Colocalization test and Macro

[Leroy Olivier]

Dear ImageJ list,

I am trying to call "Colocalization test" function from a Macro but I am not able to.

"Colocalization test" function is working fine, I get expected results when I use it manually (Analyze > Colocalization > Colocalization test).
But if the Macro recorder is open, in order to get the macro command line, when I run "colocalization test" function, I get an error message from the recorder :

Duplicate keyword :
Command "Colocalization Test"
Keyword "Channel"
Value: <name of my 2nd channel image>
Add an underscore to the corresponding label in the dialog to make the first word unique.

At the end, I still get a command line in the recorder :

run("Colocalization Test", "channel=red.tif channel=green.tif roi=None randomization=[Costes approximation (smoothed noise)] pixel=0.040 channel=520 na=1.40 iterations=75 psf=10");

But this command does not run the "Colocalization Test" function, it seems nothing happen.
If anyone knows how to call this function from a macro, this would be very helpful.
With Best regards,

Olivier

******************************************************
Olivier Leroy

Plateau d'imagerie cellulaire et tissulaire<http://ugbdd.curie.fr/fr/imagerie>
Unité de génétique et biologie du développement<http://ugbdd.curie.fr/fr>

Centre de Recherche de l'Institut Curie
* : + 33 (0)1 56 24 64 02
* : [hidden email]<mailto:[hidden email]>
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[Gabriel Landini]

On Thursday 16 Jun 2016 14:33:13 you wrote:

> Dear ImageJ list,
>
> I am trying to call "Colocalization test" function from a Macro but I am not
> able to.
>
> "Colocalization test" function is working fine, I get expected results when
> I use it manually (Analyze > Colocalization > Colocalization test). But if
> the Macro recorder is open, in order to get the macro command line, when I
> run "colocalization test" function, I get an error message from the
> recorder :
>
> Duplicate keyword :
> Command "Colocalization Test"
> Keyword "Channel"

I think that this is because there are several "Channel" parameters in the
dialog, so it becomes ambiguous. Change the names of the parameters so there
are no clashes.

Cheers

Gabriel

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[Leroy Olivier]

Dear Gabriel,

Thank you for your reply.
I agree, the problem seems to come from the same two "channels" parameters name but I have no clue about how to work around.
What do you mean by "changing the name of parameters" ?
Best regards,

Olivier

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Gabriel Landini
Envoyé : jeudi 16 juin 2016 16:44
À : [hidden email]
Objet : Re: Colocalization test and Macro

On Thursday 16 Jun 2016 14:33:13 you wrote:

> Dear ImageJ list,
>
> I am trying to call "Colocalization test" function from a Macro but I
> am not able to.
>
> "Colocalization test" function is working fine, I get expected results
> when I use it manually (Analyze > Colocalization > Colocalization
> test). But if the Macro recorder is open, in order to get the macro
> command line, when I run "colocalization test" function, I get an
> error message from the recorder :
>
> Duplicate keyword :
> Command "Colocalization Test"
> Keyword "Channel"

I think that this is because there are several "Channel" parameters in the dialog, so it becomes ambiguous. Change the names of the parameters so there are no clashes.

Cheers

Gabriel

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[Jan Eglinger]

Hi Olivier,

as Gabriel says (and the error message suggests), it's a problem having
the keyword "channel" twice in the call to "Colocalization Test".

This needs to be fixed by the maintainers of the Colocalization Test
plugin [1]. I submitted a pull request:
https://github.com/fiji/Colocalisation_Analysis/pull/47/files

As soon as this gets merged and uploaded to the Fiji update site, the
Colocalization Test plugin should be macro recordable. Please note that
the Coloc_2 plugin is meant to replace the other colocalization plugins
in the future and is being actively developed.

Hope that helps.
Jan

[1]:
https://github.com/fiji/Colocalisation_Analysis/blob/master/src/main/java/Colocalisation_Test.java#L175



On 16.06.2016 16:44, Gabriel Landini wrote:

> On Thursday 16 Jun 2016 14:33:13 you wrote:
>> Dear ImageJ list,
>>
>> I am trying to call "Colocalization test" function from a Macro but I am not
>> able to.
>>
>> "Colocalization test" function is working fine, I get expected results when
>> I use it manually (Analyze > Colocalization > Colocalization test). But if
>> the Macro recorder is open, in order to get the macro command line, when I
>> run "colocalization test" function, I get an error message from the
>> recorder :
>>
>> Duplicate keyword :
>> Command "Colocalization Test"
>> Keyword "Channel"
>
> I think that this is because there are several "Channel" parameters in the
> dialog, so it becomes ambiguous. Change the names of the parameters so there
> are no clashes.
>
> Cheers
>
> Gabriel
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[ctrueden]

Hi all,

> As soon as this gets merged and uploaded to the Fiji update site, the
> Colocalization Test plugin should be macro recordable.

The fix has been merged, released and uploaded. Let us know how it works
for you.

