Calculator Plus

[Thomas Eschner]

Dear all,
 
I am trying to illustrate artefacts introduced by storing files as jpg by showing the difference of two identical 16-bit images, one stored as jpg and one as tiff.
 
With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16, I end up with files having their values set to 65535 exclusively.
 
Only with k2 = 0 I seem to get more or less reasonable results, but I lose negative values.
 
Could please anybody give me a hint?
 
Thank you.
 
Kind regards,
Thomas

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

[Herbie]

Good day Thomas,

you wrote:

"[...] by showing the difference of two identical 16-bit images, one
stored as jpg and one as tiff.""

How did you manage to get a 16bit JPEG-compressed image? As far as I
know JPEG-compression is limited to 8bit (RGB) images.

Just curious

Herbie

::::::::::::::::::::::::::::::::::::::::::::
Am 27.03.17 um 13:50 schrieb Thomas Eschner:

> Dear all,
>
> I am trying to illustrate artefacts introduced by storing files as
> jpg by showing the difference of two identical 16-bit images, one
> stored as jpg and one as tiff.
>
> With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16,
> I end up with files having their values set to 65535 exclusively.
>
> Only with k2 = 0 I seem to get more or less reasonable results, but I
> lose negative values.
>
> Could please anybody give me a hint?
>
> Thank you.
>
> Kind regards, Thomas
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Joel Sheffield]

Hi Thomas,

Why not try one of the colocalization programs?  For identical images,  all
the points on one image should correspond to those on the other.  The
differences between jpeg and tiff should be apparent.

Joel



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*

On Mon, Mar 27, 2017 at 7:50 AM, Thomas Eschner <[hidden email]>
wrote:

> Dear all,
>
> I am trying to illustrate artefacts introduced by storing files as jpg by
> showing the difference of two identical 16-bit images, one stored as jpg
> and one as tiff.
>
> With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16, I end
> up with files having their values set to 65535 exclusively.
>
> Only with k2 = 0 I seem to get more or less reasonable results, but I lose
> negative values.
>
> Could please anybody give me a hint?
>
> Thank you.
>
> Kind regards,
> Thomas
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Michael Schmid]

Hi Thomas,

if you want to subtract 16-bit data and get a signed result, the easiest
is using Process>Image Calculator and select "32-bit (float) result".
The other option is 'difference' instead of 'subtract' mode, it will
give you the absolute value of the difference.

By the way, if you save a 16-bit image as jpg, it will be converted to 8
bits on all programs that I am aware of.


Michael
________________________________________________________________
On 27/03/2017 13:50, Thomas Eschner wrote:

> Dear all,
>
> I am trying to illustrate artefacts introduced by storing files as
> jpg by showing the difference of two identical 16-bit images, one
> stored as jpg and one as tiff.
>
> With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16,
> I end up with files having their values set to 65535 exclusively.
>
> Only with k2 = 0 I seem to get more or less reasonable results, but I
> lose negative values.
>
> Could please anybody give me a hint?
>
> Thank you.
>
> Kind regards, Thomas
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[ctrueden]

Hi Thomas,

I usually do these sorts of comparisons using the Image Calculator command,
subtracting one image from the other, and checking the "32-bit result" box.
This is fine if your goal is to illustrate visually as you say. For
quantitative comparison, I agree with Joel that it's better to be more
rigorous, with something like colocalization.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Mon, Mar 27, 2017 at 6:50 AM, Thomas Eschner <[hidden email]>
wrote:

> Dear all,
>
> I am trying to illustrate artefacts introduced by storing files as jpg by
> showing the difference of two identical 16-bit images, one stored as jpg
> and one as tiff.
>
> With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16, I end
> up with files having their values set to 65535 exclusively.
>
> Only with k2 = 0 I seem to get more or less reasonable results, but I lose
> negative values.
>
> Could please anybody give me a hint?
>
> Thank you.
>
> Kind regards,
> Thomas
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Thomas Eschner]

 
Hi Curtis, hi all,
 
thank you for your input. As i understand - the quirk is there, but there's  also a workaround. That should do it at the moment.

Thanks once more.

Kind regards,
Thomas

 

Gesendet: Montag, 27. März 2017 um 18:03 Uhr
Von: "Curtis Rueden" <[hidden email]>
An: [hidden email]
Betreff: Re: Calculator Plus
Hi Thomas,

I usually do these sorts of comparisons using the Image Calculator command,
subtracting one image from the other, and checking the "32-bit result" box.
This is fine if your goal is to illustrate visually as you say. For
quantitative comparison, I agree with Joel that it's better to be more
rigorous, with something like colocalization.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden[https://imagej.net/User:Rueden]
Did you know ImageJ has a forum? http://forum.imagej.net/[http://forum.imagej.net/]


On Mon, Mar 27, 2017 at 6:50 AM, Thomas Eschner <[hidden email]>
wrote:

> Dear all,
>
> I am trying to illustrate artefacts introduced by storing files as jpg by
> showing the difference of two identical 16-bit images, one stored as jpg
> and one as tiff.
>
> With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16, I end
> up with files having their values set to 65535 exclusively.
>
> Only with k2 = 0 I seem to get more or less reasonable results, but I lose
> negative values.
>
> Could please anybody give me a hint?
>
> Thank you.
>
> Kind regards,
> Thomas
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html[http://imagej.nih.gov/ij/list.html]
>

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

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

[ctrueden]

Hi Thomas,

> As i understand - the quirk is there, but there's  also a workaround.

