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Macro to save plot profile data as text

arobisson
Hello,

I am new to macro.. and cannot get this to work. I am trying to save my plot profile automatically in a txt or csv file. The macro below gives me a log window but not a txt file. Ultimately, I will need to plot and save this on each image from an image sequence…

Your input is welcome, Agathe

xcenter=1658;
ycenter=306;
makeLine(xcenter,ycenter+1100, xcenter, ycenter+1900);
run("Plot Profile");
Plot.getValues(x, y);
  for (i=0; i<x.length; i++)
     print(x[i], y[i]);
path = getDirectory("home")+"profile.csv";
saveAs("Results", path);
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Re: Macro to save plot profile data as text

Volko Straub
Dear Agathe,

The problem is that your focus is not on the log window when you try to
save its content. Also, I don't think the 'Results' option will work
with the log window. Change

saveAs("Results", path);

to  

selectWindow("Log");
saveAs("Text", path);


A quick websearch shows some similar questions (e.g.
http://stackoverflow.com/questions/29879988/solvedimagej-macro-how-to-save-plot-profile-data-in-a-text-file)
that use a results window rather than the log window to list the plot
values. Hope this helps, Volko


On 07/05/2017 03:36, arobisson wrote:

> Hello,
>
> I am new to macro.. and cannot get this to work. I am trying to save my plot
> profile automatically in a txt or csv file. The macro below gives me a log
> window but not a txt file. Ultimately, I will need to plot and save this on
> each image from an image sequence…
>
> Your input is welcome, Agathe
>
> xcenter=1658;
> ycenter=306;
> makeLine(xcenter,ycenter+1100, xcenter, ycenter+1900);
> run("Plot Profile");
> Plot.getValues(x, y);
>    for (i=0; i<x.length; i++)
>       print(x[i], y[i]);
> path = getDirectory("home")+"profile.csv";
> saveAs("Results", path);
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Macro-to-save-plot-profile-data-as-text-tp5018666.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ---
> This email has been checked for viruses by AVG.
> http://www.avg.com
>


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RE: [Ext] Re: Macro to save plot profile data as text

arobisson

Hi Volko,

 

It works. Thank you!

Yes, I used the example from this discussion.. but I got stuck… I guess I have still a bit to learn to write my own macro…

Thank you,

Agathe

 

From: Volko Straub [via ImageJ] [mailto:ml+[hidden email]]
Sent: 07 May, 2017 2:30 AM
To: Agathe Robisson <[hidden email]>
Subject: [Ext] Re: Macro to save plot profile data as text

 

Dear Agathe,

The problem is that your focus is not on the log window when you try to
save its content. Also, I don't think the 'Results' option will work
with the log window. Change

saveAs("Results", path);

to  

selectWindow("Log");
saveAs("Text", path);


A quick websearch shows some similar questions (e.g.
http://stackoverflow.com/questions/29879988/solvedimagej-macro-how-to-save-plot-profile-data-in-a-text-file)
that use a results window rather than the log window to list the plot
values. Hope this helps, Volko


On 07/05/2017 03:36, arobisson wrote:


> Hello,
>
> I am new to macro.. and cannot get this to work. I am trying to save my plot
> profile automatically in a txt or csv file. The macro below gives me a log
> window but not a txt file. Ultimately, I will need to plot and save this on
> each image from an image sequence…
>
> Your input is welcome, Agathe
>
> xcenter=1658;
> ycenter=306;
> makeLine(xcenter,ycenter+1100, xcenter, ycenter+1900);
> run("Plot Profile");
> Plot.getValues(x, y);
>    for (i=0; i<x.length; i++)
>       print(x[i], y[i]);
> path = getDirectory("home")+"profile.csv";
> saveAs("Results", path);
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Macro-to-save-plot-profile-data-as-text-tp5018666.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ---
> This email has been checked for viruses by AVG.
> http://www.avg.com
>



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Re: [Ext] Re: Macro to save plot profile data as text

Andy Schofield
Hi All,

I'm having a similar problem where the SaveAs is failing in a macro when I try to save my bespoke table window as a CSV file.

