Rename output from "Straighten..." (as a function argument)

[wirthvolker]

Hi,
my macro is using the command Edit>Selection>Straighten in a loop to
extract lines from several ROIs on a stack. The code looks like this:

... in a loop
{
     selectWindow(rawStack);
     roiManager("Select", currROIindex);
     run("Straighten...", "line=20 process");
     rename(currOutputName);
}

The problem with this is that sometimes the "rename"-command is
applied on the raw stack image instead of the straightened output
image. I cannot exclude that it is a problem with users' impatience
(and clicking on images at the wrong time), but it might help to make
it more stable, anyway.

Is there an option for Straighten to do the renaming immediately? I
imagine something like:

run("Straighten...", "line=20 output=whateverWeWantToCallTheOutput");

If there is no such option, could someone give me a hint to the place
where I can modify it myself (my Java skills are limited, but I would
give it a shot)?

Thanks a lot!

Best regards,
Volker

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[Gabriel Landini]

On Tuesday 06 May 2014 10:00:34 you wrote:

> Hi,
> my macro is using the command Edit>Selection>Straighten in a loop to
> extract lines from several ROIs on a stack. The code looks like this:
>
> ... in a loop
> {
>      selectWindow(rawStack);
>      roiManager("Select", currROIindex);
>      run("Straighten...", "line=20 process");
>      rename(currOutputName);
> }
>
> The problem with this is that sometimes the "rename"-command is
> applied on the raw stack image instead of the straightened output
> image. I cannot exclude that it is a problem with users' impatience
> (and clicking on images at the wrong time), but it might help to make
> it more stable, anyway.
>
> Is there an option for Straighten to do the renaming immediately? I
> imagine something like:

Not in the macro language.

You could specify again the selected image that needs to be renamed.
Assuming that the window has no extension, the straightened image name should
be predictable: the original name +"-1".

Something like:

 {
    selectWindow(rawStack);
    roiManager("Select", currROIindex);
    run("Straighten...", "line=20 process");
    selectWindow(originalName+"-1");
    rename(currOutputName);
}


Cheers

Gabriel

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[wirthvolker]

Hi Gabriel,
thank you for the quick reply, I will implement it like that.
Cheers,
Volker

2014-05-06 10:12 GMT+02:00 Gabriel Landini <[hidden email]>:

> On Tuesday 06 May 2014 10:00:34 you wrote:
>> Hi,
>> my macro is using the command Edit>Selection>Straighten in a loop to
>> extract lines from several ROIs on a stack. The code looks like this:
>>
>> ... in a loop
>> {
>>      selectWindow(rawStack);
>>      roiManager("Select", currROIindex);
>>      run("Straighten...", "line=20 process");
>>      rename(currOutputName);
>> }
>>
>> The problem with this is that sometimes the "rename"-command is
>> applied on the raw stack image instead of the straightened output
>> image. I cannot exclude that it is a problem with users' impatience
>> (and clicking on images at the wrong time), but it might help to make
>> it more stable, anyway.
>>
>> Is there an option for Straighten to do the renaming immediately? I
>> imagine something like:
>
> Not in the macro language.
>
> You could specify again the selected image that needs to be renamed.
> Assuming that the window has no extension, the straightened image name should
> be predictable: the original name +"-1".
>
> Something like:
>
>  {
>     selectWindow(rawStack);
>     roiManager("Select", currROIindex);
>     run("Straighten...", "line=20 process");
>     selectWindow(originalName+"-1");
>     rename(currOutputName);
> }
>
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Krs5]

Hi Volker,

If this does not solve the problem it is possible that the Straighten image is not created yet when you try to rename it. As a result the raw image is renamed. If so, add:  wait(100); before rename. You can change the 100 to any number that works (1000 = 1 second).

