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Meta lost on concatenation

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CARL Philippe (LBP)

Meta lost on concatenation

Dear all,
Given that I perform a "quite big" acquisition protocol, my tif pictures got split into three single files by the used acquisition software.
It is of course easy to stick again these 3 pictures together using the Image>Stacks>Tools>Concatenete... tool.
Nevertheless, when I do so all the "nice meta data" I had within these pictures get erased.
And given that I want later on the information stored within the meta data, this is a kind of pity.
Thus is it obvious for you that the meta data get lost upon a concatenation process or should they rather 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

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Fred Damen

Re: Meta lost on concatenation

Greetings,

I have faced this issue in the past(/currently). There is a method,
copyAttributes(ImagePlus) in ImagePlus.java that copies this information,
albeit, it refuses to perform said action when the source ImagePlus has a
current ImageWindow. I have resorted to copying the guts of this method
into my code when this information is important to me.

Is there a problem with the source ImagePlus being displayed when copying
the Meta data?

Enjoy,

Fred

On Wed, August 12, 2020 8:52 am, CARL Philippe (LBP) wrote:

> Dear all,
> Given that I perform a "quite big" acquisition protocol, my tif pictures
> got split into three single files by the used acquisition software.
> It is of course easy to stick again these 3 pictures together using the
> Image>Stacks>Tools>Concatenete... tool.
> Nevertheless, when I do so all the "nice meta data" I had within these
> pictures get erased.
> And given that I want later on the information stored within the meta
> data, this is a kind of pity.
> Thus is it obvious for you that the meta data get lost upon a
> concatenation process or should they rather be saved ?
> My best regards,
> Philippe
>
>
> Philippe CARL
> Laboratoire de Bioimagerie et Pathologies
> UMR 7021 CNRS - UniversitÃ© de Strasbourg
> FacultÃ© de Pharmacie
> 74 route du Rhin
> 67401 ILLKIRCH
> Tel : +33(0)3 68 85 42 89
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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CARL Philippe (LBP)

Re: Meta lost on concatenation

Dear Fred,
I could simply do something like:
selectWindow("window1");
data = getMetadata("Info");
selectWindow("window2");
setMetadata("Info", data);
But for me the MetaData should be saved given especially that they are identical within the three pictures.
My best regards,
Philippe

----- Mail original -----
De: "Fred Damen" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Mercredi 12 Août 2020 19:14:20
Objet: Re: Meta lost on concatenation

Greetings,

I have faced this issue in the past(/currently). There is a method,
copyAttributes(ImagePlus) in ImagePlus.java that copies this information,
albeit, it refuses to perform said action when the source ImagePlus has a
current ImageWindow. I have resorted to copying the guts of this method
into my code when this information is important to me.

Is there a problem with the source ImagePlus being displayed when copying
the Meta data?

Enjoy,

Fred

On Wed, August 12, 2020 8:52 am, CARL Philippe (LBP) wrote:

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Wayne Rasband-2

Re: Meta lost on concatenation

In reply to this post by CARL Philippe (LBP)

> On Aug 12, 2020, at 9:52 AM, CARL Philippe (LBP) <[hidden email]> wrote:
>
> Dear all,
> Given that I perform a "quite big" acquisition protocol, my tif pictures got split into three single files by the used acquisition software.
> It is of course easy to stick again these 3 pictures together using the Image>Stacks>Tools>Concatenete... tool.
> Nevertheless, when I do so all the "nice meta data" I had within these pictures get erased.
> And given that I want later on the information stored within the meta data, this is a kind of pity.
> Thus is it obvious for you that the meta data get lost upon a concatenation process or should they rather be saved ?
> My best regards,

Upgrade to the ImageJ 1.53d66 daily build and the Image>Stacks>Tools>Concatenate command will copy the metadata from the first input image (or stack) to the output stack.

-wayne
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CARL Philippe (LBP)

Re: Meta lost on concatenation

Thanks a lot Wayne!

Take care,

Philippe

----- Mail original -----
De: "Wayne Rasband" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Jeudi 13 Août 2020 23:29:01
Objet: Re: Meta lost on concatenation

> On Aug 12, 2020, at 9:52 AM, CARL Philippe (LBP) <[hidden email]> wrote:
>
> Dear all,
> Given that I perform a "quite big" acquisition protocol, my tif pictures got split into three single files by the used acquisition software.
> It is of course easy to stick again these 3 pictures together using the Image>Stacks>Tools>Concatenete... tool.
> Nevertheless, when I do so all the "nice meta data" I had within these pictures get erased.
> And given that I want later on the information stored within the meta data, this is a kind of pity.
> Thus is it obvious for you that the meta data get lost upon a concatenation process or should they rather be saved ?
> My best regards,

Upgrade to the ImageJ 1.53d66 daily build and the Image>Stacks>Tools>Concatenate command will copy the metadata from the first input image (or stack) to the output stack.

-wayne
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