[Insight-users] Composing an image using two input images
Luis Ibanez
luis.ibanez at kitware.com
Tue Mar 10 16:58:31 EDT 2009
Hi David,
You may find a way what you describe by combining the
following two filters:
PadImageFilter
http://www.itk.org/Insight/Doxygen/html/classitk_1_1PadImageFilter.html
PasteImageFilter
http://www.itk.org/Insight/Doxygen/html/classitk_1_1PasteImageFilter.html
If you have your two images A and B, then
You can pad A by an amount large enough to be able
to paste B on top of it.
Regards,
Luis
-------------------
David Pastor wrote:
> Hi,
>
> 2. Use itk::ImageRegionIterators to copy from the original image into
> the larger image at a particular offset.
>
> This is what is was trying now and it'll give me the solution, but I was
> hoping there was a shorter way. I meant just the opposite operation to a
> "crop image filter". The result would be a larger image with the same
> content in the same scaling than the original one. Problem was that
> tiling images with different sizes dont align the images in their
> original position.
>
> For example tiling a 5x5x5 with a 3x3x3 image will return a 5x5x5x2
> image, but the second frame will be located in a corner of the volume
> and not in its original position. That's why I need to create a larger
> image embedding the original.
>
> It's true that you need another image, it was just bad speaking.
>
> thanks!
>
> david
>
>
>
> ----- Original Message ----- From: <insight-users-request at itk.org>
> To: <insight-users at itk.org>
> Sent: Tuesday, March 10, 2009 1:48 PM
> Subject: Insight-users Digest, Vol 59, Issue 33
>
>
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>> Today's Topics:
>>
>> 1. Segmentation filters (Eduardo - LNCC)
>> 2. Enlarge the image (David Pastor)
>> 3. Re: Enlarge the image (kent williams)
>> 4. Re: Enlarge the image (Andreas Schuh)
>> 5. Re: Segmentation filters (Luis Ibanez)
>> 6. Re: Curves2DExtractor not working (Luis Ibanez)
>> 7. Re: Curves2DExtractor not working (Rick Giuly)
>> 8. Re: Validation of deformable registration (Marta)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 9 Mar 2009 14:53:22 -0300
>> From: Eduardo - LNCC <camargo at lncc.br>
>> Subject: [Insight-users] Segmentation filters
>> To: insight-users at itk.org
>> Message-ID:
>> <846025900903091053k2943ddd4w6d836b5e7550d470 at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi,
>>
>>
>> Can I replace the itkFastMarchingImageFilter class by class
>> itkDanielssonDistanceMapImageFilter without have problems in the
>> segmentation filters below?
>>
>>
>> - itkShapeDetectionLevelSetImageFilter
>> - itkGeodesicActiveContourLeveSetImageFilter
>> - itkThresholdSegmentationLevelSetImageFilter
>> - itkCannySegmentationLevelSetImageFilter
>> - itkLaplacianSegmentationLevelSetImageFilter
>>
>>
>>
>> Sorry for my english
>>
>> --
>> Atenciosamente,
>>
>> Eduardo Camargo
>> Analista de Sistemas
>> HeMoLab - http://hemolab.lncc.br/equipe/desenv/eduardo.htm
>> Laborat?rio Nacional de Computa??o Cient?fica - LNCC
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 9 Mar 2009 19:13:11 +0100
>> From: "David Pastor" <david.pastor at die.upm.es>
>> Subject: [Insight-users] Enlarge the image
>> To: <insight-users at itk.org>
>> Message-ID: <006001c9a0e2$b4a22cb0$a337048a at POSEIDON>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hello,
>>
>> I need to enlarge an image, change its size type to a bigger one
>> without modifying the content of the original one, so there is no
>> rescaling. Any direct filter for this?
>>
>> cheers
>> david
>> -------------- next part --------------
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>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Mon, 9 Mar 2009 14:55:07 -0500
>> From: kent williams <nkwmailinglists at gmail.com>
>> Subject: Re: [Insight-users] Enlarge the image
>> To: itk users <Insight-users at itk.org>
>> Message-ID:
>> <44f773f50903091255q41e0edecid3b5ed6c96572bae at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> What you said, as it stands, makes no sense. First of all, the
>> default behavior is to not to modify the input image at all. A new
>> image is generated. There are some special cases of 'in place' filters
>> that are supposed to change the input, because the input and output
>> are the same image.
>>
>> Second of all, if you resize an image, you're going to be resampling.
>>
>> What I think you mean is you either want to go from 2D to 3D (for
>> example), or embed an image unmodified inside a larger image.
>>
>> In the former case, you can use itk::CastImageFilter. In the latter
>> case, it's more complicated.
>>
>> 1. Create and Allocate the larger output image.
>> 2. Use itk::ImageRegionIterators to copy from the original image into
>> the larger image at a particular offset.
>>
>> If you can clarify what you're trying to do we can provide a better
>> answer.
