETATION = 3
I guess this information is also used for the image info.
"Bits per pixel: 8 (color LUT)"

"the problem of how that name gets updated remains."

If you have the LUT-name in the subtitle and save the image, the name is
saved as well. If you replace the LUT-name in the subtitle and again
save the image, it will be stored. If you don't save the image you can
recall the current LUT-name form the subtitle.

In short, I don't understand the problem.

"So I am guessing that the answer to my question is  "no" (we cannot
retrieve the name)."

Without some code, e.g. using *setMetadata("Label", string)*, it appears
that currently it is impossible to retrieve the name. At least I didn't
find it in the TIFF-header.

"There is always brute: generate a dictionary of the LUTs in the LUT
folder and try to match the current image LUT with an entry in the
dictionary."

I'd prefer to store the LUT-name with the image in which way ever.

Kind regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 23.06.20 um 15:36 schrieb Gabriel Landini:

> On Tuesday, 23 June 2020 13:33:40 BST [hidden email] wrote:
>> the most convenient way to achieve what you want is the display of the
>> LUT-name as a subtitle-label, as with the inverted LUT. I think you can
>> easily write either some simple macro- or plugin-code to achieve this.
>
> Hi Herbie,
> Yes that would work, if the LUT is stored in the TIFF header, it
> could store the name as well but the problem of how that name gets updated
> remains.
>
> So I am guessing that the answer to my question is  "no" (we cannot retrieve
> the name).
>
> There is always brute: generate a dictionary of the LUTs in the LUT folder and
> try to match the current image LUT with an entry in the dictionary.
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Current lut?

Gabriel Landini
Hi Herbie,

> I'm not perfectly sure where you see a problem.

I do not see any :-) I meant (probably expressed it wrong): If the LUT is
stored in the image  then one could store the LUT name too. I did not want to
suggest the values (as they are already stored in a palette somewhere in the
TIFF file).
 
> "the problem of how that name gets updated remains."
> In short, I don't understand the problem.

The problem is this: You apply a LUT (which has a name, let's say Fire) then
when imagine changing the LUT programmatically, not by loading a new LUT file
but by editing some (or all) palette entries.
What results from the editing is not the Fire LUT anymore, so unless one
catches that the LUT has been edited, one risks storing the Fire name in the
header when saving that image.

That seems to be current situation with the Inverted LUT. If you edit it via
LUT Edit, the image frame still says that there is an Inverting LUT active,
but the original entries have been changed and so there is no guarantee that
the LUT looks like the one in the name, i.e. "inverting LUT".

Perhaps there should be a flag that records whether the LUT values have been
altered/edited.  If so, the LUT name is not really a valid name and should be
changed or added a "*" at the end or something similar to indicate that fact.

Hope it clarifies it.

Cheers

Gabriel

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Re: Current lut?

Herbie
Dear Gabriel!

"Hope it clarifies it."

It does, and it explains that the problem is not with the LUT-name per
se, but with the fact that an edited LUT doesn't immediately get a new name!

This sounds to possibly become an interesting suggestion. As you write:
A LUT that has been modified but not yet save under a new name should
receive an indicator similar to files that have been modified but not
yet saved...

If this may perhaps be realized by Wayne, storing the current LUT-name
could accompany this endeavour...

Thanks

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 23.06.20 um 16:31 schrieb Gabriel Landini:

