Determining origin of Z coordinates

[Stein Rørvik]

ImageJ allows you to define an origin elsewhere than the upper left corner of the image,
allowing measurements in physical coordinates where applicable.

This works well for both XY and Z coordinates.
For example, we can define the origin of the "T1 Head" sample stack as the centre of the middle slice:

run("T1 Head (2.4M, 16-bits)");
run("Properties...", "origin=128,128,64");

What I need to do is to determine the location of this origin later, from a macro.

For XY, this is easy. I just convert scaled position 0,0 to pixel coordinates:

x = 0;
y = 0;
toUnscaled(x, y);
print("x: " + x);
print("y: " + y);

But how can I get the pixel Z coordinate of the origin?

toUnscaled(x, y, z) does not work.

The easy fix to this would be to allow this third Z parameter in the toScaled and toUnscaled macro commands, for consistency.

Perhaps even better, a getOrigin(x,y,z) command?


Stein


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[Wayne Rasband-2]

> On Mar 9, 2018, at 3:04 AM, Stein Rørvik <[hidden email]> wrote:
>
> ImageJ allows you to define an origin elsewhere than the upper left corner of the image,
> allowing measurements in physical coordinates where applicable.
>
> This works well for both XY and Z coordinates.
> For example, we can define the origin of the "T1 Head" sample stack as the centre of the middle slice:
>
> run("T1 Head (2.4M, 16-bits)");
> run("Properties...", "origin=128,128,64");
>
> What I need to do is to determine the location of this origin later, from a macro.
>
> For XY, this is easy. I just convert scaled position 0,0 to pixel coordinates:
>
> x = 0;
> y = 0;
> toUnscaled(x, y);
> print("x: " + x);
> print("y: " + y);
>
> But how can I get the pixel Z coordinate of the origin?
>
> toUnscaled(x, y, z) does not work.

Upgrade to the latest daily build (1.52a4) and toUnscaled(x, y, z) will work. Both toScaled() and toUnscaled() now support a third z argument.  Here is an updated version of your example:

  run("T1 Head (2.4M, 16-bits)");
  run("Properties...", "origin=128,128,64");
  x=0; y=0; z=0;
  toUnscaled(x, y, z);
  print("x origin: " + x);
  print("y origin: " + y);
  print("z origin: " + z);

-wayne


> The easy fix to this would be to allow this third Z parameter in the toScaled and toUnscaled macro commands, for consistency.
>
> Perhaps even better, a getOrigin(x,y,z) command?
>
>
> Stein

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[Stein Rørvik]

Thanks, works great!

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Wayne Rasband
Sent: 14. mars 2018 21:21
To: [hidden email]
Subject: Re: Determining origin of Z coordinates

...

Upgrade to the latest daily build (1.52a4) and toUnscaled(x, y, z) will work. Both toScaled() and toUnscaled() now support a third z argument.  Here is an updated version of your example:

  run("T1 Head (2.4M, 16-bits)");
  run("Properties...", "origin=128,128,64");
  x=0; y=0; z=0;
  toUnscaled(x, y, z);
  print("x origin: " + x);
  print("y origin: " + y);
  print("z origin: " + z);

-wayne


> The easy fix to this would be to allow this third Z parameter in the toScaled and toUnscaled macro commands, for consistency.
>
> Perhaps even better, a getOrigin(x,y,z) command?
>
>
> Stein

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