ObjectJ Tree Rings/Otolith Macro questions

[Jens Hegg]

I've successfully used the ObjectJ tree ring/otolith project to do growth analysis on juvenile salmon otoliths. There are a few things that I'd like to be able to change in the macro but I don't know how.

1) the table output is really useful, but it would be nice to be able to put the image name at the top of each column rather than the generic obj1, obj2...

2) I'd like to change the keystroke combination to delete a point with the gun tool. It's far too easy to delete all of your work by forgetting to hold down the option key when deleting a single point...I'm not a fan of having to redo a hundred points because I tried to delete a single misplaced one.

3) The F7 combination to do auto-detection always ends up giving me multiple objects on the same otolith, which makes the process much more difficult. Can anyone explain to me how to correctly use it within an object without creating a new object each time, or is this the default?

Are these manageable changes for a newbie? Can anyone point me toward how to change this macro? I'm having trouble figuring out how the ImageJ macro system works.

Thanks

[vischer]

Hi Jens,


> On 20. May 2016, at 23:25, Jens Hegg <[hidden email]> wrote:
>
> I've successfully used the tree ring/otolith project to do growth analysis on
> juvenile salmon otoliths. There are a few things that I'd like to be able to
> change in the macro but I don't know how.
>
> 1) the table output is really useful, but it would be nice to be able to put
> the image name at the top of each column rather than the generic obj1,
> obj2...

in function doOutput(format),

replace
                for (obj = 1; obj<= maxObj; obj++)
                        hdr = hdr + "\t" + "obj-"+obj;
by:

                for (obj = 1; obj<= maxObj; obj++)
                        hdr = hdr + "\t" + ojOwnerName(obj);

In TreeRings-13, this is on line 371. It will show the file name instead the object number as header.
Click "Install In ObjectJ menu" to make the change active.



> 2) I'd like to change the keystroke combination to delete a point with the
> gun tool. It's far too easy to delete all of your work by forgetting to hold
> down the option key when deleting a single point...I'm not a fan of having
> to redo a hundred points because I tried to delete a single misplaced one.

Are your juvenile otoliths hundreds of years old?
Unfortunately, there is no Undo Kill (like in real life).
We usually didn't have hundreds of points per trajectory.
But I could try to create a special "kill closest point" shortcut key...



> 3) The F7 combination to do auto-detection always ends up giving me multiple
> objects on the same otolith, which makes the process much more difficult.
> Can anyone explain to me how to correctly use it within an object without
> creating a new object each time, or is this the default?
>

In TreeRings-13, F7 is used to insert a point into the selected trajectory, whereas the auto-repeat function of key F2 is used to detect more rings while you move the mouse, which can then be confirmed with F3. So it is not clear to me what you mean. Is your "Composite Objects" button in ObjectJ Tools correctly set?

> Are these manageable changes for a newbie? Can anyone point me toward how to
> change this macro? I'm having trouble figuring out how the ImageJ macro
> system works.
>
> Thanks


Best regards, Norbert
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jens Hegg]

Thanks for the reply!

This is a real noob question, but how do you open the file to edit it? Opening in TextEdit comes out as gibberish and I can't find a way to open it directly in ImageJ.

No, the fish aren't hundreds of years old. I am measuring daily growth increments, so there are many more of them than if I was only counting yearly bands. It would be nice if the "Kill single point" were the simplest keystroke and "kill all points" required an extra keystroke. This would guard against accidentally deleting an entire object. I suppose doing that gets deeper into how ObjectJ is written though.

I'm sorry, I mistyped. The auto-detect is F2 as you say. My Composite box is checked. Should it be?

Thanks.