profile extraction

[Braekevelt Martin]

Dear all,

I am only starting using imageJ, but I am doing metallograpy for 30 years already.
In the past I was using an open software platform software, with macro scripting and module building, now we are forced to change due to windows 7 to change for other software, so that's how I find imageJ.
My most urgent concern is to transform our roughness measurement module.
All I need is to collect the xy coordinates from a profile determined by a circle segment.
I included an example image in annex.
With the old software this was done by simple tresholding to select the data for segmenting.
I think within imagej there are multiple ways to get this profile plot.
It would be a great help to get some advice from experienced users, what would be the best way to extract that profile and record the xy coordinates into a txt format for further processing with our dedicated roughness software.
I know that imagej is mainly used by people from the biological, medical science, I am interested if there are also other metallography science users.

Braekevelt Martin
Global Metallographic Lab Process Owner(GLaM)
Oude Heerweg 5
8540 DEERLIJK
Tel. [phone]
Mobile :[phone]

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[Peter Haub]

Dear Martin,

here is a VERY simple macro that extracts some information of the edge
profile.
Copy it into a macro window and run :

setOption("BlackBackground", false);
run("Make Binary");
run("Invert");
run("Select All");
run("Plot Profile");

Maybe this is all you need.

But this information can not be used as a direct roughness measurement
since it is distributed along a circular shape. A better strategy would
be to approximate a circle to this 'simple' data and to measure the edge
positions in the original image with sub-pixel accuracy along this circle.

Regards,

Peter

On 14.12.2015 02:22, Braekevelt Martin wrote:

> Dear all,
>
> I am only starting using imageJ, but I am doing metallograpy for 30 years already.
> In the past I was using an open software platform software, with macro scripting and module building, now we are forced to change due to windows 7 to change for other software, so that's how I find imageJ.
> My most urgent concern is to transform our roughness measurement module.
> All I need is to collect the xy coordinates from a profile determined by a circle segment.
> I included an example image in annex.
> With the old software this was done by simple tresholding to select the data for segmenting.
> I think within imagej there are multiple ways to get this profile plot.
> It would be a great help to get some advice from experienced users, what would be the best way to extract that profile and record the xy coordinates into a txt format for further processing with our dedicated roughness software.
> I know that imagej is mainly used by people from the biological, medical science, I am interested if there are also other metallography science users.
>
> Braekevelt Martin
> Global Metallographic Lab Process Owner(GLaM)
> Oude Heerweg 5
> 8540 DEERLIJK
> Tel. [phone]
> Mobile :[phone]
>
> ::DISCLAIMER:: This e-mail is confidential and intended for use by the addressee only. If you are not the intended recipient, please notify us immediately and delete this e-mail, as well as any attachment.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Braekevelt Martin]

Dear Peter,

Thanks for the help.
What the roughness as such concerns is not a problem because I use a dedicated software for that, allowing me measuring according DIN, ASTM norms with cut-off filtering and related roughness parameters.

I will test the little macro and see from there.

Braekevelt Martin
Global Metallographic Lab Process Owner(GLaM)
Oude Heerweg 5
8540 DEERLIJK
Tel. [phone]
Mobile :[phone]


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Peter Haub
Sent: Monday, December 14, 2015 9:59 AM
To: [hidden email]
Subject: Re: profile extraction

Dear Martin,

here is a VERY simple macro that extracts some information of the edge profile.
Copy it into a macro window and run :

setOption("BlackBackground", false);
run("Make Binary");
run("Invert");
run("Select All");
run("Plot Profile");

Maybe this is all you need.

But this information can not be used as a direct roughness measurement since it is distributed along a circular shape. A better strategy would be to approximate a circle to this 'simple' data and to measure the edge positions in the original image with sub-pixel accuracy along this circle.

