Re: area calculations - discrepancy in the manual and batch results

Posted by Brandon Hurr on Jan 25, 2016; 5:28pm
URL: http://imagej.273.s1.nabble.com/area-calculations-discrepancy-in-the-manual-and-batch-results-tp5015432p5015457.html

Ram,

Your previously attached code has no perpendicular calculations in it.
Also, the approach you've laid out seems dangerous to me because given a
line (slope + intercept) there are infinite perpendicular lines. How are
you anchoring it? Are you predrawing your dark blue lines and then drawing
the line perpendicular to that?

Attached I've included the ability to select a folder and loop through that
folder. I've also included a results table that stores the area to the
right and left of your line that are "black" pixels as defined by your
color thresholding step.

If you can explain better why you want to draw a perpendicular line, and
how you would anchor that line, I might be able to adapt the macro to that.
I have recently developed code for computing perpendiculars but relative to
the midpoint of the drawn line, but this code doesn't seem to apply in your
situation (in my opinion).


HTH,
B


On Sun, Jan 24, 2016 at 4:25 PM, ram prasad <[hidden email]> wrote:

> 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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> > >
> >
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> >
>
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