>>
>> On Mon, Mar 9, 2009 at 1:13 PM, David Pastor <david.pastor at die.upm.es>
>> wrote:
>>
>>> Hello,
>>>
>>> I need to enlarge an image, change its size type to a bigger one without
>>> modifying the content of the original one, so there is no rescaling. Any
>>> direct filter for this?
>>>
>>> cheers
>>> david
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
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>>> 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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>>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 09 Mar 2009 22:39:28 +0100
>> From: Andreas Schuh <andreas.schuh.84 at googlemail.com>
>> Subject: Re: [Insight-users] Enlarge the image
>> To: kent williams <nkwmailinglists at gmail.com>
>> Cc: itk users <Insight-users at itk.org>
>> Message-ID: <49B58C90.2070902 at googlemail.com>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi,
>>
>> my first thought was that you, David, might want to change just the
>> spacing of the image such that it is physically bigger than before.
>> Let's consider this as zooming. If this is what you want, you wouldn't
>> need any filter as you can just reset the spacing of the image manually.
>> On the other side, if you meant to keep the continuous image in physical
>> space constant but change the size of the grid this continuous image is
>> sampled on, you may have a look at the ResampleImageFilter. As the name
>> implies, this filter resamples an image sampled on one grid on another
>> one. Thus, if "I need to enlarge an image, change its size (type) to a
>> bigger one" meant to increase the number of pixels of the discrete
>> image, this may be what you're looking for.
>>
>> --
>> regards
>> Andreas
>>
>> kent williams schrieb:
>>
>>> What you said, as it stands, makes no sense. First of all, the
>>> default behavior is to not to modify the input image at all. A new
>>> image is generated. There are some special cases of 'in place' filters
>>> that are supposed to change the input, because the input and output
>>> are the same image.
>>>
>>> Second of all, if you resize an image, you're going to be resampling.
>>>
>>> What I think you mean is you either want to go from 2D to 3D (for
>>> example), or embed an image unmodified inside a larger image.
>>>
>>> In the former case, you can use itk::CastImageFilter. In the latter
>>> case, it's more complicated.
>>>
>>> 1. Create and Allocate the larger output image.
>>> 2. Use itk::ImageRegionIterators to copy from the original image into
>>> the larger image at a particular offset.
>>>
>>> If you can clarify what you're trying to do we can provide a better
>>> answer.
>>>
>>> On Mon, Mar 9, 2009 at 1:13 PM, David Pastor
>>> <david.pastor at die.upm.es> wrote:
>>>
>>>> Hello,
>>>>
>>>> I need to enlarge an image, change its size type to a bigger one
>>>> without
>>>> modifying the content of the original one, so there is no rescaling.
>>>> Any
>>>> direct filter for this?
>>>>
>>>> cheers
>>>> david
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.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
>>>
>>> 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
>>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Mon, 09 Mar 2009 19:26:04 -0400
>> From: Luis Ibanez <luis.ibanez at kitware.com>
>> Subject: Re: [Insight-users] Segmentation filters
>> To: camargo at lncc.br
>> Cc: insight-users at itk.org
>> Message-ID: <49B5A58C.6050201 at kitware.com>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>> Hi Eduardo,
>>
>> Yes,
>>
>> You could replace the FastMarching filter with a
>> DanielssonDistanceMap filter.
>>
>> Just create a binary image that is set to zeros everywhere,
>> and only set to ones the pixels corresponding to the seed
>> points that are now being passed to the FastMarching filter.
>> Then use that image as input to the Danielsson distance map
>> filter.
>>
>>
>> Notice however that:
>>
>>
>> A) In some of the examples, the seed points are set
>> to initial negative values, in order to be able to
>> define the initial level set as the iso-value == 0.
>>
>>
>> B) The FastMarching filter is a lot faster than the
>> Danielson Filter for the purpose of computing that
>> distance map
>>
>>
>> C) If you really want to stick to a distance filter,
>> then you may want to try the SignedMaurer distance
>> filter that is equivalent to the Danielson filter,
>> but it executes a lot faster.
>>
>>
>>
>> Regards,
>>
>>
>> Luis
>>
>>
>>
>> --------------------
>> Eduardo - LNCC wrote:
>>
>>> Hi,
>>>
>>>
>>> Can I replace the itkFastMarchingImageFilter class by class
>>> itkDanielssonDistanceMapImageFilter without have problems in the
>>> segmentation filters below?