I create my table as such

        titleRG="RedtoGreen";
        tblRG = "["+titleRG+"]";
        fRG = tblRG;
        run("New... ", "name="+tblRG+" type=Table");

and then populate it using

        print(fRG,(CurrCol+CHIPWIDTH/2) + "\t" + (CurrRow+CHIPHEIGHT/2) + "\t" + lastline[4] + "\t" + lastline[6]);

and finally save the table as

        selectWindow("RedtoGreen");
        saveAs(titleRG, ImageDir+"\\"+titleRG+".csv");


When I run the macro, the RedtoGreen table is created OK with tab separated fields but the saveAs reports:-

        Unsupported save() or saveAs() file format: "redtogreen"

I can choose the RedtoGreen table manually and choose File->Save As. The default filename name displayed is RedtoGreen.txt but I can change that to redtoGreen.csv and the tbale saves as expected (i.e. a comma separated file) so it would seem the behaviour is different between the GUI and the macro handler (or that I'm missing something obvious ;-) )

Cheers
Andy

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of arobisson
Sent: 08 May 2017 02:36
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi Volko,

It works. Thank you!
Yes, I used the example from this discussion.. but I got stuck… I guess I have still a bit to learn to write my own macro… Thank you, Agathe

From: Volko Straub [via ImageJ] [mailto:[hidden email]]
Sent: 07 May, 2017 2:30 AM
To: Agathe Robisson <[hidden email]>
Subject: [Ext] Re: Macro to save plot profile data as text

Dear Agathe,

The problem is that your focus is not on the log window when you try to save its content. Also, I don't think the 'Results' option will work with the log window. Change

saveAs("Results", path);

to

selectWindow("Log");
saveAs("Text", path);


A quick websearch shows some similar questions (e.g.
http://stackoverflow.com/questions/29879988/solvedimagej-macro-how-to-save-plot-profile-data-in-a-text-file<https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_29879988_solvedimagej-2Dmacro-2Dhow-2Dto-2Dsave-2Dplot-2Dprofile-2Ddata-2Din-2Da-2Dtext-2Dfile&d=CwMFaQ&c=uGuXJ43KPkPWEl2imVFDmZQlhQUET7pVRA2PDIOxgqw&r=ZSB5F8Ew5Pfa9PJrJrErd_qpXmtjZqfSdSGDjHk5aOs&m=EqPFXdRMzDelyEe4t7UBrRoYEh-gjrJIEA8keliIpPk&s=Hhcyi80Y9Tsz892UNZVr3AF1vXfI4bjG9HnOyUyJGIk&e=>)
that use a results window rather than the log window to list the plot values. Hope this helps, Volko


On 07/05/2017 03:36, arobisson wrote:

> Hello,
>
> I am new to macro.. and cannot get this to work. I am trying to save
> my plot profile automatically in a txt or csv file. The macro below
> gives me a log window but not a txt file. Ultimately, I will need to
> plot and save this on each image from an image sequence…
>
> Your input is welcome, Agathe
>
> xcenter=1658;
> ycenter=306;
> makeLine(xcenter,ycenter+1100, xcenter, ycenter+1900); run("Plot
> Profile"); Plot.getValues(x, y);
>    for (i=0; i<x.length; i++)
>       print(x[i], y[i]);
> path = getDirectory("home")+"profile.csv";
> saveAs("Results", path);
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Macro-to-save-plot-profile-data-as-te
> xt-tp5018666.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__
> imagej.1557.x6.nabble.com_Macro-2Dto-2Dsave-2Dplot-2Dprofile-2Ddata-2D
> as-2Dtext-2Dtp5018666.html&d=CwMFaQ&c=uGuXJ43KPkPWEl2imVFDmZQlhQUET7pV
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Re: [Ext] Re: Macro to save plot profile data as text

Volko Straub
Hi Andy,
I think your problem is that you use your window title as the first argument in the SaveAs command. The first argument should be format argument (see macro function documentation). Try replacing
saveAs(titleRG, ImageDir+"\\"+titleRG+".csv");
with
saveAs("text", ImageDir+"\\"+titleRG+".csv");

Hope this helps,
Volko


-----Original Message-----
From: Andy Schofield [mailto:[hidden email]]
Sent: 09 May 2017 10:31
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi All,

I'm having a similar problem where the SaveAs is failing in a macro when I try to save my bespoke table window as a CSV file.