Best wishes

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Volker Wirth
Sent: 06 May 2014 09:56
To: [hidden email]
Subject: Re: Rename output from "Straighten..." (as a function argument)

Hi Gabriel,
thank you for the quick reply, I will implement it like that.
Cheers,
Volker

2014-05-06 10:12 GMT+02:00 Gabriel Landini <[hidden email]>:

> On Tuesday 06 May 2014 10:00:34 you wrote:
>> Hi,
>> my macro is using the command Edit>Selection>Straighten in a loop to
>> extract lines from several ROIs on a stack. The code looks like this:
>>
>> ... in a loop
>> {
>>      selectWindow(rawStack);
>>      roiManager("Select", currROIindex);
>>      run("Straighten...", "line=20 process");
>>      rename(currOutputName);
>> }
>>
>> The problem with this is that sometimes the "rename"-command is
>> applied on the raw stack image instead of the straightened output
>> image. I cannot exclude that it is a problem with users' impatience
>> (and clicking on images at the wrong time), but it might help to make
>> it more stable, anyway.
>>
>> Is there an option for Straighten to do the renaming immediately? I
>> imagine something like:
>
> Not in the macro language.
>
> You could specify again the selected image that needs to be renamed.
> Assuming that the window has no extension, the straightened image name
> should be predictable: the original name +"-1".
>
> Something like:
>
>  {
>     selectWindow(rawStack);
>     roiManager("Select", currROIindex);
>     run("Straighten...", "line=20 process");
>     selectWindow(originalName+"-1");
>     rename(currOutputName);
> }
>
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Rasband, Wayne (NIH/NIMH) [E]]

On May 6, 2014, at 4:00 AM, Volker Wirth wrote:

> Hi,
> my macro is using the command Edit>Selection>Straighten in a loop to
> extract lines from several ROIs on a stack. The code looks like this:
>
> ... in a loop
> {
>     selectWindow(rawStack);
>     roiManager("Select", currROIindex);
>     run("Straighten...", "line=20 process");
>     rename(currOutputName);
> }
>
> The problem with this is that sometimes the "rename"-command is
> applied on the raw stack image instead of the straightened output
> image. I cannot exclude that it is a problem with users' impatience
> (and clicking on images at the wrong time), but it might help to make
> it more stable, anyway.
>
> Is there an option for Straighten to do the renaming immediately? I
> imagine something like:
>
> run("Straighten...", "line=20 output=whateverWeWantToCallTheOutput");

The Edit>Selection>Straighten command in the latest ImageJ daily build (1.49a16) adds a "Title:" field to its dialog so you can use something like

   run("Straighten...", "line=20 title=OutputTitle");

in a macro.

-wayne

> If there is no such option, could someone give me a hint to the place
> where I can modify it myself (my Java skills are limited, but I would
> give it a shot)?
>
> Thanks a lot!
>
> Best regards,
> Volker

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[wirthvolker]

Thanks a lot!
Cheers,
Volker

2014-05-07 17:17 GMT+02:00 Rasband, Wayne (NIH/NIMH) [E]
<[hidden email]>:

> On May 6, 2014, at 4:00 AM, Volker Wirth wrote:
>
>> Hi,
>> my macro is using the command Edit>Selection>Straighten in a loop to
>> extract lines from several ROIs on a stack. The code looks like this:
>>
>> ... in a loop
>> {
>>     selectWindow(rawStack);
>>     roiManager("Select", currROIindex);
>>     run("Straighten...", "line=20 process");
>>     rename(currOutputName);
>> }
>>
>> The problem with this is that sometimes the "rename"-command is
>> applied on the raw stack image instead of the straightened output
>> image. I cannot exclude that it is a problem with users' impatience
>> (and clicking on images at the wrong time), but it might help to make
>> it more stable, anyway.
>>
>> Is there an option for Straighten to do the renaming immediately? I
>> imagine something like:
>>
>> run("Straighten...", "line=20 output=whateverWeWantToCallTheOutput");
>
> The Edit>Selection>Straighten command in the latest ImageJ daily build (1.49a16) adds a "Title:" field to its dialog so you can use something like
>
>    run("Straighten...", "line=20 title=OutputTitle");
>
> in a macro.
>
> -wayne
>
>> If there is no such option, could someone give me a hint to the place
>> where I can modify it myself (my Java skills are limited, but I would
>> give it a shot)?
>>
>> Thanks a lot!
>>
>> Best regards,
>> Volker
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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