Posted by
ram prasad on
Jan 25, 2016; 12:25am
URL: http://imagej.273.s1.nabble.com/area-calculations-discrepancy-in-the-manual-and-batch-results-tp5015432p5015445.html
Hi Brandon,
Thank you very much for your reply. I really appreciate it.
A line was drawn by me on the vein which was then perpendicular'd to give
that blue line you see on that image. So just to make it more convenient, I
included that rotate line step in my script so that all I had to do was to
give it the first line and then let the tool rotate it by 90.
And yes, this script does exactly what I wanted it to do. I was under the
impression that looping through a series of images and putting it in the
batchmode are one and the same thing. Is there a way to do that? Almost
every hit I see on google talks about running things in batchmode or
running it as an image sequence but neither works for me.
Cheers,
Ram
On Sun, Jan 24, 2016 at 7:07 AM, Brandon Hurr <
[hidden email]>
wrote:
> The logic in your workflow doesn't make sense here:
> 1) Select the line tool
> 2) Wait for my input
> 3) Rotate my line by 90 degrees.
> 3) Calculate slope and extrapolate the line to the edges of my image.
> 4) Make a polygon from the line coordinates and add it to ROI
> 5) Inverse my selection and add it to ROI
> 6) Duplicate the original image
> 7) Select ROI 0
> 8) Set foreground colour to blue
> 9) Fill the other slice with foreground colour.
> 10) Use thresholder to identify black pixels and make a selection
> 11) Restore selction on the original image and calculate the area of the
> selection.
> 12) Repeat 6-11 for ROI 1.
>
> You don't need to perpendicular line. You need the continuation of your
> line to the edges of the image. I already gave you code for steps 1-5 and
> it did work (but I fixed a potential bug in it related to completely
> vertical line selections).
>
> Also, you've got it set up for potentially going into batch mode. When you
> do that, the image will not be displayed and your user will not be able to
> input the initial line. If you want to loop through a series of images,
> that's different than just putting it in batchmode.
>
> I've changed some things and functionalized your segmentation (since it's
> the same) and it seems to be working for me. Can you test again with this
> and report back?
>
> HTH,
> B
>
> On Fri, Jan 22, 2016 at 5:32 AM, Ramprasad Neethiraj <
[hidden email]
> >
> wrote:
>
> > Hi all,
> >
> > I just realized that I had sent a different version of my script from the
> > one I was using for testing. Please find the script attached.
> >
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http://imagej.nih.gov/ij/list.html> >
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