http://imagej.273.s1.nabble.com/How-is-the-line-plot-profile-generated-tp5015838p5015870.html
far as I can see. That's perhaps clearer if you use the "live" mode of the
can try to estimate continuous parameters from pixel data. i.e., sub-pixel
> HTH
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::
> Am 13.03.16 um 20:50 schrieb Emmanuel Levy:
>
>> Dear All,
>>
>> I wished to add a piece of macro to illustrate the behaviour I observed
>> and
>> was describing (see below).
>>
>> Discussing offline with Avital made it clear what happens: pixel values
>> are
>> represented by the image-coordinate system and this introduces asymmetry -
>> let's consider 3 pixels:
>> - x=0,y=0 (black)
>> - x=0,y=1 (white)
>> -x=0,y=2 (black)
>>
>> If I draw two horizontal lines at y=0.5 and y=2.5. They are both
>> equidistant from the white pixel on the image (i.e., it looks symmetric)
>> but they are not equidistant in the coordinate system, the line at y=0.5
>> is
>> only 0.5 pixels far from the while pixel's origin (at x=0,y=1), while the
>> line at y=2.5 is 1.5 pixels away. This introduces asymmetry when plot
>> profile calculates values.
>>
>> Would anyone know of a way of producing a symmetric behaviour for plot
>> profile?
>>
>> Thanks for your help,
>> All the best,
>>
>> Emmanuel
>>
>>
>> ===========
>>
>> The macro below creates a whitish region at the centre of a 17 by 17px
>> image, and adds a white pixel at the top of the image as well. It then
>> draws two pairs of lines. I would expect the profile for the two pairs to
>> be identical because the pixel environment is identical. However, the two
>> profiles within each pair are different. e.g., if the line is 0.5 pixel
>> above or below a white pixel will yield a very different outcome.
>>
>> newImage("Untitled", "8-bit Black", 17, 17, 1);
>> makeRectangle(8, 8, 1, 1);
>> run("Clear", "slice");
>> run("Select All");
>> run("Gaussian Blur...", "sigma=2");
>> makeRectangle(7, 1, 1, 1);
>> run("Clear", "slice");
>> run("Enhance Contrast", "saturated=0.35");
>>
>> ///// FIRST PAIR OF PROFILES (left and right to the whitish spot)
>> selectWindow("Untitled");
>> makeLine(4.5, 5.5, 4.5, 11.5);
>> run("Plot Profile");
>>
>> selectWindow("Untitled");
>> makeLine(12.5, 5.5, 12.5, 11.5);
>> run("Plot Profile");
>>
>>
>> ///// SECOND PAIR OF PROFILES (top and bottom to the white pixel)
>> selectWindow("Untitled");
>> makeLine(5.5, 0.5, 9.5, 0.5);
>> run("Plot Profile");
>>
>> selectWindow("Untitled");
>> makeLine(5.5, 2.5, 9.5, 2.5);
>> run("Plot Profile");
>>
>> On 10 March 2016 at 10:06, Jan Eglinger <
[hidden email]> wrote:
>>
>> Dear Avital and Emmanuel,
>>>
>>> On 9 March 2016 at 21:28, Avital Steinberg <
[hidden email]>
>>>> wrote:
>>>>
>>>>> Herbie helped me in the other ImageJ forum
>>>>>
>>>>
>>> Let's be nice and link to this discussion, so others can follow:
>>>
http://forum.imagej.net/t/how-is-the-plot-profile-calculated/1070>>>
>>>
>>> On 10.03.2016 07:26, Emmanuel Levy wrote:
>>>
>>> I would have expected that, by default, only the pixels onto which the
>>>> line
>>>> is drawn are used and interpolated when calculating the profile. Is this
>>>> non-symmetric behaviour of the interpolation an intended behaviour?
>>>>
>>>>
>>> I agree that there are inconsistencies between how lines and segmented
>>> line selection are displayed on the image and the measurements of those
>>> lines. Please see also my following related post on the forum:
>>>
>>>
>>>
>>>
http://forum.imagej.net/t/change-in-pixels-using-reslice-function/999/2?u=imagejan>>>
>>>
>>> I remember previous discussions about rectangular selections and the
>>> behavior of the Fill and Draw commands that by now have been fixed. It
>>> would be great to have a consistent ROI behavior through all types of
>>> selections in ImageJ.
>>>
>>> Cheers,
>>> Jan
>>>
>>>
>>>
>>>
>>>
>>>> On 9 March 2016 at 21:28, Avital Steinberg <
[hidden email]>
>>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>>> When I use ImageJ's graphical user interface and draw a line and then
>>>>> select Analyze, plot profile (with the default settings), I get a plot
>>>>> of
>>>>> intensities vs. the distance from the beginning of the line. I was
>>>>> wondering how the plot is generated, in terms of which pixels in the
>>>>> neighborhood are taken into the weighted average, and how the weights
>>>>> are
>>>>> determined.
>>>>>
>>>>> Herbie helped me in the other ImageJ forum by suggesting that I plot a
>>>>> ramp
>>>>> image. Now I can sometimes predict the values that will appear in the
>>>>> profile plot. (but only in some simple cases) After experimenting with
>>>>> an
>>>>> image, I noticed that the plot's x-axis scale changes abruptly from 1.5
>>>>> to
>>>>> 2.0 (for example) and I was wondering if the distance between 2
>>>>> adjacent
>>>>> points changes when the scale suddenly changes.
>>>>>
>>>>> Thank you,
>>>>> Avital
>>>>>
>>>>>
>>>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>>
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