>>>
>>> * itkShapeDetectionLevelSetImageFilter
>>> * itkGeodesicActiveContourLeveSetImageFilter
>>> * itkThresholdSegmentationLevelSetImageFilter
>>> * itkCannySegmentationLevelSetImageFilter
>>> * itkLaplacianSegmentationLevelSetImageFilter
>>>
>>>
>>>
>>> Sorry for my english
>>>
>>> --
>>> Atenciosamente,
>>>
>>> Eduardo Camargo
>>> Analista de Sistemas
>>> HeMoLab - http://hemolab.lncc.br/equipe/desenv/eduardo.htm
>>> Laborat?rio Nacional de Computa??o Cient?fica - LNCC
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.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
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Mon, 09 Mar 2009 19:28:02 -0400
>> From: Luis Ibanez <luis.ibanez at kitware.com>
>> Subject: Re: [Insight-users] Curves2DExtractor not working
>> To: Rick Giuly <rgiuly at gmail.com>
>> Cc: insight users <insight-users at itk.org>
>> Message-ID: <49B5A602.7000507 at kitware.com>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>> Hi Rick,
>>
>> Could you post to a public web site the image that you are using
>> as input to the Curve2DExtractor ?
>>
>>
>> (Please do not send executables to the mailing list).
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> ------------------
>> Rick Giuly wrote:
>>
>>> Hello All,
>>>
>>> Using Insight Applications 3.12.0 on windows, Curves2DExtractor does
>>> nothing when I run it. (No error messages show up in the CMD box and no
>>> gui appears.) I used fltk-1.1.7 and built it with CMake and Eclipse
>>>
>>> The build output is attached. It seemed to build with no errors.
>>>
>>> Any help is appreciated
>>>
>>> -Rick
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.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
>>
>>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Tue, 10 Mar 2009 05:06:01 -0700
>> From: Rick Giuly <rgiuly at gmail.com>
>> Subject: Re: [Insight-users] Curves2DExtractor not working
>> To: Luis Ibanez <luis.ibanez at kitware.com>
>> Cc: insight users <insight-users at itk.org>
>> Message-ID: <49B657A9.9020603 at gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>> Hi Luis,
>>
>> As I understand it, running Curve2DExtractor should bring up a GUI where
>> an image can be chosen. But, the GUI is not coming up, so I'm not able
>> to pick an image file for input.
>>
>> -Rick
>>
>> Luis Ibanez wrote:
>>
>>>
>>> Hi Rick,
>>>
>>> Could you post to a public web site the image that you are using
>>> as input to the Curve2DExtractor ?
>>>
>>>
>>> (Please do not send executables to the mailing list).
>>>
>>>
>>> Thanks
>>>
>>>
>>> Luis
>>>
>>>
>>> ------------------
>>> Rick Giuly wrote:
>>>
>>>> Hello All,
>>>>
>>>> Using Insight Applications 3.12.0 on windows, Curves2DExtractor does
>>>> nothing when I run it. (No error messages show up in the CMD box and
>>>> no gui appears.) I used fltk-1.1.7 and built it with CMake and Eclipse
>>>>
>>>> The build output is attached. It seemed to build with no errors.
>>>>
>>>> Any help is appreciated
>>>>
>>>> -Rick
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.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
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Tue, 10 Mar 2009 13:48:46 +0100
>> From: Marta <t_s_80 at gmx.de>
>> Subject: Re: [Insight-users] Validation of deformable registration
>> To: Marta <t_s_80 at gmx.de>
>> Cc: insight-users at itk.org
>> Message-ID: <3673490C-8CA3-48E9-97E2-788ED017E944 at gmx.de>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>> Hello once again,
>>
>> I still have the questions below, but I also have a new one that
>> bothers me to the topic.
>>
>> What is a good way to find data for my synthetic deformation field? I
>> mean, it isn't enough to deform the image "anyhow", it's important to
>> have a realistic deformation, right? How can I imitate that? Are there
>> any tools to create an synthetic deformation field?
>>
>> Thanks for any comments to my questions! It's important for my master
>> thesis.
>>
>> Best regards,
>> Marta
>>
>>
>> Am 05.03.2009 um 17:38 schrieb Marta:
>>
>>> Hi,
>>>
>>> I try to validate my deformable registration method and I do already
>>> know that there is no standard for it.
>>> Anyway, I found in older posts a way to do it by generating an
>>> artificially deformation field and compare it with the result
>>> deformation field.
>>> Luis told (e.g.) so in
>>> http://www.itk.org/pipermail/insight-users/2006-July/018634.html
>>> :
>>>
>>> "The common approach is to artificially generate a
>>> deformation field by using ThinPlateSplines, use this artificial
>>> deformation field in order to create a deformed version of your image.
>>> Then use your registration method between the original and the
>>> deformed image, and finally compare the artificial deformation field
>>> against the one that
>>> you produced with the registration method."
>>>
>>> However, I'm not sure what is the best way to compare the
>>> deformation fields. Can I also use a squared image difference?
>>> Or are there any better ways?
>>>
>>> Would be happy for any suggestions!
>>>
>>> Best regards,
>>> Marta
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.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
>>
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> Insight-users mailing list
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>>
>>
>> End of Insight-users Digest, Vol 59, Issue 33
>> *********************************************
>>
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>
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