To comment on the Calculator Plus plugin [1] specifically: my understanding
is that Gabriel Landini is currently the maintainer of that plugin, which
is bundled with the Fiji distribution of ImageJ. However, essentially no
work (bug-fixes or improvements) have been done to that plugin for many
years. I do not know if Gabriel considers himself to be actively
maintaining the plugin these days -- I'll leave it to him to comment on
that. Perhaps he has insight into the behavior you observed.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

[1] https://github.com/fiji/Calculator_Plus


On Tue, Mar 28, 2017 at 4:19 AM, Thomas Eschner <[hidden email]>
wrote:

>
> Hi Curtis, hi all,
>
> thank you for your input. As i understand - the quirk is there, but
> there's  also a workaround. That should do it at the moment.
>
> Thanks once more.
>
> Kind regards,
> Thomas
>
>
>
> Gesendet: Montag, 27. März 2017 um 18:03 Uhr
> Von: "Curtis Rueden" <[hidden email]>
> An: [hidden email]
> Betreff: Re: Calculator Plus
> Hi Thomas,
>
> I usually do these sorts of comparisons using the Image Calculator command,
> subtracting one image from the other, and checking the "32-bit result" box.
> This is fine if your goal is to illustrate visually as you say. For
> quantitative comparison, I agree with Joel that it's better to be more
> rigorous, with something like colocalization.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> [https://imagej.net/User:Rueden]
> Did you know ImageJ has a forum? http://forum.imagej.net/[http:
> //forum.imagej.net/]
>
>
> On Mon, Mar 27, 2017 at 6:50 AM, Thomas Eschner <[hidden email]>
> wrote:
>
> > Dear all,
> >
> > I am trying to illustrate artefacts introduced by storing files as jpg by
> > showing the difference of two identical 16-bit images, one stored as jpg
> > and one as tiff.
> >
> > With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16, I
> end
> > up with files having their values set to 65535 exclusively.
> >
> > Only with k2 = 0 I seem to get more or less reasonable results, but I
> lose
> > negative values.
> >
> > Could please anybody give me a hint?
> >
> > Thank you.
> >
> > Kind regards,
> > Thomas
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.
> html[http://imagej.nih.gov/ij/list.html]
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.
> html[http://imagej.nih.gov/ij/list.html]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Gabriel Landini]

 On Mon, Mar 27, 2017 at 6:50 AM, Thomas Eschner <[hidden email]>
> I am trying to illustrate artefacts introduced by storing files as jpg
> by  showing the difference of two identical 16-bit images, one stored as
> jpg and one as tiff.

First of all, are there 16bit jpegs?? I do not seem to be able to create one
in IJ.

> With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16, I
> end up with files having their values set to 65535 exclusively.

The subtraction in that plugin is scaled by k1 and offset by k2. I do not
understand what is that you are tring to achieve.
Why not use just the Image Calculator (not the "Plus" one) with the result as
32 bit?

I do not think I am the maintainer of the plugin. I added the support for RGB
images, plane-wise, long ago but that was about it. I think the plugin works
fine as it is. If it doesn't, please post a macro that shows the problem.

Cheers

Gabriel

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

[Thomas Eschner]

Dear Gabriel, dear all,
 
as I explained somewhere in-between of this discussion, the order was
Taking RGB-image - Storing as jpg and tiff - difference of RGB-jpeg - RGB-tiff (working, but noisy) - 2 x transformation to 16 bit - difference of "16-bit jpeg" - "16-bit tiff" (not working as expected and reason for first of all mails).
In that sense I do have 16-bit jpegs, i.e. images containing artefacts from jpg-compression (and possibly from transformation, too).
 
And all I want to achieve is to have a difference of these images. For some reason I tried Calculatur Plus. Butd if for two quite similar images the difference scaled by k1 = 8 and offset by k2 = 128 is 65535 everywhere, I dare to say that subtraction in that plugin is _not_ scaled  by k1 and offset by k2.
 
I already learned that I should go with Image Calculator (non-Plus) and surely I will do so. However, I would have liked the idea that all offered tools work as expected/intended, even the simpler ones. I know I could/should do that myself, but let's remain realistic.
 