I create my table as such

        titleRG="RedtoGreen";
        tblRG = "["+titleRG+"]";
        fRG = tblRG;
        run("New... ", "name="+tblRG+" type=Table");

and then populate it using

        print(fRG,(CurrCol+CHIPWIDTH/2) + "\t" + (CurrRow+CHIPHEIGHT/2) + "\t" + lastline[4] + "\t" + lastline[6]);

and finally save the table as

        selectWindow("RedtoGreen");
        saveAs(titleRG, ImageDir+"\\"+titleRG+".csv");


When I run the macro, the RedtoGreen table is created OK with tab separated fields but the saveAs reports:-

        Unsupported save() or saveAs() file format: "redtogreen"

I can choose the RedtoGreen table manually and choose File->Save As. The default filename name displayed is RedtoGreen.txt but I can change that to redtoGreen.csv and the tbale saves as expected (i.e. a comma separated file) so it would seem the behaviour is different between the GUI and the macro handler (or that I'm missing something obvious ;-) )

Cheers
Andy

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of arobisson
Sent: 08 May 2017 02:36
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi Volko,

It works. Thank you!
Yes, I used the example from this discussion.. but I got stuck… I guess I have still a bit to learn to write my own macro… Thank you, Agathe

From: Volko Straub [via ImageJ] [mailto:[hidden email]]
Sent: 07 May, 2017 2:30 AM
To: Agathe Robisson <[hidden email]>
Subject: [Ext] Re: Macro to save plot profile data as text

Dear Agathe,

The problem is that your focus is not on the log window when you try to save its content. Also, I don't think the 'Results' option will work with the log window. Change

saveAs("Results", path);

to

selectWindow("Log");
saveAs("Text", path);


A quick websearch shows some similar questions (e.g.
http://stackoverflow.com/questions/29879988/solvedimagej-macro-how-to-save-plot-profile-data-in-a-text-file<https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_29879988_solvedimagej-2Dmacro-2Dhow-2Dto-2Dsave-2Dplot-2Dprofile-2Ddata-2Din-2Da-2Dtext-2Dfile&d=CwMFaQ&c=uGuXJ43KPkPWEl2imVFDmZQlhQUET7pVRA2PDIOxgqw&r=ZSB5F8Ew5Pfa9PJrJrErd_qpXmtjZqfSdSGDjHk5aOs&m=EqPFXdRMzDelyEe4t7UBrRoYEh-gjrJIEA8keliIpPk&s=Hhcyi80Y9Tsz892UNZVr3AF1vXfI4bjG9HnOyUyJGIk&e=>)
that use a results window rather than the log window to list the plot values. Hope this helps, Volko


On 07/05/2017 03:36, arobisson wrote:

> Hello,
>
> I am new to macro.. and cannot get this to work. I am trying to save
> my plot profile automatically in a txt or csv file. The macro below
> gives me a log window but not a txt file. Ultimately, I will need to
> plot and save this on each image from an image sequence…
>
> Your input is welcome, Agathe
>
> xcenter=1658;
> ycenter=306;
> makeLine(xcenter,ycenter+1100, xcenter, ycenter+1900); run("Plot
> Profile"); Plot.getValues(x, y);
>    for (i=0; i<x.length; i++)
>       print(x[i], y[i]);
> path = getDirectory("home")+"profile.csv";
> saveAs("Results", path);
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Macro-to-save-plot-profile-data-as-te
> xt-tp5018666.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__
> imagej.1557.x6.nabble.com_Macro-2Dto-2Dsave-2Dplot-2Dprofile-2Ddata-2D
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Re: [Ext] Re: Macro to save plot profile data as text

Andy Schofield
Thanks Volko.

That moves me forward a little. The file saves now but only as a tab delimited file despite the filename being a .csv. Is there a mechanism to save this as a CSV as it seems to be with the GUI SaveAs?
Do I need to use a different Type= in the original new table creation, for instance? What are the different possible types?

Cheers
Andy

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Straub, Volko A. (Dr.)
Sent: 09 May 2017 11:14
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi Andy,
I think your problem is that you use your window title as the first argument in the SaveAs command. The first argument should be format argument (see macro function documentation). Try replacing saveAs(titleRG, ImageDir+"\\"+titleRG+".csv"); with saveAs("text", ImageDir+"\\"+titleRG+".csv");

Hope this helps,
Volko


-----Original Message-----
From: Andy Schofield [mailto:[hidden email]]
Sent: 09 May 2017 10:31
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi All,

I'm having a similar problem where the SaveAs is failing in a macro when I try to save my bespoke table window as a CSV file.

