[ITK-users] vnl matrix to numpy array gives random numbers

[Samuel Gerber]

I'd guess there is something funky going with vnl_matrix_fixed. From the
docs ( https://github.com/vxl/vxl/blob/master/core/vnl/vnl_matrix_fixed.h )
it says that the data resides on the stack. From your code snippet it is
not exactly clear to me who owns the data in fixed_matrix, probably image.
Might it be that image gets removed before you use the array view?


On Mon, Aug 7, 2017 at 10:27 PM, Nick Cullen via Insight-users <

Hi Friends !!
I'm trying to use itkPyVnl directly in ITK, but I must be getting
```
typedef typename ImageType::DirectionType ImageDirectionType;
ImageDirectionType * direction = const_cast<ImageDirectionType *>(
&image->GetDirection() );
typedef typename ImageDirectionType::InternalMatrixType
DirectionInternalMatrixType;
DirectionInternalMatrixType * fixed_matrix = const_cast<DirectionInternalMatrixType
*>( &direction->GetVnlMatrix() );
const vnl_matrix<double> vnlmat1 = fixed_matrix->as_matrix();
vnl_matrix<double> * vnlmat2 = const_cast<vnl_matrix<double> *>(
&vnlmat1 );
typedef itk::PyVnl<double> PyVnlType;
PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat2
);
```
I've tried a million different things and have problems either 1) due to
the constness of ->as_matrix() and others or 2) due to "taking the address
of a temporary object" with ->as_matrix() ... -__-
```
vnl_matrix<double> * vnlmat = new vnl_matrix<double>;
vnlmat->set_size(2,3);
vnlmat->fill(0);
vnlmat->put(1,2,1.3);
vnlmat->put(1,0,2);
std::cout << vnlmat << std::endl;
typedef itk::PyVnl<double> PyVnlType;
PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat );
```
Any help above is MUCH appreciated !!!!
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[Lowekamp, Bradley (NIH/NLM/LHC) [C]]

Hello,

Is there a method named something like “_GetArrayFromVnlMatrix”? This should perform a copy of the data, as opposed to just a “view”.

Brad


From: Samuel Gerber <***@kitware.com>
Date: Tuesday, August 8, 2017 at 7:57 AM
To: Nick Cullen <***@yahoo.com>
Cc: "insight-***@itk.org" <insight-***@itk.org>
Subject: Re: [ITK] [ITK-users] vnl matrix to numpy array gives random numbers

I'd guess there is something funky going with vnl_matrix_fixed. From the docs ( https://github.com/vxl/vxl/blob/master/core/vnl/vnl_matrix_fixed.h ) it says that the data resides on the stack. From your code snippet it is not exactly clear to me who owns the data in fixed_matrix, probably image. Might it be that image gets removed before you use the array view?

On Mon, Aug 7, 2017 at 10:27 PM, Nick Cullen via Insight-users <insight-***@itk.org<mailto:insight-***@itk.org>> wrote:
Hi Friends !!

I'm trying to use itkPyVnl directly in ITK, but I must be getting something wrong with pointers... The following just gives me random numbers:

```
typedef typename ImageType::DirectionType ImageDirectionType;
ImageDirectionType * direction = const_cast<ImageDirectionType *>( &image->GetDirection() );

typedef typename ImageDirectionType::InternalMatrixType DirectionInternalMatrixType;
DirectionInternalMatrixType * fixed_matrix = const_cast<DirectionInternalMatrixType *>( &direction->GetVnlMatrix() );

const vnl_matrix<double> vnlmat1 = fixed_matrix->as_matrix();
vnl_matrix<double> * vnlmat2 = const_cast<vnl_matrix<double> *>( &vnlmat1 );

typedef itk::PyVnl<double> PyVnlType;
PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat2 );
```

I've tried a million different things and have problems either 1) due to the constness of ->as_matrix() and others or 2) due to "taking the address of a temporary object" with ->as_matrix() ... -__-


I know that this works:

```
vnl_matrix<double> * vnlmat = new vnl_matrix<double>;
vnlmat->set_size(2,3);
vnlmat->fill(0);
vnlmat->put(1,2,1.3);
vnlmat->put(1,0,2);
std::cout << vnlmat << std::endl;

typedef itk::PyVnl<double> PyVnlType;
PyObject * mymatrix = PyVnlType::_GetArrayViewFromVnlMatrix( vnlmat );
```

Any help above is MUCH appreciated !!!!

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