> Hi Herbie,
>
>> I'm not perfectly sure where you see a problem.
>
> I do not see any :-) I meant (probably expressed it wrong): If the LUT is
> stored in the image  then one could store the LUT name too. I did not want to
> suggest the values (as they are already stored in a palette somewhere in the
> TIFF file).
>  
>> "the problem of how that name gets updated remains."
>> In short, I don't understand the problem.
>
> The problem is this: You apply a LUT (which has a name, let's say Fire) then
> when imagine changing the LUT programmatically, not by loading a new LUT file
> but by editing some (or all) palette entries.
> What results from the editing is not the Fire LUT anymore, so unless one
> catches that the LUT has been edited, one risks storing the Fire name in the
> header when saving that image.
>
> That seems to be current situation with the Inverted LUT. If you edit it via
> LUT Edit, the image frame still says that there is an Inverting LUT active,
> but the original entries have been changed and so there is no guarantee that
> the LUT looks like the one in the name, i.e. "inverting LUT".
>
> Perhaps there should be a flag that records whether the LUT values have been
> altered/edited.  If so, the LUT name is not really a valid name and should be
> changed or added a "*" at the end or something similar to indicate that fact.
>
> Hope it clarifies it.
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Current lut?

Wayne Rasband-2
In reply to this post by Gabriel Landini
> On Jun 23, 2020, at 7:00 AM, Gabriel Landini <[hidden email]> wrote:
>
> Hi,
> I wonder if there is a way to retrieve what is the name of (the last?) LUT
> applied to an image.
> I appreciate that LUTs can be changed on the fly  without loading one from a
> file and therefore might not be a robust way of knowing what is being
> displayed.

Starting with the ImageJ 1.53c60 daily build, the LUT name is saved as an image property and displayed when you type “i” (Image>Show Info). The LUT name can be retrieved in a macro using Property.get("CurrentLUT”) and in a plugin or script using imp.getProp("CurrentLUT”). The name will have “(edited)” appended to it if the LUT has been edited by the Image>Color>Edit LUT tool.

-wayne

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Re: Current lut?

Herbie
Dear Wayne,

that's great news and a more than fast reaction!

Thanks and kind regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 23.06.20 um 18:32 schrieb Wayne Rasband:

>> On Jun 23, 2020, at 7:00 AM, Gabriel Landini <[hidden email]> wrote:
>>
>> Hi,
>> I wonder if there is a way to retrieve what is the name of (the last?) LUT
>> applied to an image.
>> I appreciate that LUTs can be changed on the fly  without loading one from a
>> file and therefore might not be a robust way of knowing what is being
>> displayed.
>
> Starting with the ImageJ 1.53c60 daily build, the LUT name is saved as an image property and displayed when you type “i” (Image>Show Info). The LUT name can be retrieved in a macro using Property.get("CurrentLUT”) and in a plugin or script using imp.getProp("CurrentLUT”). The name will have “(edited)” appended to it if the LUT has been edited by the Image>Color>Edit LUT tool.
>
> -wayne
>
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>

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Re: Current lut?

jmutterer
Here's a alternative solution with the linked menu tool that provides two
commands :
- Store LUT in Prefs
- Restore LUT from Prefs

https://gist.github.com/mutterer/51021eb24d117bb9d4f43e5f020b6bb8

Jerome.


On Tue, 23 Jun 2020 at 18:42, Herbie <[hidden email]> wrote:

> Dear Wayne,
>
> that's great news and a more than fast reaction!
>
> Thanks and kind regards
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::
> Am 23.06.20 um 18:32 schrieb Wayne Rasband:
> >> On Jun 23, 2020, at 7:00 AM, Gabriel Landini <[hidden email]>
> wrote:
> >>
> >> Hi,
> >> I wonder if there is a way to retrieve what is the name of (the last?)
> LUT
> >> applied to an image.
> >> I appreciate that LUTs can be changed on the fly  without loading one
> from a
> >> file and therefore might not be a robust way of knowing what is being
> >> displayed.
> >
> > Starting with the ImageJ 1.53c60 daily build, the LUT name is saved as
> an image property and displayed when you type “i” (Image>Show Info). The
> LUT name can be retrieved in a macro using Property.get("CurrentLUT”) and
> in a plugin or script using imp.getProp("CurrentLUT”). The name will have
> “(edited)” appended to it if the LUT has been edited by the
> Image>Color>Edit LUT tool.
> >
> > -wayne
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
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