Gabriel, as you are not the maintainer, I'd suggest to end the discussion at this point, but just fyi I attached two images and this macro:

selectWindow("2017010061-130-small.jpg");
run("16-bit");
selectWindow("2017010061-132-small.tif");
run("16-bit");
run("Calculator Plus", "i1=2017010061-130-small.jpg i2=2017010061-132-small.tif operation=[Subtract: i2 = (i1-i2) x k1 + k2] k1=8 k2=128 create");

 
Kind regards,
Thomas
 

Gesendet: Donnerstag, 30. März 2017 um 03:19 Uhr
Von: "Gabriel Landini" <[hidden email]>
An: [hidden email]
Betreff: Re: Calculator Plus
On Mon, Mar 27, 2017 at 6:50 AM, Thomas Eschner <[hidden email]>
> I am trying to illustrate artefacts introduced by storing files as jpg
> by showing the difference of two identical 16-bit images, one stored as
> jpg and one as tiff.

First of all, are there 16bit jpegs?? I do not seem to be able to create one
in IJ.

> With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 = 16, I
> end up with files having their values set to 65535 exclusively.

The subtraction in that plugin is scaled by k1 and offset by k2. I do not
understand what is that you are tring to achieve.
Why not use just the Image Calculator (not the "Plus" one) with the result as
32 bit?

I do not think I am the maintainer of the plugin. I added the support for RGB
images, plane-wise, long ago but that was about it. I think the plugin works
fine as it is. If it doesn't, please post a macro that shows the problem.

Cheers

Gabriel

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

--
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[Herbie]

Dear Thomas,

from my point of view you didn't specify enough of what you really want.

Comparing two RGB images isn't defined per se. You need to tell us how
you want to deal with color.

One possibility is to compare corresponding color channels.
This in turn can be done by subtracting the corresponding channels and
this can be done with and without sign, i.e. as 32bit (Subtract) or as
8bit (Difference) result.
Finally the resulting channels can again be combined to give an RGB-image.

Attached please find the RGB-result from your example image
        2017010061-132-small.tif
that I saved as JPG-image in ImageJ (with the default quality of ImageJ)
for comparison.

The resulting RGB image from channel-wise subtraction is displayed as
follows:
The three bipolar channel-wise 32bit results from the subtractions are
made to range from -20 to 20 and this span of 0...40 is finally shown as
the RGB-result.

Evidently, your original TIF-image is quite noisy and this shows up in
pronounced JPG-artifacts all over the image.

I hope this clarifies the issue a bit.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::
Am 30.03.17 um 14:03 schrieb Thomas Eschner:

> Dear Gabriel, dear all,
>
> as I explained somewhere in-between of this discussion, the order
> was Taking RGB-image - Storing as jpg and tiff - difference of
> RGB-jpeg - RGB-tiff (working, but noisy) - 2 x transformation to 16
> bit - difference of "16-bit jpeg" - "16-bit tiff" (not working as
> expected and reason for first of all mails). In that sense I do have
> 16-bit jpegs, i.e. images containing artefacts from jpg-compression
> (and possibly from transformation, too).
>
> And all I want to achieve is to have a difference of these images.
> For some reason I tried Calculatur Plus. Butd if for two quite
> similar images the difference scaled by k1 = 8 and offset by k2 = 128
> is 65535 everywhere, I dare to say that subtraction in that plugin is
> _not_ scaled  by k1 and offset by k2.
>
> I already learned that I should go with Image Calculator (non-Plus)
> and surely I will do so. However, I would have liked the idea that
> all offered tools work as expected/intended, even the simpler ones. I
> know I could/should do that myself, but let's remain realistic.
>
> Gabriel, as you are not the maintainer, I'd suggest to end the
> discussion at this point, but just fyi I attached two images and this
> macro:
>
> selectWindow("2017010061-130-small.jpg"); run("16-bit");
> selectWindow("2017010061-132-small.tif"); run("16-bit");
> run("Calculator Plus", "i1=2017010061-130-small.jpg
> i2=2017010061-132-small.tif operation=[Subtract: i2 = (i1-i2) x k1 +
> k2] k1=8 k2=128 create");
>
>
> Kind regards, Thomas
>
>
> Gesendet: Donnerstag, 30. März 2017 um 03:19 Uhr Von: "Gabriel
> Landini" <[hidden email]> An: [hidden email] Betreff: Re:
> Calculator Plus On Mon, Mar 27, 2017 at 6:50 AM, Thomas Eschner
> <[hidden email]>
>> I am trying to illustrate artefacts introduced by storing files as
>> jpg by showing the difference of two identical 16-bit images, one
>> stored as jpg and one as tiff.
>
> First of all, are there 16bit jpegs?? I do not seem to be able to
> create one in IJ.
>
>> With Calculator Plus, setting e.g. Subtract with k1 = 1 and k2 =
>> 16, I end up with files having their values set to 65535
>> exclusively.
>
> The subtraction in that plugin is scaled by k1 and offset by k2. I do
> not understand what is that you are tring to achieve. Why not use
> just the Image Calculator (not the "Plus" one) with the result as 32
> bit?
>
> I do not think I am the maintainer of the plugin. I added the support
> for RGB images, plane-wise, long ago but that was about it. I think
> the plugin works fine as it is. If it doesn't, please post a macro
> that shows the problem.
>
> Cheers
>
> Gabriel
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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