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Store convolutions in array

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PEARSON Matthew

Store convolutions in array

Hi all,

I'd like to run some convolutions on an image and rather than run each convolution in turn as the macro recorder prints it, like below:
run("Convolve...", "text1=[0 0 0 0 0\n0 -1 -1 -1 0\n0 -1 12 -1 0\n0 -1 -1 -1 0\n0 0 0 0 0\n] normalize");

I'd like to set up a loop that will run through several convolutions. I thought i could add the convolutions to an array but not quite sure of the syntax of this in the macro language. I thought i could have a string array of the convolutions and then do something like:

convolutions = newArray ("text1=[0 0 0 0 0\n0 -1 -1 -1 0\n0 -1 12 -1 0\n0 -1 -1 -1 0\n0 0 0 0 0\n] normalize");
run("Convolve…", [0]);

I know what i've done is wrong but wondering if its possible and what are the correct statements to use?

Thanks for the help,

Matt

--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU

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

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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Herbie

Re: Store convolutions in array

Good day Matt,

not sure whether it helps in your case, but I use to store the kernels
as a string in a file and then use:

kernel = File.openAsString( path2kernel );
run( "Convolve...", "text1=["+kernel+"] normalize stack" )

This should also work without storing the kernels in a file.

HTH

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 13.10.16 um 18:16 schrieb PEARSON Matthew:

> Hi all,
>
> I'd like to run some convolutions on an image and rather than run
> each convolution in turn as the macro recorder prints it, like
> below: run("Convolve...", "text1=[0 0 0 0 0\n0 -1 -1 -1 0\n0 -1 12 -1
> 0\n0 -1 -1 -1 0\n0 0 0 0 0\n] normalize");
>
> I'd like to set up a loop that will run through several convolutions.
> I thought i could add the convolutions to an array but not quite sure
> of the syntax of this in the macro language. I thought i could have
> a string array of the convolutions and then do something like:
>
> convolutions = newArray ("text1=[0 0 0 0 0\n0 -1 -1 -1 0\n0 -1 12 -1
> 0\n0 -1 -1 -1 0\n0 0 0 0 0\n] normalize"); run("Convolve…", [0]);
>
> I know what i've done is wrong but wondering if its possible and what
> are the correct statements to use?
>
> Thanks for the help,
>
> Matt
>
> -- Matt Pearson Microscopy Facility MRC Human Genetics Unit Institute
> of Genetics and Molecular Medicine (IGMM) University of Edinburgh
> Crewe Road EH4 2XU
>
>
>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

PEARSON Matthew

Fwd: Store convolutions in array

In reply to this post by PEARSON Matthew

-------- Original message --------
From: PEARSON Matthew <[hidden email]>
Date: 13/10/2016 22:53 (GMT+00:00)
To: [hidden email]
Subject: Re: Store convolutions in array

Hi Herbie,

Thanks for that it's good to know you can use a string that contains the kernel. Presumably altering this slightly as below to add in a string from an array wouldn't work.

Kernel = newArray ("kernel1", "kernel2");

run( "Convolve...", "text1=["+kernel[0]+"] normalize stack" )

I'll play around with it tomorrow. I could always do it slightly less elegantly with a for loop and a series of if and else if statements to switch the kernel to Convolve with.
run( "Convolve...", "text1=["+kernel[0]+"] normalize stack" )

Thanks,

Matt

-------- Original message --------
From: Herbie <[hidden email]>
Date: 13/10/2016 20:09 (GMT+00:00)
To: [hidden email]
Subject: Re: Store convolutions in array

Good day Matt,

not sure whether it helps in your case, but I use to store the kernels
as a string in a file and then use:

kernel = File.openAsString( path2kernel );
run( "Convolve...", "text1=["+kernel+"] normalize stack" )

This should also work without storing the kernels in a file.

HTH

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 13.10.16 um 18:16 schrieb PEARSON Matthew:

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

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

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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

PEARSON Matthew

Re: Store convolutions in array

Just wanted to confirm for anyone else who isn't sure, you can run convolutions from an array, like so:
run("Convolve...", "text1=["+convolutions[i]+"] normalize stack");

Thanks again to Herbie.

Matt

--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU

On 13 Oct 2016, at 22:56, PEARSON Matthew <[hidden email]<mailto:[hidden email]>> wrote:

-------- Original message --------
From: PEARSON Matthew <[hidden email]<mailto:[hidden email]>>
Date: 13/10/2016 22:53 (GMT+00:00)
To: [hidden email]<mailto:[hidden email]>
Subject: Re: Store convolutions in array

Hi Herbie,

Thanks for that it's good to know you can use a string that contains the kernel. Presumably altering this slightly as below to add in a string from an array wouldn't work.

Kernel = newArray ("kernel1", "kernel2");

run( "Convolve...", "text1=["+kernel[0]+"] normalize stack" )

I'll play around with it tomorrow. I could always do it slightly less elegantly with a for loop and a series of if and else if statements to switch the kernel to Convolve with.
run( "Convolve...", "text1=["+kernel[0]+"] normalize stack" )

Thanks,

Matt

-------- Original message --------
From: Herbie <[hidden email]<mailto:[hidden email]>>
Date: 13/10/2016 20:09 (GMT+00:00)
To: [hidden email]<mailto:[hidden email]>
Subject: Re: Store convolutions in array

Good day Matt,

not sure whether it helps in your case, but I use to store the kernels
as a string in a file and then use:

kernel = File.openAsString( path2kernel );
run( "Convolve...", "text1=["+kernel+"] normalize stack" )

This should also work without storing the kernels in a file.

HTH

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 13.10.16 um 18:16 schrieb PEARSON Matthew:
Hi all,

I'd like to run some convolutions on an image and rather than run
each convolution in turn as the macro recorder prints it, like
below: run("Convolve...", "text1=[0 0 0 0 0\n0 -1 -1 -1 0\n0 -1 12 -1
0\n0 -1 -1 -1 0\n0 0 0 0 0\n] normalize");

I'd like to set up a loop that will run through several convolutions.
I thought i could add the convolutions to an array but not quite sure
of the syntax of this in the macro language. I thought i could have
a string array of the convolutions and then do something like:

convolutions = newArray ("text1=[0 0 0 0 0\n0 -1 -1 -1 0\n0 -1 12 -1
0\n0 -1 -1 -1 0\n0 0 0 0 0\n] normalize"); run("Convolve…", [0]);

I know what i've done is wrong but wondering if its possible and what
are the correct statements to use?

Thanks for the help,

Matt

-- Matt Pearson Microscopy Facility MRC Human Genetics Unit Institute
of Genetics and Molecular Medicine (IGMM) University of Edinburgh
Crewe Road EH4 2XU

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

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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

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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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

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

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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