measure length of many parallel lines?

[sombreroduck]

Hi,
We have images with many more-or-less parallel lines. We can measure the spacing with FFT, but is there a way to measure all their lengths? (and/or the distribution of) Either if there is a function that could do this, or if I could write a plugin/macro?

We're looking for a software solution to extract the numbers since measuring them by hand, one at a time, could be subjective (because we know what the theory says), plus there will be many hundreds of them...

I've appended an example image, just to give you an idea of what I'm talking about. Others might have several, smaller areas with similar lines (but if need be we could crop them...)

Cheers!
R

[David Webster]

Try using a linear Hough Transform to detect the lines. There is one in
ImageJ's plugin library.


On Sat, Apr 27, 2013 at 1:18 AM, sombreroduck <[hidden email]>wrote:

> Hi,
> We have images with many more-or-less parallel lines. We can measure the
> spacing with FFT, but is there a way to measure all their lengths? (and/or
> the distribution of) Either if there is a function that could do this, or
> if
> I could write a plugin/macro?
>
> We're looking for a software solution to extract the numbers since
> measuring
> them by hand, one at a time, could be subjective (because we know what the
> theory says), plus there will be many hundreds of them...
>
> I've appended an example image, just to give you an idea of what I'm
> talking
> about. Others might have several, smaller areas with similar lines (but if
> need be we could crop them...)
>
> Cheers!
> R
>
> <http://imagej.1557.x6.nabble.com/file/n5002827/isoPP.png>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/measure-length-of-many-parallel-lines-tp5002827.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[sombreroduck]

Thanks for the tip!

I tried downloading it, unpacked to the plugin/analyze folder, but when compiling it always gives me a "plugin or class not found". I've had a bit of a look around the file, but can't see what it's complaining about. Does it require another plugin/macro? there seems to be one called "GHT_", but I can't see any reference to it in the code.

Cheers again!

R

On 27 April 2013 15:43, David Webster [via ImageJ] <[hidden email]> wrote:

Try using a linear Hough Transform to detect the lines. There is one in
ImageJ's plugin library.


On Sat, Apr 27, 2013 at 1:18 AM, sombreroduck <[hidden email]>wrote:

> Hi,
> We have images with many more-or-less parallel lines. We can measure the
> spacing with FFT, but is there a way to measure all their lengths? (and/or
> the distribution of) Either if there is a function that could do this, or
> if
> I could write a plugin/macro?
>
> We're looking for a software solution to extract the numbers since
> measuring
> them by hand, one at a time, could be subjective (because we know what the
> theory says), plus there will be many hundreds of them...
>
> I've appended an example image, just to give you an idea of what I'm
> talking
> about. Others might have several, smaller areas with similar lines (but if
> need be we could crop them...)
>
> Cheers!
> R
>
> <http://imagej.1557.x6.nabble.com/file/n5002827/isoPP.png>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/measure-length-of-many-parallel-lines-tp5002827.html

... [show rest of quote]

> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Michael Schmid]

Hi R,

don't unpack anything, just save GHT_.jar into your plugins folder (that's also what is recommended ion the web page of the plugin)

For how to use it, see the PDF file.
Note that it's not self-explanatory and you have to follow the instructions. If you don't, you will get error messages that are not necessarily saying what is wrong.

Michael
________________________________________________________________
On Apr 27, 2013, at 19:38, sombreroduck wrote:

> Thanks for the tip!
> I tried downloading it, unpacked to the plugin/analyze folder, but when
> compiling it always gives me a "plugin or class not found". I've had a bit
> of a look around the file, but can't see what it's complaining about. Does
> it require another plugin/macro? there seems to be one called "GHT_", but I
> can't see any reference to it in the code.
> Cheers again!
> R
>
>
> On 27 April 2013 15:43, David Webster [via ImageJ] <
> [hidden email]> wrote:
>
>> Try using a linear Hough Transform to detect the lines. There is one in
>> ImageJ's plugin library.
>>
>>
>> On Sat, Apr 27, 2013 at 1:18 AM, sombreroduck <[hidden email]<http://user/SendEmail.jtp?type=node&node=5002829&i=0>>wrote:
>>
>>
>>> Hi,
>>> We have images with many more-or-less parallel lines. We can measure the
>>> spacing with FFT, but is there a way to measure all their lengths?
>> (and/or
>>> the distribution of) Either if there is a function that could do this,
>> or
>>> if
>>> I could write a plugin/macro?
>>>
>>> We're looking for a software solution to extract the numbers since
>>> measuring
>>> them by hand, one at a time, could be subjective (because we know what
>> the
>>> theory says), plus there will be many hundreds of them...
>>>
>>> I've appended an example image, just to give you an idea of what I'm
>>> talking
>>> about. Others might have several, smaller areas with similar lines (but
>> if
>>> need be we could crop them...)
>>>
>>> Cheers!
>>> R
>>>
>>> <http://imagej.1557.x6.nabble.com/file/n5002827/isoPP.png>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>>
>> http://imagej.1557.x6.nabble.com/measure-length-of-many-parallel-lines-tp5002827.html
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
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>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
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>
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[sombreroduck]

Maybe it's my email, bit I don't see the URL. Do you mean this one from Burger &
Burge?
http://www.imagingbook.com/index.php?id=98

That one give me this error

David Webster wrote

Try this website and download chapter 9. I think that this is what I have.