I create my table as such

        titleRG="RedtoGreen";
        tblRG = "["+titleRG+"]";
        fRG = tblRG;
        run("New... ", "name="+tblRG+" type=Table");

and then populate it using

        print(fRG,(CurrCol+CHIPWIDTH/2) + "\t" + (CurrRow+CHIPHEIGHT/2) + "\t" + lastline[4] + "\t" + lastline[6]);

and finally save the table as

        selectWindow("RedtoGreen");
        saveAs(titleRG, ImageDir+"\\"+titleRG+".csv");


When I run the macro, the RedtoGreen table is created OK with tab separated fields but the saveAs reports:-

        Unsupported save() or saveAs() file format: "redtogreen"

I can choose the RedtoGreen table manually and choose File->Save As. The default filename name displayed is RedtoGreen.txt but I can change that to redtoGreen.csv and the tbale saves as expected (i.e. a comma separated file) so it would seem the behaviour is different between the GUI and the macro handler (or that I'm missing something obvious ;-) )

Cheers
Andy

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of arobisson
Sent: 08 May 2017 02:36
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi Volko,

It works. Thank you!
Yes, I used the example from this discussion.. but I got stuck… I guess I have still a bit to learn to write my own macro… Thank you, Agathe

From: Volko Straub [via ImageJ] [mailto:[hidden email]]
Sent: 07 May, 2017 2:30 AM
To: Agathe Robisson <[hidden email]>
Subject: [Ext] Re: Macro to save plot profile data as text

Dear Agathe,

The problem is that your focus is not on the log window when you try to save its content. Also, I don't think the 'Results' option will work with the log window. Change

saveAs("Results", path);

to

selectWindow("Log");
saveAs("Text", path);


A quick websearch shows some similar questions (e.g.
http://stackoverflow.com/questions/29879988/solvedimagej-macro-how-to-save-plot-profile-data-in-a-text-file<https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_29879988_solvedimagej-2Dmacro-2Dhow-2Dto-2Dsave-2Dplot-2Dprofile-2Ddata-2Din-2Da-2Dtext-2Dfile&d=CwMFaQ&c=uGuXJ43KPkPWEl2imVFDmZQlhQUET7pVRA2PDIOxgqw&r=ZSB5F8Ew5Pfa9PJrJrErd_qpXmtjZqfSdSGDjHk5aOs&m=EqPFXdRMzDelyEe4t7UBrRoYEh-gjrJIEA8keliIpPk&s=Hhcyi80Y9Tsz892UNZVr3AF1vXfI4bjG9HnOyUyJGIk&e=>)
that use a results window rather than the log window to list the plot values. Hope this helps, Volko


On 07/05/2017 03:36, arobisson wrote:

> Hello,
>
> I am new to macro.. and cannot get this to work. I am trying to save
> my plot profile automatically in a txt or csv file. The macro below
> gives me a log window but not a txt file. Ultimately, I will need to
> plot and save this on each image from an image sequence…
>
> Your input is welcome, Agathe
>
> xcenter=1658;
> ycenter=306;
> makeLine(xcenter,ycenter+1100, xcenter, ycenter+1900); run("Plot
> Profile"); Plot.getValues(x, y);
>    for (i=0; i<x.length; i++)
>       print(x[i], y[i]);
> path = getDirectory("home")+"profile.csv";
> saveAs("Results", path);
>
>
>
>
> --
> View this message in context:
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Re: [Ext] Re: Macro to save plot profile data as text

Andy Schofield
Ah, forget that. The .csv is case-sensitive and I was using .CSV in the macro window for testing. Using .csv seems to work fine.
Thanks for the guidance.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Andy Schofield
Sent: 09 May 2017 13:10
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Thanks Volko.

That moves me forward a little. The file saves now but only as a tab delimited file despite the filename being a .csv. Is there a mechanism to save this as a CSV as it seems to be with the GUI SaveAs?
Do I need to use a different Type= in the original new table creation, for instance? What are the different possible types?

