[Insight-users] Label Image question again...

Anja Ende anja.ende at googlemail.com
Wed May 21 06:07:37 EDT 2008 

I finally have the filling problem solved!

The PolygonSpatialObject was the one I had to use.

Thank you everyone for your help!

Cheers,
Anja

2008/5/21 Richard Beare <richard.beare at gmail.com>:
> Hi,
>
> I've not much experience with the spatial object classes, so I'll
> outline another approach.
>
> Create a destination image of the size you want, which presumably
> matches the size of the image the user marked points on.
>
> Draw the outline of the shape(s) into the image, and then fill
> it(them). If there is only one shape feed this direct to the label map
> converter class.
>
> The shape outline could be drawn using the LineIterator - you might
> want to develop a helper class to make life easier.
>
> Unfortunately I haven't managed to find a hole filling class in ITK,
> but there are a number of approaches you might use.
>
> 1) Connected component filter - invert your outline image and label
> the result. If none of your vertices are on the image border then
> label 1 will correspond to background and all others will be holes. OR
> the result with your original image to fill it.
>
> 2) Find a point that is inside your shape and figure out how to use
> the flood fill iterator to fill in the hole - maybe someone else can
> advise on that part.
>
>
>
> On Wed, May 21, 2008 at 1:20 AM, Anja Ende <anja.ende at googlemail.com> wrote:
>> Hello again......
>>
>> I tried using the BlobSpatialObject filter but it does not seem to be
>> able to converting the whole region enclosed by the ROI but only the
>> boundaries...
>>
>> So, my code is as follows:
>>
>> // Create the Blob object
>> typedef itk::BlobSpatialObject<3>  BlobType;
>> typedef BlobType::Pointer BlobPointer;
>> typedef itk::SpatialObjectPoint<3> BlobPointType;
>>
>> BlobType::PointListType list;
>> for(int i=0; i<myPoints.size(); i++)
>> {
>>   BlobPointType p;
>>   p.SetPosition(myPoints[i].x, myPoints[i].y, myPoints[i].z);
>>
>>   // This confused me as well... I just want grayscale values, so
>>   // I set all to 1.
>>   p.SetRed(1);
>>   p.SetGreen(1);
>>   p.SetBlue(1);
>>
>>   list.push_back(p);
>> }
>>
>> BlobPointer blob = BlobType::New();
>> blob->GetProperty()->SetName("Anja blob");
>> blob->SetId(1);
>> blob->SetPoints(list);
>>
>> However, now this would only set the intensities of the border pixels,
>> right? The vertices that my point describe. What I was hoping for is
>> somewhere where I can specify this boundary and the region contained
>> by this boundary would be filled with 1 and the background could be 0.
>>
>> Is there any class in ITK that can do that? So, I am specifying the
>> boundary of the 2D or 3D ROI and the ITK class hopefully could
>> generate me a binary image which would have the pixels in the ROI
>> filled with a particular intensity value (1 for example) and the
>> background as 0 (for example).
>>
>> I hate to send so many mails to the newsgroup and I apologize for
>> that. However, this seemingly simple task has taken me weeks now and I
>> am really frustrated and have got nowhere.
>>
>> Apologies again!
>>
>> Cheers,
>> Anja
>>
>>
>>
>>
>> 2008/5/20 Anja Ende <anja.ende at googlemail.com>:
>>> Hi Richard,
>>>
>>> Yes, the region conversion is where I am stuck!
>>>
>>> The points indeed do represent the vertices of the 2D polygon and
>>> drawing a line through these points would give the shape.
>>>
>>> Cheers,
>>> Anja
>>>
>>> 2008/5/20 Richard Beare <richard.beare at gmail.com>:
>>>> Hi,
>>>>
>>>> I attempted to answer this before, but obviously wasn't clear enough.
>>>>
>>>> The critical step seems to be the point to region conversion, which
>>>> depends on the meaning of the user defined points. So are these points
>>>> corners of a polygon? i.e. if you drew lines in an image (assuming 2D)
>>>> from the point 1 to 2, 2 to 3 ... and finally n to 1 to give you a
>>>> closed shape, would those lines represent the outline of the shape you
>>>> are interested in?
>>>>
>>>> On Tue, May 20, 2008 at 8:55 PM, Xabier Artaechevarria Artieda
>>>> <xabiarta at unav.es> wrote:
>>>>> You can use:
>>>>>
>>>>> http://www.itk.org/Doxygen34/html/classitk_1_1SpatialObjectToImageFilter.html
>>>>>
>>>>> However, that will give you separate points, not a contiguous irregular
>>>>> binary shape.
>>>>> I do not know of any filter that can do that, it might be that you have to
>>>>> implement this.
>>>>>
>>>>> Maybe somebody can help here?
>>>>>
>>>>> --
>>>>> Xabier Artaechevarria
>>>>> Cancer Imaging Laboratory
>>>>> Centre for Applied Medical Research
>>>>> www.cima.es
>>>>>
>>>>>
>>>>>
>>>>> Anja Ende <anja.ende at googlemail.com> ha escrito:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Actually spoke too soon! Do not see how I can convert this
