[Insight-users] Problems with ImageMaskSpatialObject

[Julien Jomier]

Hi Markus,

The index of the RequestedRegion cannot be used to set the initial 
offset of the image because the requested region can change but should 
not affect how the image is represented in the scene.
Moreover, ImageSpatialObject does not support the concept of streaming 
and regions. This should be handled at the Image level.

That's in part why the ImageMaskSpatialObject is used, i.e. to define a 
region of interest.

You can use the ExtractImageFilter beforehand to extract your region of 
interest or you can "paint" the appropriate region of your 
ImageMaskSpatialObject.

What do you mean by "the offset to compute ObjectToWorldTransform is
completely ignored"? When requested if the value at a physical point or 
if a point IsInside() the image, the full ObjectToWorldTransform is used.

Hope that helps,

Julien

Markus Mehrwald wrote:
> In addition to that the offset to compute ObjectToWorldTransform is 
> completely ignored. Maybe I am wrong with the origin and the offset but 
> I thing ignoring the offset for world transform should not happen, 
> should it?
> 
> Markus Mehrwald schrieb:
>> Hi,
>>
>> I just had a look at the code of the ImageSpatialObject. In the method 
>> SetImage there is code to compute the offset of the spatial object. In 
>> my mind it should be better to use the index of the RequestedRegion 
>> instead of the origin because in my case this is the image I want the 
>> spatial object from. In case of having the whole image origin and the 
>> index of the RequestedRegion are the same anyway.
>>
>> Regards,
>> Markus Mehrwald
>>
>> Markus Mehrwald schrieb:
>>> Hi Julien,
>>>
>>> I do not really need ValueAt() at the moment. I used this code just 
>>> for debug reasons. As I wrote before I have created my binary image 
>>> first and than want it as spatial object to save it because if I only 
>>> save the image the translation information is gone. At the moment I 
>>> need ValueAt() I do not have the translation information anymore 
>>> (after a restart of the application and without calculating 
>>> everything again).
>>> I have tried some other things with transform and offsets but the 
>>> only case in which I get the correct result (but without translation) 
>>> is if the image passed to the ImageMaskSpatialObject has its origin 
>>> at 0,0.
>>>
>>> Greetings,
>>> Markus
>>>
>>> Julien Jomier schrieb:
>>>> Hi Markus,
>>>>
>>>> Can you take into account the origin of your image when you request 
>>>> the ValueAt()?
>>>> If you are using the SpatialObjectToImageFilter to create your 
>>>> binary image you can set the origin of the output image, if you set 
>>>> it to the same origin as the input image then it should work.
>>>>
>>>> One other option is to reset the IndexToObjectTransform of your 
>>>> ImageMaskSpatialObject with an offset of zero:
>>>>
>>>>   myImageSO->GetIndexToObjectTransform()->SetOffset( offset );
>>>>   myImageSO->ComputeObjectToParentTransform();
>>>>
>>>> This will not modify the origin of the image passed using the 
>>>> SetImage() function so you can use it later.
>>>>
>>>> Hope that helps,
>>>>
>>>> Julien
>>>>
>>>> Markus Mehrwald wrote:
>>>>> Hi,
>>>>>
>>>>> I found the problem. The image starts at 180, 130 and that is the 
>>>>> problem. If I translate the image to 0, 0 the code from my last 
>>>>> mail works correct. The problem now: I need the information of the 
>>>>> translation for further calculations.
>>>>> Any suggestions how to keep the translation? I tried
>>>>>
>>>>> ImageMaskSpatialObjectType::TransformType::OffsetType offset;
>>>>> offset[0] = 
>>>>> thresholder->GetOutput()->GetRequestedRegion().GetIndex()[0];
>>>>> offset[1] = 
>>>>> thresholder->GetOutput()->GetRequestedRegion().GetIndex()[1];
>>>>> imageMaskSpatialObject->GetObjectToParentTransform()->SetOffset(offset); 
>>>>>
>>>>> imageMaskSpatialObject->ComputeObjectToParentTransform();
>>>>>
>>>>> but this leads to the same problem I had before. Also with 
>>>>> WorldTransform.
>>>>>
>>>>> Greetings,
>>>>> Markus
>>>>>
>>>>> Markus Mehrwald schrieb:
>>>>>> Hi,
>>>>>> I just implemented some code which uses a ImageMaskSpatialObject. 
>>>>>> I created a binary image in my filter chain and want this now to 
>>>>>> be a spatial object so I use the SetImage method of the spatial 
>>>>>> object but nothing happens. The output of the object looks good. 
>>>>>> Coordinates (, ...) are correct but at every point of the so 
>>>>>> created object ValueAt gives me 0. The code looks like the following:
>>>>>>
>>>>>> thresholder->Update();
>>>>>> ImageMaskSpatialObjectType::PointType point;
>>>>>> imageMaskSpatialObject = ImageMaskSpatialObjectType::New();
>>>>>> imageMaskSpatialObject->SetImage(thresholder->GetOutput());
>>>>>> imageMaskSpatialObject->SetRequestedRegion(thresholder->GetOutput()->GetRequestedRegion()); 
>>>>>>
>>>>>> imageMaskSpatialObject->Update();
>>>>>> imageMaskSpatialObject->UpdateOutputInformation();
>>>>>> imageMaskSpatialObject->ComputeObjectToWorldTransform();
>>>>>> double ret;
>>>>>> for (int i = 0; i < 640; i++)
>>>>>> {
>>>>>>    for (int j = 0; j < 512; j++)
>>>>>>    {
>>>>>>        point[0] = i;
>>>>>>        point[1] = j;
>>>>>>        imageMaskSpatialObject->ValueAt(point, ret);
>>>>>>        if (ret != 0)
>>>>>>            std::cout << "ret: " << ret << std::endl;
>>>>>>    }
>>>>>> }
>>>>>>
>>>>>>
>>>>>> The image coming from the thresholder has indeed a size of 300x280 
>>>>>> but changing the for-loops has no consequence on the outcome.
>>>>>> I took a look at the image coming from the thresholder and it is 
>>>>>> what it should be, a binary image with white areas too. The code 
>>>>>> above never writes anything to the standard output because it does 
>>>>>> not find any values differing to 0.
>>>>>> Did I anything wrong or is it a problem of the 
>>>>>> ImageMaskSpatialObject?
>>>>>>
>>>>>> Thanks in advance,
>>>>>> Markus
>>>>>> _______________________________________________
>>>>>> Insight-users mailing list
>>>>>> Insight-users at itk.org
>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
> 
>