A problem with this approach, and possibly all approaches is the subjective difference between one line with gaps and 2 or more parallel lines with longitudinal offsets

I've had another look, and still can't see what it doesn't like...

[Herbie-2]

For IJ-PlugIns the first place to look in my opinion is

        <http://rsb.info.nih.gov/ij/plugins/index.html>

There you will find a link to

        <http://rsb.info.nih.gov/ij/plugins/ght/index.html>

where you can download the PlugIn and read:

"Installation: Drag and drop GHT_.jar onto the "ImageJ" window."

HTH

Herbie

__________________________________________
On 29.04.13 11:09, sombreroduck wrote:

> Maybe it's my email, bit I don't see the URL. Do you mean this one from
> Burger&
> Burge?
> http://www.imagingbook.com/index.php?id=98
>
> That one give me this error
> <http://imagej.1557.x6.nabble.com/file/n5002846/linearHT_CompileError.png>
>
>
> David Webster wrote
>> Try this website and download chapter 9. I think that this is what I have.
>>
>> A problem with this approach, and possibly all approaches is the
>> subjective difference between one line with gaps and 2 or more parallel
>> lines with longitudinal offsets
>
>
> I've had another look, and still can't see what it doesn't like...
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/measure-length-of-many-parallel-lines-tp5002827p5002846.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[sombreroduck]

Thanks Michael and Herbie,
The GHT wasn't the one I'd been working with, it was the one from Burger&Burge I mentioned in the post above. I foudn your replies this a.m. and have been trying the GHT for a bit now, and one the +side it runs, but on the - it gives a rather curious output for my test images. I've been using these three (not to scale)

called "reference_object.jpg", "Image1.jpg" and Image2.jpg" resp.

The plugin it either finds 0 objects, or anything between 17 and 194. It is probably my choice of parameters, you're right that it isn't intuitive, even with the PDF, but why does it search for the reference object in the image named "reference_object"?! and how can it find it 134 times?!

Two parameters I don't understand at all are the Size and Angle delta. Is this merely the difference between the max and min? (in which case why can't it figure that out for itsself?)

If I can figure this out, would the GHT be able to detect simple, straight lines too?
Cheers!
R

Michael Schmid-3 wrote

Hi R,

don't unpack anything, just save GHT_.jar into your plugins folder (that's also what is recommended ion the web page of the plugin)

For how to use it, see the PDF file.
Note that it's not self-explanatory and you have to follow the instructions. If you don't, you will get error messages that are not necessarily saying what is wrong.

Herbie-2 wrote

For IJ-PlugIns the first place to look in my opinion is

        <http://rsb.info.nih.gov/ij/plugins/index.html>

There you will find a link to

        <http://rsb.info.nih.gov/ij/plugins/ght/index.html>

where you can download the PlugIn and read:

"Installation: Drag and drop GHT_.jar onto the "ImageJ" window."

HTH

[Herbie-2]

It's always a good idea to start with what was stated first in a thread.
Hence, I just had look at the original image in which--I must admit--I
can't see any parallel lines but more or less aligned parallel
structures (sequences of dots). For me it makes no sense to apply the
Hough transform to such images (for an analysis of the elongation of
these structures) without heavy preprocessing.

In any case, the term "lines" is definitely wrong in the context of the
sample image and to realize this fact may lead to more promising
approaches to solve your task.

HTH

Herbie

_____________________________________
On 27.04.13 10:18, sombreroduck wrote:

> Hi,
> We have images with many more-or-less parallel lines. We can measure the
> spacing with FFT, but is there a way to measure all their lengths? (and/or
> the distribution of) Either if there is a function that could do this, or if
> I could write a plugin/macro?
>
> We're looking for a software solution to extract the numbers since measuring
> them by hand, one at a time, could be subjective (because we know what the
> theory says), plus there will be many hundreds of them...
>
> I've appended an example image, just to give you an idea of what I'm talking
> about. Others might have several, smaller areas with similar lines (but if
> need be we could crop them...)
>
> Cheers!
> R
>
> <http://imagej.1557.x6.nabble.com/file/n5002827/isoPP.png>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/measure-length-of-many-parallel-lines-tp5002827.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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