>>>>>> BlobSpatialObject to a binary itk::Image.
>>>>>>
>>>>>> It seems to be very difficult to be able to create a binary image by
>>>>>> hand unless you use one of the itk filters...
>>>>>>
>>>>>> Cheers,
>>>>>> Anja
>>>>>>
>>>>>> 2008/5/20 Anja Ende <anja.ende at googlemail.com>:
>>>>>>>
>>>>>>> Hi Xabi,
>>>>>>>
>>>>>>> Thanks for your reply!
>>>>>>>
>>>>>>> 4. So, now the problem is how to compute a binary region from those
>>>>>>> points. What do you want exactly? Is it the bounding box? You can get
>>>>>>> this with SpatialObjects (BlobSpatialObject).
>>>>>>>
>>>>>>> I actually need the shape that the points represent. It is not really
>>>>>>> a rectangle but an irregular shape. I think the BlobSpatialObject
>>>>>>> might be the thing that I need as it seems to be able to represent any
>>>>>>> amorphous shape. I will give this a shot now!
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Anja
>>>>>>>
>>>>>>> 2008/5/20 Xabier Artaechevarria Artieda <xabiarta at unav.es>:
>>>>>>>>
>>>>>>>> Hi Anja,
>>>>>>>>
>>>>>>>> Let's see if I can help a bit with some points.
>>>>>>>>
>>>>>>>> 1. The article you mentioned is an Insight Journal contribution.  As
>>>>>>>> such, it
>>>>>>>> includes the code needed to reproduce the results. You need this  code,
>>>>>>>> which
>>>>>>>> you can find in
>>>>>>>>
>>>>>>>> http://insight-journal.org/InsightJournalManager/view_reviews.php?pubid=176.
>>>>>>>> This includes the LabelImage class, the classes to convert different
>>>>>>>> images
>>>>>>>> to a LabelMap, and so on.
>>>>>>>>
>>>>>>>> 2. At least that I know, there is no straighforward way to create a
>>>>>>>> LabelImage based on a user defined contour. What you need, though, is a
>>>>>>>> LabelMap.
>>>>>>>>
>>>>>>>> 3. You must do it in two steps. First convert your points to binary
>>>>>>>> image,
>>>>>>>> and then this image to a label map. You can convert a Binary image to a
>>>>>>>> label map easily with the itkBinaryImageToBinaryMapFilter.
>>>>>>>>
>>>>>>>> 4. So, now the problem is how to compute a binary region from those
>>>>>>>> points.
>>>>>>>> What do you want exactly? Is it the bounding box? You can get this with
>>>>>>>> SpatialObjects (BlobSpatialObject).
>>>>>>>>
>>>>>>>> Hope that helps,
>>>>>>>> Xabi
>>>>>>>>
>>>>>>>> --
>>>>>>>> Xabier Artaechevarria
>>>>>>>> Cancer Imaging Laboratory
>>>>>>>> Centre for Applied Medical Research
>>>>>>>> www.cima.es
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Anja Ende <anja.ende at googlemail.com> ha escrito:
>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I am really frustrated at my inability to achieve this and hope
>>>>>>>>> someone can help me with a few lines of code on how to achieve this:
>>>>>>>>>
>>>>>>>>> - I have an itk::Image object and a set of points in the image
>>>>>>>>> coordinates that represent a ROI.
>>>>>>>>> - I cannot for saving my life figure out how to generate a LabelObject
>>>>>>>>> based on this.... I have had some help when I asked this question
>>>>>>>>> before but there seems to be a disconnect somewhere and I am missing a
>>>>>>>>> step.
>>>>>>>>>
>>>>>>>>> I guess I have to figure out a way to render the region defined by
>>>>>>>>> these points into another image and somehow use this image as a mask
>>>>>>>>> on the original image. However, I just do not know how to achieve this
>>>>>>>>> with the ITK classes. The document entitled "Label Object
>>>>>>>>> representation and manipulation with ITK" somehow (I think) assumes
>>>>>>>>> that the LabelImage is easily created, but I am finding it very
>>>>>>>>> difficult to actually create this LabelImage!
>>>>>>>>>
>>>>>>>>> Is there any documentation on how one can create a LabelImage based on
>>>>>>>>> a user defined contour???
>>>>>>>>>
>>>>>>>>> Please help!
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Cheers,
>>>>>>>>>
>>>>>>>>> Anja
>>>>>>>>> _______________________________________________
>>>>>>>>> Insight-users mailing list
>>>>>>>>> Insight-users at itk.org
>>>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ----------------------------------------------------------------
>>>>>>>> Este mensaje ha sido enviado desde https://webmail.unav.es
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Insight-users mailing list
>>>>>>>> Insight-users at itk.org
>>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Anja
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Cheers,
>>>>>>
>>>>>> Anja
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------
>>>>> Este mensaje ha sido enviado desde https://webmail.unav.es
>>>>>
>>>>> _______________________________________________
>>>>> Insight-users mailing list
>>>>> Insight-users at itk.org
>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Cheers,
>>>
>>> Anja
>>>
>>
>>
>>
>> --
>> Cheers,
>>
>> Anja
>>
>



-- 
Cheers,

Anja

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