[Insight-users] How to turn Off sorting by size in RelabelComponentFilter

Richard Beare richard.beare at gmail.com
Tue Aug 10 00:53:48 EDT 2010 

The original one produced a random ordering, which could then be
relabeled according to size. The one that has been there for a number
of years labels according to raster order. However raster order means
that a objects struck first in a raster order scan will have lower
labels, and this often isn't obvious to the eye. For example an object
may have a higher label than one that is further right because the
right object has a voxel with a lower y value and is therefore struck
first in a raster order scan.

On Tue, Aug 10, 2010 at 2:20 PM, Arpit Agrawal <arpit392 at gmail.com> wrote:
> hello guyz,
> i have a doubt...as far as i know even ConnectedComponentFilter does not
> produce labels in raster order...it also labels the components according to
> the size and the relabel image filter assigns only just a predefined
> specific color according the label...
>
> plz tell me if i m wrong...
>
> On Tue, Aug 10, 2010 at 5:10 AM, Richard Beare <richard.beare at gmail.com>
> wrote:
>>
>> The default labeling behavior provided in the
>> itk::ConnectedComponentImageFilter does this. If you are starting with
>> a binary image and want to label separate components then
>> ConnectedComponentImageFilter will produce labels in raster order. If
>> you already have a labelled image then different strategies might be
>> needed, depending on how it was produced and what the characteristics
>> are (i.e whether labelled regions touch.)
>>
>> On Tue, Aug 10, 2010 at 8:45 AM, Emma Ryan <eryanvtk at yahoo.com> wrote:
>> > Hello All,
>> >
>> >    By default the itk::RelabelComponentImageFilter  seems to be sorting
>> > the
>> > labels by size. I would like the label to be number according to their
>> > raster position. Is there a way to turn off the sorting ?
>> >
>> > Thank you,
>> > Emma
>> >
>> > ________________________________
>> > From: "insight-users-request at itk.org" <insight-users-request at itk.org>
>> > To: insight-users at itk.org
>> > Sent: Mon, August 9, 2010 12:42:15 PM
>> > Subject: Insight-users Digest, Vol 76, Issue 24
>> >
>> > Send Insight-users mailing list submissions to
>> >     insight-users at itk.org
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>> >
>> > Today's Topics:
>> >
>> >   1. Tcon Agenda Posted (Tuesday 1pm EST) (Luis Ibanez)
>> >   2. Re: Tcon Agenda Posted (Tuesday 1pm EST) (Bradley Lowekamp)
>> >   3. Re: [Insight-developers] Tcon Agenda Posted    (Tuesday 1pm EST)
>> >       (Arnaud GELAS)
>> >   4. itk::BilateralImageFilter extremely slow (Oleksandr Dzyubak)
>> >   5. Re: Problem with passing images to functions (habibbaluwala2010)
>> >
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Mon, 9 Aug 2010 14:35:09 -0400
>> > From: Luis Ibanez <luis.ibanez at kitware.com>
>> > Subject: [Insight-users] Tcon Agenda Posted (Tuesday 1pm EST)
>> > To: itk <Insight-users at itk.org>,    Insight Developers
>> >     <Insight-developers at itk.org>
>> > Message-ID:
>> >     <AANLkTi=OgJ1OyJRuRDOqY=t70iSYpWT1JAVZcj_5HC5Y at mail.gmail.com>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > The Agenda for tomorrow's tcon has been posted at:
>> >
>> > http://www.itk.org/Wiki/Agenda%26Status_081010
>> >
>> > As discussed in the last tcon,
>> > we are inverting the order of the agenda,
>> > in order to address some topics for which
>> > we have run out of time in previous calls.
>> >
>> > Please feel free to add any topics of your interest.
>> >
>> >
>> >     Luis
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
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>> >
>> > <http://www.itk.org/pipermail/insight-users/attachments/20100809/286a83b3/attachment-0001.htm>
>> >
>> > ------------------------------
>> >
>> > Message: 2
>> > Date: Mon, 9 Aug 2010 15:06:45 -0400
>> > From: Bradley Lowekamp <blowekamp at mail.nih.gov>
>> > Subject: Re: [Insight-users] Tcon Agenda Posted (Tuesday 1pm EST)
>> > To: Luis Ibanez <luis.ibanez at kitware.com>
>> > Cc: itk <Insight-users at itk.org>,    Insight Developers
>> >     <Insight-developers at itk.org>
>> > Message-ID: <3640D14E-D614-41AA-BE09-5223002184CB at mail.nih.gov>
>> > Content-Type: text/plain; charset="us-ascii"
>> >
>> > Hello Luis,
>> >
>> > Looking over the agenda for tomorrow, I can't help but think  that the
>> > Microscopy should be a break out t-con (unless I missed it, and this is
>> > a
>> > summary). I have had experience with streaming and many related issues
>> > to
>> > the large datasets complications, so I would like to participate in such
>> > a
>> > break out.
