Scaling of / measuring inside a profile plot window

[madmark666]

I am trying to measure within a profile plot window. But even if I scale the original window, the scale of the profile plot window isn't set properly.

What I want to do:
1. Create a profile plot through some image features using the straight line selection.
2. Measure a distance between two peaks inside the profile plot using the straight line selection inside the plot window.

The coordinates shown at the bottom of the plot windows are correct, but the data shown for the lenght of the straight line selection shown in the ImageJ command window aren't scaled right. It seems to me as if the scale/calibaration of the profile window itself isn't set at all? How could I fix this?

Best regards and thanks for the great program,

Mad

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[Wayne Rasband]

> I am trying to measure within a profile plot window. But even if I
> scale the original window, the scale of the profile plot window isn't
> set properly.
>
> What I want to do:
> 1. Create a profile plot through some image features using the
> straight line selection.
> 2. Measure a distance between two peaks inside the profile plot using
> the straight line selection inside the plot window.
>
> The coordinates shown at the bottom of the plot windows are correct,
> but the data shown for the lenght of the straight line selection shown
> in the ImageJ command window aren't scaled right. It seems to me as if
> the scale/calibaration of the profile window itself isn't set at all?
> How could I fix this?

The plot window scale is not set. I will fix this but I won't be able
to get to it for a couple of weeks. In the meantime, you can set the
scale by setting "Pixel Width" and "Pixel Height" in the
Image>Properties dialog, where

     Pixel Width = (xmax-xmin)/<length of x-axis in pixels>
     Pixel Height = (ymax-ymin)/<length of y-axis in pixels>

The length of the x and y axis in pixels can be found in the
Edit>Options>Profile Plot Options dialog box.

-wayne

[Jonathan Hilmer]

The scale of a profile plot window is hard-coded into the plot.java
file.  The coordinates you see while moving the cursor in a plot
window also come from the same file (getCoordinates), and they are
correct because getCoordinates() uses xValues[] and yValues[]
(containing the plot data) to produce the displayed text.

However, if you're using a straight line selection to perform
measurements on the profile plot window, the displayed coordinates for
the selection come from the cursor coordinates and the image
calibration (pixel height, length, voxel depth, and units).  Although
I'm not sure where to find this code, it's fairly obvious from use
that the function has no knowledge of stored lists containing a plot
profile.

The easiest solution would be to edit the way plots are drawn to
include a calibration based upon the plot dimensions and the final
plot size.  In my opinion, this is something that should be added to
the ImageJ base, since I'm sure few people care about the pixel
measurements of a plot (rather than the data actually being plotted).
Making the plots at least 1:1 to the original selection would also be
nice to see, but this is just my personal preference.



Jonathan Hilmer
Bothner Research Group
Montana State University


On 7/26/06, madmark666 <[hidden email]> wrote:

> I am trying to measure within a profile plot window. But even if I scale the original window, the scale of the profile plot window isn't set properly.
>
> What I want to do:
> 1. Create a profile plot through some image features using the straight line selection.
> 2. Measure a distance between two peaks inside the profile plot using the straight line selection inside the plot window.
>
> The coordinates shown at the bottom of the plot windows are correct, but the data shown for the lenght of the straight line selection shown in the ImageJ command window aren't scaled right. It seems to me as if the scale/calibaration of the profile window itself isn't set at all? How could I fix this?
>
> Best regards and thanks for the great program,
>
> Mad