dolfin team mailing list archive

[A Navaei <axnavaei@xxxxxxxxxxxxxx>]

2009/2/19 Johan Hake <hake@xxxxxxxxx>:
> On Thursday 19 February 2009 17:51:12 A Navaei wrote:
>> 2009/2/19 Anders Logg <logg@xxxxxxxxx>:
>> > On Thu, Feb 19, 2009 at 02:53:52PM +0000, A Navaei wrote:
>> >> ---------- Forwarded message ----------
>> >> From: A Navaei <axnavaei@xxxxxxxxxxxxxx>
>> >> Date: 2009/2/19
>> >> Subject: Re: [DOLFIN-dev] A minimal c++ Function test and some bugs
>> >> To: Johan Hake <hake@xxxxxxxxx>
>> >>
>> >> 2009/2/19 Johan Hake <hake@xxxxxxxxx>:
>> >> > On Thursday 19 February 2009 14:54:57 A Navaei wrote:
>> >> >> 2009/2/19 Johan Hake <hake@xxxxxxxxx>:
>> >> >> > On Thursday 19 February 2009 14:46:18 A Navaei wrote:
>> >> >> >> 2009/2/19 Garth N. Wells <gnw20@xxxxxxxxx>:
>> >> >> >> > A Navaei wrote:
>> >> >> >> >> 2009/2/19 Johan Hake <hake@xxxxxxxxx>:
>> >> >> >> >>> The previous email was sent a bit premature...
>> >> >> >> >>>
>> >> >> >> >>> [snip]
>> >> >> >> >>>
>> >> >> >> >>>>> I have also thought of this :)
>> >> >> >> >>>>>
>> >> >> >> >>>>> Then you can take an ordered mesh, iterate over the
>> >> >> >> >>>>> vertices, and use the
>> >> >> >> >>>>> present implementation of the eval function (which in its
>> >> >> >> >>>>> present shape is a piecewise constant interpolator isn't
>> >> >> >> >>>>> it?), to fill the new _vector,
>> >> >> >> >>>>> all done in the constructor. Then you have a discrete
>> >> >> >> >>>>> function in the first place :)
>> >> >> >> >>>>
>> >> >> >> >>>> Is it possible to set the pointer to _vector data directly
>> >> >> >> >>>> where we can pass the pointer to image data? If this works,
>> >> >> >> >>>> no loop will be involve in data conversion and it will be
>> >> >> >> >>>> super fast.
>> >> >> >> >>>
>> >> >> >> >>> Yes but you do not know how the mesh is ordered.
>> >> >> >> >>
>> >> >> >> >> Consider a 2D image data mapped on a structured grid, with size
>> >> >> >> >> (number of nodes in each direction) of (sx, sy), the value of
>> >> >> >> >> image brightness at coordinate (i, j) is given by I(k), where:
>> >> >> >> >>
>> >> >> >> >> k = i + sx * j
>> >> >> >> >>
>> >> >> >> >> Is this not enough information to create the mesh?
>> >> >> >> >>
>> >> >> >> >>>> It seems _vector.set()
>> >> >> >> >>>>
>> >> >> >> >>>> (http://www.fenics.org/pub/documents/dolfin/dolfin-progr-refe
>> >> >> >> >>>>rence/ d6/ da4/c
>> >> >> >> >>>> lassdolfin_1_1GenericVector.html#bc4ecede55f2846ecadae02426df
>> >> >> >> >>>>8f63) accepts
>> >> >> >> >>>> the pointer to each row, is that right?
>> >> >> >> >>>
>> >> >> >> >>> There is no such thing as a row in a vector. It stores the
>> >> >> >> >>> data in a contigouos way (if not distributed).
>> >> >> >> >>
>> >> >> >> >> No idea why it says rows: virtual void
>> >> >> >> >> dolfin::GenericVector::set (const double *block, const uint
>> >> >> >> >> *num_rows, const uint *const * rows).
>> >> >> >> >
>> >> >> >> > You can set as few or as many entries as you wish at once.
>> >> >> >> > 'block' contains the values you want to set, 'num_rows' are the
>> >> >> >> > number of entries you wish to set, and 'rows' are the positions
>> >> >> >> > into which the entries should be inserted.
>> >> >> >>
>> >> >> >> I hate to say this, but _vector is private!
>> >> >> >
>> >> >> > ... and perfectly accesable through vector()
>> >> >>
>> >> >> ... and perfectly read-only through vector()
>> >> >
>> >> > I past from Function.h
>> >> >
>> >> >    /// Return the vector of expansion coefficients, automatically
>> >> >    /// initialized to zero if coefficients have not been computed
>> >> > (non-const version)
>> >> >    GenericVector& vector();
>> >> >
>> >> >    /// Return the vector of expansion coefficients, automatically
>> >> >    /// initialized to zero if coefficients have not been computed
>> >> > (const version)
>> >> >    const GenericVector& vector() const;
>> >> >
>> >> > So one const version and one that is not.
>> >>
>> >> Would this be the right way of initialising _vector in the subclass? :
>> >>
>> >>      DefaultFactory factory;
>> >>      vector() =
>> >> *(boost::shared_ptr<GenericVector>(factory.create_vector()));
>> >>
>> >> Try attached in your sandbox.
>> >
>> > No, just do
>> >
>> >  vector();
>> >
>> > That will initialize a zero vector of correct size.
>>
>> These two work:
>>
>>   Function1(boost::shared_ptr<const Image> image) : Function()
>>   {
>>   };
>>
>>   Function1() : Function()
>>   {
>>     vector();
>>   };
>>
>> But the combination generates a segmentation fault:
>>
>> class Function2 : public Function
>> {
>> public:
>>   Function2(boost::shared_ptr<const Image> image) : Function()
>>   {
>>     vector();
>>   };
>> };
>>
>> The trace includes /libdolfin.so.0(_ZN6dolfin8Function6vectorEv+0x38).
>> Example attached.
>
> I get:
>
> terminate called after throwing an instance of 'std::runtime_error'
>  what():  *** Assertion (_function_space) [at
> dolfin/function/Function.cpp:303 in init()]
>
> You need to attach a FunctionSpace before you call vector() otherwise it
> cannot know how long the vector should be.

The vector length is supposed to be initialised directly using the
image size, not FunctionSpace:

class LinearDiscreteImageFunction : public Function
{
public:
  LinearDiscreteImageFunction(boost::shared_ptr<Image> image) : Function()
  {
  int N = image->get_size()[0] * image->get_size()[1];
  vector(); // segmentation fault
  vector().resize(N);
  vector().set(image->get_data());
  };
};


-Ali

>
> The first constructor is not called (for what reason I do not know) and wont
> trigger the assertion.
>
> Johan
>