http://imagej.273.s1.nabble.com/area-calculations-discrepancy-in-the-manual-and-batch-results-tp5015432p5015471.html
Yes that should work very well. Just add the one line after the user input
> HI Brandon,
>
> Thank you very much for the script. Works like a charm.
>
> As for the perpendicular line, I'm trying to draw a line perpendicular to
> the central vein. To achieve that, first, I draw a line as shown in
> step1.png (attached) and then rotate the selection around the midpoint by
> 90degrees to get step2.png (attached). So if I just draw the first line and
> then ask the macro to rotate it by 90degress, that should work, no?
>
> Cheers,
> Ram
>
> On Mon, Jan 25, 2016 at 6:38 PM, Brandon Hurr <
[hidden email]>
> wrote:
>
> > 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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> >
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>
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