Maxima in a plot profile

[ERIC]

Dear All,
I would like to know how the values are calculated in a plot profile :
I have a small image (Stack-2.tif) in which I draw a line over the pixel
of maximum intensity (value : 2068).
The line is traced
  If I use Analyze/Plot Profile and list the values from a 1 pixel width
line the maximum is 1921.58 (Values on the left of plot profile.png). On
the right it's with a width of 3 pixels.
How does the values are calculated ? How can I get the real max value (
in this case 2068) of a line across a picture ?

Thanks for your comment

-- ich

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/


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[Jerome Mutterer-3]

Hi Eric,

You must have Edit > Options > Profile Plot Options > Interpolate line
profiles option checked.
Uncheck it if you want uninterpolated pixel values.

The pixel values along a line are retrieved like this:
https://github.com/fiji/imagej1/blob/master/ij/gui/Line.java#L394

For 1 pixel wide lines like yours the interpolation code is there:
https://github.com/fiji/imagej1/blob/master/ij/process/ImageProcessor.java#L962

and finally calls the getInterpolatedValue(x,y) method here:
https://github.com/fiji/imagej1/blob/master/ij/process/ImageProcessor.java#L1694

Sincerely,

Jerome.

On 28 June 2013 08:44, Eric Denarier <[hidden email]> wrote:

> Dear All,
> I would like to know how the values are calculated in a plot profile :
> I have a small image (Stack-2.tif) in which I draw a line over the pixel
> of maximum intensity (value : 2068).
> The line is traced
>  If I use Analyze/Plot Profile and list the values from a 1 pixel width
> line the maximum is 1921.58 (Values on the left of plot profile.png). On
> the right it's with a width of 3 pixels.
> How does the values are calculated ? How can I get the real max value ( in
> this case 2068) of a line across a picture ?
>
> Thanks for your comment
>
> -- ich
>
> Eric Denarier
> Grenoble Institut des Neurosciences
> Inserm U836
> Chemin Fortuné Ferrini
> 38700 La Tronche
> France
>
>
> Tél :[phone]
> Fax :[phone]
>
> http://neurosciences.ujf-**grenoble.fr/<http://neurosciences.ujf-grenoble.fr/>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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[ERIC]

Thanks Jerome,
That was the problem.
But I have an other one : If I draw a segmented line and
Edit/Selection/Straigthen, it makes a curve that doesn't overlay the
original line. Can it be fix ?

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 28/06/2013 09:49, Jerome Mutterer a écrit :

> Hi Eric,
>
> You must have Edit > Options > Profile Plot Options > Interpolate line
> profiles option checked.
> Uncheck it if you want uninterpolated pixel values.
>
> The pixel values along a line are retrieved like this:
> https://github.com/fiji/imagej1/blob/master/ij/gui/Line.java#L394
>
> For 1 pixel wide lines like yours the interpolation code is there:
> https://github.com/fiji/imagej1/blob/master/ij/process/ImageProcessor.java#L962
>
> and finally calls the getInterpolatedValue(x,y) method here:
> https://github.com/fiji/imagej1/blob/master/ij/process/ImageProcessor.java#L1694
>
> Sincerely,
>
> Jerome.
>
> On 28 June 2013 08:44, Eric Denarier <[hidden email]> wrote:
>
>> Dear All,
>> I would like to know how the values are calculated in a plot profile :
>> I have a small image (Stack-2.tif) in which I draw a line over the pixel
>> of maximum intensity (value : 2068).
>> The line is traced
>>   If I use Analyze/Plot Profile and list the values from a 1 pixel width
>> line the maximum is 1921.58 (Values on the left of plot profile.png). On
>> the right it's with a width of 3 pixels.
>> How does the values are calculated ? How can I get the real max value ( in
>> this case 2068) of a line across a picture ?
>>
>> Thanks for your comment
>>
>> -- ich
>>
>> Eric Denarier
>> Grenoble Institut des Neurosciences
>> Inserm U836
>> Chemin Fortuné Ferrini
>> 38700 La Tronche
>> France
>>
>>
>> Tél :[phone]
>> Fax :[phone]
>>
>> http://neurosciences.ujf-**grenoble.fr/<http://neurosciences.ujf-grenoble.fr/>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Jerome Mutterer-3]

Eric,
As far as I know, the Straightener always fits a spline before
straightening. What you can do to get a fitted spline closer to your
original polygon line, is interpolate it at 1 pixel intervals before
straightening, using the Edit > Selection > Interpolate command.
Jerome

On 28 June 2013 10:09, Eric Denarier <[hidden email]> wrote:

