http://imagej.273.s1.nabble.com/Pixel-inspector-rugosity-tp5010138p5010150.html
pretty low, any sort of filter throws it off way too much. I have found
> Hi Keyvan,
>
> as long as the slope angles are low, it seems to me that rugosity can be
> approximated by
> 1 + 0.5((dv/dx)^2 + (dv/dy)^2)
> where v is the pixel value.
>
> This is essentially 1 + 0.5 times the square of the Sobel operator.
>
http://en.wikipedia.org/wiki/Sobel_operator> The Sobel operator is implemented in ImageJ as Process>Find Edges.
>
> For higher slopes, you need 1/cos(Sobel_output). In any case, make sure
> that your z units are the same as the distance between the pixels (use a
> 32-bit image, i.e. floating-point precision).
>
> You can then average over the rugosity in any area by Analyze>Measure.
>
> The result will be slightly different than what you get when calculating
> rugosity from the single pixel values because the Sobel operator does
> slight smoothing of the data (to avoid that, you may resize the image to
> twice or 3x the original size with bicubic interpolation).
>
> ---
>
> The reason why the Pixel Inspector is limited in size is showing no more
> data than what fits the typical screen size, but also performance: When
> writing the plugin, I did not expect that any one would ever use it for
> sizes larger than roughly 7x7, so I simply took a jawa.awt.Label for each
> single number. This becomes quite slow for large amounts of numbers.
>
> ---
>
> Another option if you need the pixel values for a larger area: Duplicate
> the selection and save as Text Image. Then you can read the values into
> your own program to calculate rugosity by the method of your choice. Or
> implement that method directly in an ImageJ macro or plugin.
>
>
> Michael
> ________________________________________________________________
> On Oct 21, 2014, at 20:03, Balazadeh Mohtadi, Carlos wrote:
>
> > Hi everyone,
> >
> > I'm currently looking at trying to generate a value for rugosity or
> average
> > roughness from a set number of pixels or a frame within a grayscale
> image.
> >
> > Pixel inspector gives me a wide array of pixel data with intensity values
> > per pixel which can be translated into a surface plot easily. I would
> like
> > to translate that data into a rugosity measurement of the plot generated,
> > in this case, height would be designated by max peaks recorded in the
> pixel
> > data frame.
> >
> > One issue I have with pixel inspector is that it can only give me a pixel
> > inspection radius of 10 pixels. I need something slightly bigger and I'm
> > not sure if I could potentially override this setting or not.
> >
> > I'm linking an image of the surface plot I'm generating within a
> specified
> > area using the rectangle tool (unfortunately, I don't know if I can
> extract
> > pixel data for the rectangle tool).
> > The next image is an example of the surface plot I'm generating using the
> > pixel inspector along with a .csv that contains the pixel data for that
> > plot.
> >
> > 1 - rectangle tool surface plot ROI
> >
https://www.dropbox.com/s/jim0svvd0h8ycou/1.bmp?dl=0> >
> > 2 - Pixel inspector ROI surface plot (much smaller than the first
> >
https://www.dropbox.com/s/bh061xdl8y3yrzk/2.bmp?dl=0> >
> > Pixel data2 - Pixel data for image "2".
> >
> >
https://www.dropbox.com/s/43dpfffifv4bfof/Pixel%20data2.csv?dl=0> >
> > I'm converting all my images to 8-bit before generating these.
> > As you see with picture 1, there is plenty of peaks and valleys that can
> be
> > used to assess a rugosity value or roughness.
> >
> > If anyone has done similar work I'd greatly appreciate the help.
> >
> > Best regards,
> >
> > Keyvan Balazadeh
> >
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