[Insight-users] Volume not perfectly rotated

[Luis Ibanez]

Hi Nic,

Can you please post your code to the list ?

and also post the basic information about your image ?

The best way of doing this is to send the output of:

      reader->GetOutput()->Print( std::cout );


    Thanks


       Luis


-----------------
Nic wrote:
> Hi Luis,
>    I replace my quaternion code with your code, but I get exactly the 
> same result, the first slide (magenta ) is half cut, sic..
> http://itk.fete.ch/perso/testCodeLuis01.jpg
> 
> 
> 
> ----- Original Message ----- From: "Luis Ibanez" <luis.ibanez at kitware.com>
> To: "Nic" <itk at fete.ch>
> Cc: "Insight Users" <insight-users at itk.org>
> Sent: Thursday, October 11, 2007 5:44 PM
> Subject: Re: [Insight-users] Volume not perfectly rotated
> 
> 
>>
>> Hi Nic,
>>
>>
>> It seems that you have not initialized the Center of Rotation of the
>> VersorRigid3DTransform.
>>
>> By default that center is at (0,0,0), so it is likely that your image
>> if being flipped around the corner of the image, not around the center
>> of the image.
>>
>> You may want to compute the center of the image in physical coordinates
>> and use that as the center of rotation for the VersorRigid3DTransform.
>>
>> You will find examples on how to compute the center of the image in
>> the ITK Software Guide.
>>
>>       http://www.itk.org/ItkSoftwareGuide.pdf
>>
>>
>> It comes down to
>>
>>     for( i=0; i<3; i++)
>>       {
>>       Center[i] = Origin[i] + Size[i] * Spacing[i] / 2.0
>>       }
>>
>> -----
>>
>>
>> Also, Please aware that *you are not using the Quaternion correctly*.
>>
>>
>>   //: Construct quaternion from Euler Angles,
>>   // That is a rotation about the X axis, followed by Y, followed by
>>   // the Z axis, using a fixed reference frame.
>>   vnl_quaternion(T theta_X, T theta_Y, T theta_Z);
>>
>>
>>
>> That is not the order of the rotational sequence that you are assuming.
>>
>>
>>
>> It is too bad that so many people have grown used to Euler angles.
>> They are one of the *worst things* that have made their way in
>> computer graphics. They are clumsy and provide a very poor
>> representation of the SO(3) rotational space
>>
>>          http://en.wikipedia.org/wiki/SO%283%29
>>
>> Euler angles have impoverished the understanding of generations of
>> engineers on the nature of rotational space and crippled them to
>> think in Cartesian schems instead of embracing the natural properties
>> of the rotational space. That results in uncountable pieces of software
>> that require "if" conditions when computing rotational components.
>>
>>
>>
>> ---------
>>
>> The correct way of composing rotations in space when using
>> Quaternions is to define a quaternion for each one of the
>> intermediate rotations and then use the Quaternion composition
>> method:
>>
>>     vnl_quaternion::operator*()   in VNL
>>
>> or
>>
>>     itkVersor::operator*()   in ITK
>>
>>
>> In your case:
>>
>> > What I do is simply initialize the versorRigid3dTransform with a 180°
>> > rotation around y-axis and -94.55 rotation around z-axis.
>>
>>
>> You should do:
>>
>> typedef itk::Versor<double>      VersorType;
>> typedef VersorType::VectorType   AxisType;
>> typedef VersorType::ValueType    ValueType;
>>
>> AxisType axis1;   // Rotation Axis = Y
>> axis1[0] = 0.0;
>> axis1[0] = 1.0;
>> axis1[0] = 0.0;
>>
>> ValueType angle1 = 3.141516...
>>
>> VersorType versor1;
>> versor1.Set( axis1, angle1 ); // 180 degrees around Y
>>
>>
>> AxisType axis2;   // Rotation Axis = Z
>> axis2[0] = 0.0;
>> axis2[0] = 0.0;
>> axis2[0] = 1.0;
>>
>> ValueType angle2 = 3.141516 * ( -94.55 ) / 180.0;
>>
>> VersorType versor2;
>> versor2.Set( axis2, angle2 ); // -94.55 degrees around Z
>>
>>
>>      VersorType versor3 = versor2 * versor1;
>>
>>
>> The last variable "versor3" will contain the correct rotation
>> expressed in terms of a unit quaternion.
>>
>>
>> Note that most of the time, when people use Quaternions,
>> what they actually want to use are Versors.
>>
>> Quaternions can represent rotation *and scaling* in space,
>> while Versors are limited to rotations. Versors are equivalent
>> to Unit-Quaternions.
>>
>>
>> You may want to read more about Quaternions and their properties:
>> http://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation
>>
>> and the ITK Quaternion Tutorials:
>>
>> http://www.itk.org/CourseWare/Training/QuaternionsI.pdf
>> http://www.itk.org/CourseWare/Training/QuaternionsII.pdf
>>
>>
>>    Regards,
>>
>>
>>       Luis
>>
>>
>>
>> ----------------
>> Nic wrote:
>>
>>> Hi all,
>>>     I have a strange behaviour I would like to correct in my 
>>> initialisation.
>>> I used quaternion for rotation initialisation like this, as previously
>>> adviced :
>>>
>>> *******************************************************
>>> double RotX = angleX * vnl_math::pi / 180.0;
>>> double RotY = angleY * vnl_math::pi / 180.0;
>>> double RotZ = angleZ * vnl_math::pi / 180.0;
>>> vnl_quaternion<double> RR(RotX,RotY,RotZ);
>>> rotation.Set(RR);
>>> transform->SetRotation( rotation );
>>>
>>> [...]
>>> // Checking
>>> VersorType rotationInitiale = transform->GetVersor();
>>> vnl_vector_fixed<double,3> anglesEuleriensInitiaux = 
>>> (rotationInitiale.GetVnlQuaternion()).rotation_euler_angles();
>>> cout << "Angles d'Euler (initiaux): " << 
>>> (anglesEuleriensInitiaux*180.0/vnl_math::pi) << endl;
>>>
>>> ********************************************************
>>>
>>> What I doesn't understand actually is why by flipping around X or Y 
>>> axis by 180°, I get an "half image" at the beginning of the stack
>>> Is this behavious linked to the Quaternions ? Is there a special case 
>>> for a pi angle ? Is there a way to avoid this behaviour ?
>>>  Images:
>>> http://itk.fete.ch/perso/Rot_0_0_0.jpg
>>> http://itk.fete.ch/perso/Rot_0_180_0.jpg
>>> http://itk.fete.ch/perso/Rot_180_0_0.jpg
>>>  ------------------------------------------------------------------------ 
>>>
>>>
>>> _______________________________________________
>>> Insight-users mailing list
>>> Insight-users at itk.org
>>> http://www.itk.org/mailman/listinfo/insight-users
>>
>>
> 
>