>> >
>> > Perhaps the agenda item should just be to schedule such a meeting?
>> >
>> > Brad
>> >
>> > On Aug 9, 2010, at 2:35 PM, Luis Ibanez wrote:
>> >
>> >>
>> >> The Agenda for tomorrow's tcon has been posted at:
>> >>
>> >> http://www.itk.org/Wiki/Agenda%26Status_081010
>> >>
>> >> As discussed in the last tcon,
>> >> we are inverting the order of the agenda,
>> >> in order to address some topics for which
>> >> we have run out of time in previous calls.
>> >>
>> >> Please feel free to add any topics of your interest.
>> >>
>> >>
>> >>    Luis
>> >>
>> >>
>> >> <ATT00001..txt>
>> >
>> > ========================================================
>> > Bradley Lowekamp
>> > Lockheed Martin Contractor for
>> > Office of High Performance Computing and Communications
>> > National Library of Medicine
>> > blowekamp at mail.nih.gov
>> >
>> >
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
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>> >
>> > <http://www.itk.org/pipermail/insight-users/attachments/20100809/bd7b55cd/attachment-0001.htm>
>> >
>> > ------------------------------
>> >
>> > Message: 3
>> > Date: Mon, 9 Aug 2010 15:16:54 -0400
>> > From: Arnaud GELAS <arnaud_gelas at hms.harvard.edu>
>> > Subject: Re: [Insight-users] [Insight-developers] Tcon Agenda Posted
>> >     (Tuesday 1pm EST)
>> > To: Bradley Lowekamp <blowekamp at mail.nih.gov>
>> > Cc: itk <Insight-users at itk.org>,    Insight Developers
>> >     <Insight-developers at itk.org>,    Luis Ibanez
>> > <luis.ibanez at kitware.com>,
>> >     "Megason,    Sean" <Sean_Megason at hms.harvard.edu>
>> > Message-ID: <4C605426.4080103 at hms.harvard.edu>
>> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>> >
>> >   Hi Brad,
>> >
>> > I think we should do both, first to present problems from the microscopy
>> > community. At least everyone can understand some of the related problems
>> > in terms of design. Then interested people and people that have ideas on
>> > how to address these issues can then meet in another break out t-con.
>> >
>> > It seems to be important to discuss at least in the main t-conf:
>> >
>> >     * how to deal with time?
>> >     * how to deal with channels? (Note that for one channel, the pixel
>> >       type could be a scalar, vector or tensor)...
>> >
>> > Then we could discuss other details in the break out one...
>> >
>> > Arnaud
>> >
>> > On 08/09/2010 03:06 PM, Bradley Lowekamp wrote:
>> >> Hello Luis,
>> >>
>> >> Looking over the agenda for tomorrow, I can't help but think  that the
>> >> Microscopy should be a break out t-con (unless I missed it, and this
>> >> is a summary). I have had experience with streaming and many related
>> >> issues to the large datasets complications, so I would like to
>> >> participate in such a break out.
>> >>
>> >> Perhaps the agenda item should just be to schedule such a meeting?
>> >>
>> >> Brad
>> >>
>> >> On Aug 9, 2010, at 2:35 PM, Luis Ibanez wrote:
>> >>
>> >>>
>> >>> The Agenda for tomorrow's tcon has been posted at:
>> >>>
>> >>> http://www.itk.org/Wiki/Agenda%26Status_081010
>> >>>
>> >>> As discussed in the last tcon,
>> >>> we are inverting the order of the agenda,
>> >>> in order to address some topics for which
>> >>> we have run out of time in previous calls.
>> >>>
>> >>> Please feel free to add any topics of your interest.
