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batch mode scale bar macro

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PEARSON Matthew

batch mode scale bar macro

Hi all,

I'm trying to write my own macro that uses batch mode to open a folder
of images, set a scale and place a scale bar on all of them then save
away to a specified folder.

I'm using the run("Set Scale...") function to set the scale of each
image which seems to work fine. I've then created my own dialog which
replicates the info needed for the inbuilt scale bar plus dialog- i
don't use that as it requires an image to be open and i want the
dialog to open at the start and then be used for all images before
batch mode begins.

The result of the macro is a white bar along the lower right of the
image, no text is seen and i can't change the colour. Basically the
run(scale bar...) function doesn't seem to 'see' or accept the
variables i've created which i've plugged into the run(scale bar...)
function. I think i've maybe made an error putting my variables into
run(scale bar...) function so i've attached that bit of code to the
email.

I know there are other ways to make scale bars by not using the scale
bar function by making rectangles of a certain size etc but this is
the easiest method for me to get my head around.

Thanks for the advice!
Matt

See extracted code below:

colours = newArray("White", "Black", "Red", "Green", "Blue");
locations = newArray("Lower Left", "Lower Right", "Upper Left", "Upper
Right");

Dialog.create("Scale Bar Options");
Dialog.addMessage("Fill in parameters");
Dialog.addNumber("Width of SB", 100);
Dialog.addNumber("Height of SB", 3);
Dialog.addNumber("Font Size", 14);
Dialog.addChoice("Colour", colours);
Dialog.addChoice("Location", locations);
Dialog.show();

width = Dialog.getNumber();
height = Dialog.getNumber();
font = Dialog.getNumber();
color = Dialog.getChoice();
location = Dialog.getChoice();

setBatchMode(true); // runs up to 6 times faster
for (i=0; i<list.length; i++) {
path = dir+list[i];
open(path);
title = getTitle();

run("Set Scale...", "distance=scale known=1 pixel=1 unit=um");
run("Scale Bar...", "width, height, font, color, background=None,
location, bold");

saveAs("tiff", dirsave + title);
close();
}

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Scotland, with registration number SC005336.

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LIM Soon Yew John (IMB)

Re: batch mode scale bar macro

Hi Matt,

If your images are not in RGB, then the colour of your scalebar will follow the LUT colour. You can add "overlay" into run("Scale Bar...",...) so that the scalebar is an overlay on top of your image.

Best Regards,
John
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Matthew Pearson [[hidden email]]
Sent: Thursday, July 12, 2012 5:56 PM
To: [hidden email]
Subject: batch mode scale bar macro

Hi all,

I'm trying to write my own macro that uses batch mode to open a folder
of images, set a scale and place a scale bar on all of them then save
away to a specified folder.

I'm using the run("Set Scale...") function to set the scale of each
image which seems to work fine. I've then created my own dialog which
replicates the info needed for the inbuilt scale bar plus dialog- i
don't use that as it requires an image to be open and i want the
dialog to open at the start and then be used for all images before
batch mode begins.

The result of the macro is a white bar along the lower right of the
image, no text is seen and i can't change the colour. Basically the
run(scale bar...) function doesn't seem to 'see' or accept the
variables i've created which i've plugged into the run(scale bar...)
function. I think i've maybe made an error putting my variables into
run(scale bar...) function so i've attached that bit of code to the
email.

I know there are other ways to make scale bars by not using the scale
bar function by making rectangles of a certain size etc but this is
the easiest method for me to get my head around.

Thanks for the advice!
Matt

See extracted code below:

colours = newArray("White", "Black", "Red", "Green", "Blue");
locations = newArray("Lower Left", "Lower Right", "Upper Left", "Upper
Right");

Dialog.create("Scale Bar Options");
Dialog.addMessage("Fill in parameters");
Dialog.addNumber("Width of SB", 100);
Dialog.addNumber("Height of SB", 3);
Dialog.addNumber("Font Size", 14);
Dialog.addChoice("Colour", colours);
Dialog.addChoice("Location", locations);
Dialog.show();

width = Dialog.getNumber();
height = Dialog.getNumber();
font = Dialog.getNumber();
color = Dialog.getChoice();
location = Dialog.getChoice();

setBatchMode(true); // runs up to 6 times faster
for (i=0; i<list.length; i++) {
path = dir+list[i];
open(path);
title = getTitle();

run("Set Scale...", "distance=scale known=1 pixel=1 unit=um");
run("Scale Bar...", "width, height, font, color, background=None,
location, bold");

saveAs("tiff", dirsave + title);
close();
}

--
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

Re: batch mode scale bar macro

Hi John,

Yes thanks thats a good point. However i changed some test images to
RGB and tried again but still got only a white rectangle and no text.
Perhaps you just can't use the scale bar plus in a macro..