Regards,
Curtis

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


On Thu, Jun 16, 2016 at 10:04 AM, Jan Eglinger <[hidden email]>
wrote:

> Hi Olivier,
>
> as Gabriel says (and the error message suggests), it's a problem having
> the keyword "channel" twice in the call to "Colocalization Test".
>
> This needs to be fixed by the maintainers of the Colocalization Test
> plugin [1]. I submitted a pull request:
> https://github.com/fiji/Colocalisation_Analysis/pull/47/files
>
> As soon as this gets merged and uploaded to the Fiji update site, the
> Colocalization Test plugin should be macro recordable. Please note that the
> Coloc_2 plugin is meant to replace the other colocalization plugins in the
> future and is being actively developed.
>
> Hope that helps.
> Jan
>
> [1]:
> https://github.com/fiji/Colocalisation_Analysis/blob/master/src/main/java/Colocalisation_Test.java#L175
>
>
>
>
> On 16.06.2016 16:44, Gabriel Landini wrote:
>
>> On Thursday 16 Jun 2016 14:33:13 you wrote:
>>
>>> Dear ImageJ list,
>>>
>>> I am trying to call "Colocalization test" function from a Macro but I am
>>> not
>>> able to.
>>>
>>> "Colocalization test" function is working fine, I get expected results
>>> when
>>> I use it manually (Analyze > Colocalization > Colocalization test). But
>>> if
>>> the Macro recorder is open, in order to get the macro command line, when
>>> I
>>> run "colocalization test" function, I get an error message from the
>>> recorder :
>>>
>>> Duplicate keyword :
>>> Command "Colocalization Test"
>>> Keyword "Channel"
>>>
>>
>> I think that this is because there are several "Channel" parameters in the
>> dialog, so it becomes ambiguous. Change the names of the parameters so
>> there
>> are no clashes.
>>
>> 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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[Jan Eglinger]

Hi all,

On 16.06.2016 17:04, Jan Eglinger wrote:
> This needs to be fixed by the maintainers of the Colocalization Test
> plugin [1]. I submitted a pull request:
> https://github.com/fiji/Colocalisation_Analysis/pull/47/files

Thanks to Curtis Rueden, the fix is now merged and available by running
'Help > Update...' in Fiji.

When you now run Colocalization Test, the recorder records:

*****
     run("Colocalization Test", "channel_1=green.tif channel_2=red.tif
roi=None randomization=[Costes approximation (smoothed noise)]
pixel=0.04 channel_2_wavelength=520 na=1.40 iterations=25 psf_radius=10");
*****

Cheers
Jan

>
>
> On 16.06.2016 16:44, Gabriel Landini wrote:
>> On Thursday 16 Jun 2016 14:33:13 you wrote:
>>> Dear ImageJ list,
>>>
>>> I am trying to call "Colocalization test" function from a Macro but I
>>> am not
>>> able to.
>>>
>>> "Colocalization test" function is working fine, I get expected
>>> results when
>>> I use it manually (Analyze > Colocalization > Colocalization test).
>>> But if
>>> the Macro recorder is open, in order to get the macro command line,
>>> when I
>>> run "colocalization test" function, I get an error message from the
>>> recorder :
>>>
>>> Duplicate keyword :
>>> Command "Colocalization Test"
>>> Keyword "Channel"
>>
>> I think that this is because there are several "Channel" parameters in
>> the
>> dialog, so it becomes ambiguous. Change the names of the parameters so
>> there
>> are no clashes.
>>
>> Cheers
>>
>> Gabriel
>>

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[Leroy Olivier]

Dear Curtis, Jan and Gabriel,

This is now working perfectly fine.
Thank you so much !
Best Regards,

Olivier

-----Message d'origine-----
De : Jan Eglinger [mailto:[hidden email]]
Envoyé : jeudi 16 juin 2016 17:41
À : [hidden email]; Leroy Olivier
Objet : Re: Colocalization test and Macro

Hi all,

On 16.06.2016 17:04, Jan Eglinger wrote:
> This needs to be fixed by the maintainers of the Colocalization Test
> plugin [1]. I submitted a pull request:
> https://github.com/fiji/Colocalisation_Analysis/pull/47/files

Thanks to Curtis Rueden, the fix is now merged and available by running 'Help > Update...' in Fiji.

When you now run Colocalization Test, the recorder records:

*****
     run("Colocalization Test", "channel_1=green.tif channel_2=red.tif roi=None randomization=[Costes approximation (smoothed noise)]
pixel=0.04 channel_2_wavelength=520 na=1.40 iterations=25 psf_radius=10");
*****

Cheers
Jan

>
>
> On 16.06.2016 16:44, Gabriel Landini wrote:
>> On Thursday 16 Jun 2016 14:33:13 you wrote:
>>> Dear ImageJ list,
>>>
>>> I am trying to call "Colocalization test" function from a Macro but
>>> I am not able to.
>>>
>>> "Colocalization test" function is working fine, I get expected
>>> results when I use it manually (Analyze > Colocalization >
>>> Colocalization test).
>>> But if
>>> the Macro recorder is open, in order to get the macro command line,
>>> when I run "colocalization test" function, I get an error message
>>> from the recorder :
>>>
>>> Duplicate keyword :
>>> Command "Colocalization Test"
>>> Keyword "Channel"
>>
>> I think that this is because there are several "Channel" parameters
>> in the dialog, so it becomes ambiguous. Change the names of the
>> parameters so there are no clashes.
>>
>> Cheers
>>
>> Gabriel
>>

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