Cheers
Andy

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Straub, Volko A. (Dr.)
Sent: 09 May 2017 11:14
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi Andy,
I think your problem is that you use your window title as the first argument in the SaveAs command. The first argument should be format argument (see macro function documentation). Try replacing saveAs(titleRG, ImageDir+"\\"+titleRG+".csv"); with saveAs("text", ImageDir+"\\"+titleRG+".csv");

Hope this helps,
Volko


-----Original Message-----
From: Andy Schofield [mailto:[hidden email]]
Sent: 09 May 2017 10:31
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi All,

I'm having a similar problem where the SaveAs is failing in a macro when I try to save my bespoke table window as a CSV file.

I create my table as such

        titleRG="RedtoGreen";
        tblRG = "["+titleRG+"]";
        fRG = tblRG;
        run("New... ", "name="+tblRG+" type=Table");

and then populate it using

        print(fRG,(CurrCol+CHIPWIDTH/2) + "\t" + (CurrRow+CHIPHEIGHT/2) + "\t" + lastline[4] + "\t" + lastline[6]);

and finally save the table as

        selectWindow("RedtoGreen");
        saveAs(titleRG, ImageDir+"\\"+titleRG+".csv");


When I run the macro, the RedtoGreen table is created OK with tab separated fields but the saveAs reports:-

        Unsupported save() or saveAs() file format: "redtogreen"

I can choose the RedtoGreen table manually and choose File->Save As. The default filename name displayed is RedtoGreen.txt but I can change that to redtoGreen.csv and the tbale saves as expected (i.e. a comma separated file) so it would seem the behaviour is different between the GUI and the macro handler (or that I'm missing something obvious ;-) )

Cheers
Andy

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of arobisson
Sent: 08 May 2017 02:36
To: [hidden email]
Subject: Re: [Ext] Re: Macro to save plot profile data as text

Hi Volko,

It works. Thank you!
Yes, I used the example from this discussion.. but I got stuck… I guess I have still a bit to learn to write my own macro… Thank you, Agathe

From: Volko Straub [via ImageJ] [mailto:[hidden email]]
Sent: 07 May, 2017 2:30 AM
To: Agathe Robisson <[hidden email]>
Subject: [Ext] Re: Macro to save plot profile data as text

Dear Agathe,

The problem is that your focus is not on the log window when you try to save its content. Also, I don't think the 'Results' option will work with the log window. Change

saveAs("Results", path);

to

selectWindow("Log");
saveAs("Text", path);


A quick websearch shows some similar questions (e.g.
http://stackoverflow.com/questions/29879988/solvedimagej-macro-how-to-save-plot-profile-data-in-a-text-file<https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_29879988_solvedimagej-2Dmacro-2Dhow-2Dto-2Dsave-2Dplot-2Dprofile-2Ddata-2Din-2Da-2Dtext-2Dfile&d=CwMFaQ&c=uGuXJ43KPkPWEl2imVFDmZQlhQUET7pVRA2PDIOxgqw&r=ZSB5F8Ew5Pfa9PJrJrErd_qpXmtjZqfSdSGDjHk5aOs&m=EqPFXdRMzDelyEe4t7UBrRoYEh-gjrJIEA8keliIpPk&s=Hhcyi80Y9Tsz892UNZVr3AF1vXfI4bjG9HnOyUyJGIk&e=>)
that use a results window rather than the log window to list the plot values. Hope this helps, Volko


On 07/05/2017 03:36, arobisson wrote:

> Hello,
>
> I am new to macro.. and cannot get this to work. I am trying to save
> my plot profile automatically in a txt or csv file. The macro below
> gives me a log window but not a txt file. Ultimately, I will need to
> plot and save this on each image from an image sequence…
>
> Your input is welcome, Agathe
>
> xcenter=1658;
> ycenter=306;
> makeLine(xcenter,ycenter+1100, xcenter, ycenter+1900); run("Plot
> Profile"); Plot.getValues(x, y);
>    for (i=0; i<x.length; i++)
>       print(x[i], y[i]);
> path = getDirectory("home")+"profile.csv";
> saveAs("Results", path);
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Macro-to-save-plot-profile-data-as-te
> xt-tp5018666.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__
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