Regards,

Peter

On 14.12.2015 02:22, Braekevelt Martin wrote:

> Dear all,
>
> I am only starting using imageJ, but I am doing metallograpy for 30 years already.
> In the past I was using an open software platform software, with macro scripting and module building, now we are forced to change due to windows 7 to change for other software, so that's how I find imageJ.
> My most urgent concern is to transform our roughness measurement module.
> All I need is to collect the xy coordinates from a profile determined by a circle segment.
> I included an example image in annex.
> With the old software this was done by simple tresholding to select the data for segmenting.
> I think within imagej there are multiple ways to get this profile plot.
> It would be a great help to get some advice from experienced users, what would be the best way to extract that profile and record the xy coordinates into a txt format for further processing with our dedicated roughness software.
> I know that imagej is mainly used by people from the biological, medical science, I am interested if there are also other metallography science users.
>
> Braekevelt Martin
> Global Metallographic Lab Process Owner(GLaM) Oude Heerweg 5
> 8540 DEERLIJK
> Tel. [phone]
> Mobile :[phone]
>
> ::DISCLAIMER:: This e-mail is confidential and intended for use by the addressee only. If you are not the intended recipient, please notify us immediately and delete this e-mail, as well as any attachment.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Gabriel Landini]

On Monday 14 Dec 2015 09:59:08 Peter Haub wrote:

> here is a VERY simple macro that extracts some information of the edge
> profile.
> Copy it into a macro window and run :
>
> setOption("BlackBackground", false);
> run("Make Binary");
> run("Invert");
> run("Select All");
> run("Plot Profile");
>
> Maybe this is all you need.

The above is, unfortunately, not a robust method. If there are any overhangs
in the profile the will be missed with "plot profile". If you rotate the
image, the profile will be different too.

It is not clear if the chained boundary is required (maybe the analysis can
work with just the image of the boundary). But if you do, what I would do is
binarise the boundary coordinates of the material and identify a start point
and an end point. Then link (using for example 8-pixel connectivity) from the
start to the end point (and all the points in between, so this is essentially
"walking along the boundary"). Each time you step on a next unvisited pixel
you store the coordinates in an array of x and y positions. This procedure
stores them in the walking order.
Search the literature for 'Freeman chain encoding' for details on the
algorithm to do this, because the above is just a simplification.

Cheers

Gabriel

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[Peter Haub]

Hi Martin,

if you wonder about the values displayed in the plot ..
.. they are calculated by :
     y*255/h   ( = mean intensity of image column )
where y is the y-position measured from the bottom line of the image and
h is the height of the image.

Peter

On 14.12.2015 10:06, Braekevelt Martin wrote:

> Dear Peter,
>
> Thanks for the help.
> What the roughness as such concerns is not a problem because I use a dedicated software for that, allowing me measuring according DIN, ASTM norms with cut-off filtering and related roughness parameters.
>
> I will test the little macro and see from there.
>
> Braekevelt Martin
> Global Metallographic Lab Process Owner(GLaM)
> Oude Heerweg 5
> 8540 DEERLIJK
> Tel. [phone]
> Mobile :[phone]
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Peter Haub
> Sent: Monday, December 14, 2015 9:59 AM
> To: [hidden email]
> Subject: Re: profile extraction
>
> Dear Martin,
>
> here is a VERY simple macro that extracts some information of the edge profile.
> Copy it into a macro window and run :
>
> setOption("BlackBackground", false);
> run("Make Binary");
> run("Invert");
> run("Select All");
> run("Plot Profile");
>
> Maybe this is all you need.
>
> But this information can not be used as a direct roughness measurement since it is distributed along a circular shape. A better strategy would be to approximate a circle to this 'simple' data and to measure the edge positions in the original image with sub-pixel accuracy along this circle.
>
> Regards,
>
> Peter
>
> On 14.12.2015 02:22, Braekevelt Martin wrote:
>> Dear all,
>>
>> I am only starting using imageJ, but I am doing metallograpy for 30 years already.
>> In the past I was using an open software platform software, with macro scripting and module building, now we are forced to change due to windows 7 to change for other software, so that's how I find imageJ.
>> My most urgent concern is to transform our roughness measurement module.
>> All I need is to collect the xy coordinates from a profile determined by a circle segment.
>> I included an example image in annex.
>> With the old software this was done by simple tresholding to select the data for segmenting.
>> I think within imagej there are multiple ways to get this profile plot.
>> It would be a great help to get some advice from experienced users, what would be the best way to extract that profile and record the xy coordinates into a txt format for further processing with our dedicated roughness software.
>> I know that imagej is mainly used by people from the biological, medical science, I am interested if there are also other metallography science users.
>>
>> Braekevelt Martin
>> Global Metallographic Lab Process Owner(GLaM) Oude Heerweg 5
>> 8540 DEERLIJK
>> Tel. [phone]
>> Mobile :[phone]
>>
>> ::DISCLAIMER:: This e-mail is confidential and intended for use by the addressee only. If you are not the intended recipient, please notify us immediately and delete this e-mail, as well as any attachment.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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