>> >>>
>> >>>
>> >>>    Luis
>> >>>
>> >>>
>> >>> <ATT00001..txt>
>> >>
>> >> ========================================================
>> >>
>> >> Bradley Lowekamp
>> >>
>> >> Lockheed Martin Contractor for
>> >>
>> >> Office of High Performance Computing and Communications
>> >>
>> >> National Library of Medicine
>> >>
>> >> blowekamp at mail.nih.gov <mailto:blowekamp at mail.nih.gov>
>> >>
>> >>
>> >>
>> >
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> > URL:
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>> > <http://www.itk.org/pipermail/insight-users/attachments/20100809/424eaff2/attachment-0001.htm>
>> >
>> > ------------------------------
>> >
>> > Message: 4
>> > Date: Mon, 09 Aug 2010 14:35:37 -0500
>> > From: Oleksandr Dzyubak <adzyubak at gmail.com>
>> > Subject: [Insight-users] itk::BilateralImageFilter extremely slow
>> > To: insight-users <Insight-users at itk.org>
>> > Message-ID: <4C605889.6020103 at gmail.com>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> >
>> > Dear ITK users and developers,
>> >
>> > A while ago for my experiments I ran into a need of using
>> > a narrow kernel bilateral filter so I decided to give
>> > the itk:: BilateralImageFilter class a try.
>> > After some pre-tests with small test images, I ran a filter on real
>> > images.
>> > Well, my first impression is somewhat discouraging.
>> > But it might be that I am doing some terrible mistake which I do not
>> > see.
>> >
>> > My setup.
>> > 1) Hardware: 4x4 core server with 64 bit Debian Linux.
>> > 2) ITK-3.18 with p-threads support ON.
>> > 3) Image 561x561x478.
>> >
>> > I followed the recommendations from the ITK user guide
>> > and below are results.
>> >
>> > dzyubak at helium: /H61_Mo_721Views_July_31_2009$ time
>> > ./Bilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds05_rs4.hdr 0.5
>> > 4.0
>> >
>> > With all 16 CPUs 100% busy after 1241m29.741s it was still running.
>> > Thus I should cancel the run not having an output.
>> >
>> > real    1241m29.741s
>> > user    19600m14.380s
>> > sys    6m33.993s
>> >
>> > After I changed the parameters, I got something but it was not what I
>> > wanted.
>> >
>> > dzyubak at helium: /H61_Mo_721Views_July_31_2009$ time
>> > ./Bilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds005_rs4.hdr
>> > 0.05 4.0
>> >
>> > real    63m46.774s
>> > user    764m24.782s
>> > sys    0m18.849s
>> >
>> > Since this filter worked extremely slow even with 16 horses under the
>> > hood,
>> > I started digging the Insight Journal and found the contribution
>> > "A Fast Approximation to the Bilateral Filter for ITK" by J. Woehr.
>> >
>> > I was attracted by the word "Fast" since it quite often means "faster
>> > performance".
>> > Even though I did not like the author's note "it is single threaded",
>> > I decided to eventually try it and, to be fair,
>> > I used exactly the same parameters as for itk:: BilateralImageFilter.
>> >
>> > dzyubak at helium: /H61_Mo_721Views_July_31_2009$  time
>> > ./FastBilateral_LessAgressive h61_with_psf.hdr h61_with_psf_ds05_rs4.hdr
>> > 0.5 4.0
>> > ImageFileName: h61_with_psf.img
>> >
>> > real    4m49.325s
>> > user    4m35.085s
>> > sys    0m5.804s
>> >
>> > In the submission description J. Woehr said that FastBilateral
>> > performs poorer for the narrow kernels thus if someone is
>> > in a need of such cases (it is exactly me!),
>> > then the itk:: BilateralImageFilter should be used instead.
>> >
>> > Well, I would like to but FastBilateral performed 200 times
>> > as much vs itk:: BilateralImageFilter.
>> > And in addition to that, for some kernel sizes it never
>> > went out of the loop.
>> >
>> > What am I missing here?
>> > Did someone experience the same filter behaver?
>> > Is it wrong conditional causing such a "prolongated" loop?
>> > Is there any recipe I could used to shorten
>> > such unacceptable long run time of itk:: BilateralImageFilter?
>> >
>> > I appreciate any suggestions/discussions on this matter.
>> >
>> > Regards,
>> >
>> > Alex
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 5
>> > Date: Mon, 9 Aug 2010 12:42:12 -0700 (PDT)
>> > From: habibbaluwala2010 <habibbaluwala at gmail.com>
>> > Subject: Re: [Insight-users] Problem with passing images to functions
>> > To: insight-users at itk.org
>> > Message-ID: <29391440.post at talk.nabble.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> >
>> > Hello Sergio,
>> >                 Can you give me an example of how to use this in context
>> > with the syntax? I am really thankful for the help.