> Thanks Jerome,
> That was the problem.
> But I have an other one : If I draw a segmented line and
> Edit/Selection/Straigthen, it makes a curve that doesn't overlay the
> original line. Can it be fix ?
>
>
> Eric Denarier
> Grenoble Institut des Neurosciences
> Inserm U836
> Chemin Fortuné Ferrini
> 38700 La Tronche
> France
>
>
> Tél :[phone]
> Fax :[phone]
>
> http://neurosciences.ujf-**grenoble.fr/<http://neurosciences.ujf-grenoble.fr/>
>
> Le 28/06/2013 09:49, Jerome Mutterer a écrit :
>
>> Hi Eric,
>>
>> You must have Edit > Options > Profile Plot Options > Interpolate line
>> profiles option checked.
>> Uncheck it if you want uninterpolated pixel values.
>>
>> The pixel values along a line are retrieved like this:
>> https://github.com/fiji/**imagej1/blob/master/ij/gui/**Line.java#L394<https://github.com/fiji/imagej1/blob/master/ij/gui/Line.java#L394>
>>
>> For 1 pixel wide lines like yours the interpolation code is there:
>> https://github.com/fiji/**imagej1/blob/master/ij/**
>> process/ImageProcessor.java#**L962<https://github.com/fiji/imagej1/blob/master/ij/process/ImageProcessor.java#L962>
>>
>> and finally calls the getInterpolatedValue(x,y) method here:
>> https://github.com/fiji/**imagej1/blob/master/ij/**
>> process/ImageProcessor.java#**L1694<https://github.com/fiji/imagej1/blob/master/ij/process/ImageProcessor.java#L1694>
>>
>> Sincerely,
>>
>> Jerome.
>>
>> On 28 June 2013 08:44, Eric Denarier <[hidden email]**>
>> wrote:
>>
>>  Dear All,
>>> I would like to know how the values are calculated in a plot profile :
>>> I have a small image (Stack-2.tif) in which I draw a line over the pixel
>>> of maximum intensity (value : 2068).
>>> The line is traced
>>>   If I use Analyze/Plot Profile and list the values from a 1 pixel width
>>> line the maximum is 1921.58 (Values on the left of plot profile.png). On
>>> the right it's with a width of 3 pixels.
>>> How does the values are calculated ? How can I get the real max value (
>>> in
>>> this case 2068) of a line across a picture ?
>>>
>>> Thanks for your comment
>>>
>>> -- ich
>>>
>>> Eric Denarier
>>> Grenoble Institut des Neurosciences
>>> Inserm U836
>>> Chemin Fortuné Ferrini
>>> 38700 La Tronche
>>> France
>>>
>>>
>>> Tél :[phone]
>>> Fax :[phone]
>>>
>>> http://neurosciences.ujf-**gre**noble.fr/ <http://grenoble.fr/><http://*
>>> *neurosciences.ujf-grenoble.fr/ <http://neurosciences.ujf-grenoble.fr/>*
>>> *>
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>> >
>>>
>>>  --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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[Michael Schmid]

Hi Eric,

Edit>Selection>Straighten works only with lines that are smooth; it does not work if there are sharp corners. Thus, if you don't have 'Spline Fit' clicked to get a smooth line, it does that for you.

Imagine a segmented line with a sharp corner, and you cut out a band with a given width along the segmented line from a rubber sheet. Then you want to straighten it: at the inner (concave) side, when you try to straighten it, it will break. In other words, the pixel values of the straightened selection are undefined.

In any case, I am not sure what it should be good for to straighten a segmented selection that is not splined.
What's the idea behind it, i.e. why do you need it?
If you are interested in the profile along the line, you can get it with 'Plot profile' or the getProfile() macro call anyhow.

Michael
________________________________________________________________
On Jun 28, 2013, at 10:09, Eric Denarier wrote:

> Thanks Jerome,
> That was the problem.
> But I have an other one : If I draw a segmented line and Edit/Selection/Straigthen, it makes a curve that doesn't overlay the original line. Can it be fix ?
>
> Eric Denarier
> Grenoble Institut des Neurosciences
> Inserm U836
> Chemin Fortuné Ferrini
> 38700 La Tronche
> France

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ERIC]

Thank you Jerome and Michael,

Now I know how it works and I will deal with it..
Thank you both for your explanations.

Eric

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 28/06/2013 13:55, Michael Schmid a écrit :

> Hi Eric,
>
> Edit>Selection>Straighten works only with lines that are smooth; it does not work if there are sharp corners. Thus, if you don't have 'Spline Fit' clicked to get a smooth line, it does that for you.
>
> Imagine a segmented line with a sharp corner, and you cut out a band with a given width along the segmented line from a rubber sheet. Then you want to straighten it: at the inner (concave) side, when you try to straighten it, it will break. In other words, the pixel values of the straightened selection are undefined.
>
> In any case, I am not sure what it should be good for to straighten a segmented selection that is not splined.
> What's the idea behind it, i.e. why do you need it?
> If you are interested in the profile along the line, you can get it with 'Plot profile' or the getProfile() macro call anyhow.
>
> Michael
> ________________________________________________________________
> On Jun 28, 2013, at 10:09, Eric Denarier wrote:
>
>> Thanks Jerome,
>> That was the problem.
>> But I have an other one : If I draw a segmented line and Edit/Selection/Straigthen, it makes a curve that doesn't overlay the original line. Can it be fix ?
>>
>> Eric Denarier
>> Grenoble Institut des Neurosciences
>> Inserm U836
>> Chemin Fortuné Ferrini
>> 38700 La Tronche
>> France
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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