Thanks,
Matt
On 12 Jul 2012, at 11:28, LIM Soon Yew John (IMB) wrote:

> Hi Matt,
>
> If your images are not in RGB, then the colour of your scalebar will
> follow the LUT colour. You can add "overlay" into run("Scale
> Bar...",...) so that the scalebar is an overlay on top of your image.
>
> Best Regards,
> John
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] On Behalf Of
> Matthew Pearson [[hidden email]]
> Sent: Thursday, July 12, 2012 5:56 PM
> To: [hidden email]
> Subject: batch mode scale bar macro
>
> Hi all,
>
> I'm trying to write my own macro that uses batch mode to open a folder
> of images, set a scale and place a scale bar on all of them then save
> away to a specified folder.
>
> I'm using the run("Set Scale...") function to set the scale of each
> image which seems to work fine. I've then created my own dialog which
> replicates the info needed for the inbuilt scale bar plus dialog- i
> don't use that as it requires an image to be open and i want the
> dialog to open at the start and then be used for all images before
> batch mode begins.
>
> The result of the macro is a white bar along the lower right of the
> image, no text is seen and i can't change the colour. Basically the
> run(scale bar...) function doesn't seem to 'see' or accept the
> variables i've created which i've plugged into the run(scale bar...)
> function. I think i've maybe made an error putting my variables into
> run(scale bar...) function so i've attached that bit of code to the
> email.
>
> I know there are other ways to make scale bars by not using the scale
> bar function by making rectangles of a certain size etc but this is
> the easiest method for me to get my head around.
>
> Thanks for the advice!
> Matt
>
> See extracted code below:
>
> colours = newArray("White", "Black", "Red", "Green", "Blue");
> locations = newArray("Lower Left", "Lower Right", "Upper Left", "Upper
> Right");
>
> Dialog.create("Scale Bar Options");
> Dialog.addMessage("Fill in parameters");
> Dialog.addNumber("Width of SB", 100);
> Dialog.addNumber("Height of SB", 3);
> Dialog.addNumber("Font Size", 14);
> Dialog.addChoice("Colour", colours);
> Dialog.addChoice("Location", locations);
> Dialog.show();
>
> width = Dialog.getNumber();
> height = Dialog.getNumber();
> font = Dialog.getNumber();
> color = Dialog.getChoice();
> location = Dialog.getChoice();
>
> setBatchMode(true); // runs up to 6 times faster
> for (i=0; i<list.length; i++) {
> path = dir+list[i];
> open(path);
> title = getTitle();
>
> run("Set Scale...", "distance=scale known=1 pixel=1 unit=um");
> run("Scale Bar...", "width, height, font, color, background=None,
> location, bold");
>
> saveAs("tiff", dirsave + title);
> close();
> }
>
> --
> 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
>

--
Matt Pearson
Microscopy and Imaging Facility
MRC Human Genetics Unit
University of Edinburgh
Crewe Road
Edinburgh
EH4 2XU

Tel: 0131 467 8425

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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

Tiago Ferreira-2

Re: batch mode scale bar macro

Dear Matt,

> However i changed some test images to RGB and tried again but still got only a
> white rectangle and no text.

The problem is that you are not passing a single string with keyword=value pairs
to the ScaleBar command. See Jérôme's guide at
<http://imagej.nih.gov/ij/docs/macro_reference_guide.pdf> and compare the output
of the Macro Recorder to the call you are making. You will have to use string
concatenation such as

run("Scale Bar...", "width="+ width +" height="+ height +" font="
+ font +" color="+ color);
or

run("Scale Bar...", "width=&width height=&height font=&font color=&color);

HTH,
-tiago;
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