>> >
>> >
>> > Kind regards,
>> >
>> > Habib Baluwala
>> >
>> >
>> >
>> >
>> > Sergio Vera wrote:
>> >>
>> >> Following advices from Luis Iba?ez in a previous mail of the list, we
>> >> now
>> >> use the following rules:
>> >>
>> >> const ITKImgType *ImgIn  when images are input to a method and
>> >>
>> >> ITKImgType::Pointer &ImgOut  when the image will be created inside the
>> >> function
>> >>
>> >> regards
>> >>
>> >> 2010/8/6 D?enan Zuki? <dzenanz at gmail.com>
>> >>
>> >>> Use ImageType::Pointer. Here is an example:
>> >>>
>> >>> void calc2DJointHistogram(VisualizingImageType::Pointer x,
>> >>> VisualizingImageType::Pointer y, std::string savefilename)
>> >>> {
>> >>> ...
>> >>> }
>> >>>
>> >>> //calling it
>> >>> VisualizingImageType::Pointer lVis, hVis;
>> >>> ...
>> >>> hVis=hReader->GetOutput();
>> >>> calc2DJointHistogram(lVis, hVis, fnNoExt+"_LH.png");
>> >>>
>> >>> D?enan
>> >>>
>> >>> On Fri, Aug 6, 2010 at 15:32, habibbaluwala2010
>> >>> <habibbaluwala at gmail.com>wrote:
>> >>>
>> >>>>
>> >>>> Hi Everyone,
>> >>>>                I am a biot confused on how can i pass an image with
>> >>>> smart
>> >>>> pointers to an outside function . I basically need this to avoid
>> >>>> reproducing
>> >>>> the code again and again and also to avoid composite filters. It
>> >>>> would
>> >>>> be
>> >>>> very helpful if you can provide an example which does the job!!!
>> >>>> Anyways
>> >>>> looking forward to your replies.
>> >>>> --
>> >>>> View this message in context:
>> >>>>
>> >>>>
>> >>>> http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29356451.html
>> >>>> Sent from the ITK - Users mailing list archive at Nabble.com.
>> >>>>
>> >>>> _____________________________________
>> >>>> Powered by www.kitware.com
>> >>>>
>> >>>> Visit other Kitware open-source projects at
>> >>>> http://www.kitware.com/opensource/opensource.html
>> >>>>
>> >>>> Kitware offers ITK Training Courses, for more information visit:
>> >>>> http://www.kitware.com/products/protraining.html
>> >>>>
>> >>>> Please keep messages on-topic and check the ITK FAQ at:
>> >>>> http://www.itk.org/Wiki/ITK_FAQ
>> >>>>
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>> >>>>
>> >>>
>> >>>
>> >>> _____________________________________
>> >>> Powered by www.kitware.com
>> >>>
>> >>> Visit other Kitware open-source projects at
>> >>> http://www.kitware.com/opensource/opensource.html
>> >>>
>> >>> Kitware offers ITK Training Courses, for more information visit:
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>> >>>
>> >>> Please keep messages on-topic and check the ITK FAQ at:
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>> >>>
>> >>
>> >>
>> >> --
>> >> Sergio Vera
>> >>
>> >>  Alma IT Systems
>> >>  C/ Vilana, 4B, 4? 1?
>> >>  08022 Barcelona
>> >>  T. (+34) 932 380 592
>> >>  www.alma3d.com
>> >>
>> >> _____________________________________
>> >> Powered by www.kitware.com
>> >>
>> >> Visit other Kitware open-source projects at
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>> >> Kitware offers ITK Training Courses, for more information visit:
>> >> http://www.kitware.com/products/protraining.html
>> >>
>> >> Please keep messages on-topic and check the ITK FAQ at:
>> >> http://www.itk.org/Wiki/ITK_FAQ
>> >>
>> >> Follow this link to subscribe/unsubscribe:
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>> >>
>> >>
>> >
>> > --
>> > View this message in context:
>> >
>> > http://old.nabble.com/Problem-with-passing-images-to-functions-tp29356451p29391440.html
>> > Sent from the ITK - Users mailing list archive at Nabble.com.
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > Insight-users mailing list
>> > Insight-users at itk.org
>> > http://www.itk.org/mailman/listinfo/insight-users
>> >
>> >
>> > End of Insight-users Digest, Vol 76, Issue 24
>> > *********************************************
>> >
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.html
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://www.itk.org/mailman/listinfo/insight-users
>> >
>> >
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
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>
>
>
> --
> Arpit Agrawal
> Junior Undergraduate,
> Dual Degree Communication and Signal Processing ,
> Dept. of Electrical Engg, IITB.
>

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