Re: [Rd] .Call - applying setAttrib(x, R_DimSymbol, s) to a matrix being an element of a list

From: Oleg Sklyar <osklyar_at_ebi.ac.uk>
Date: Thu 17 Mar 2005 - 15:16:53 GMT

Thanks a lot for your comments. In fact I had an idea that maybe it is a pointer that is transferred after Simon's yesterday's commnent. So generally I should always allocVector for imgSize before passing it and just let the garbage collector to clean them afterwards if I understand right.

Best regards
Oleg

Dr Oleg Sklyar
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD
England
phone/fax +44(0)1223 49 4478/4468
e-mail osklyar@ebi.ac.uk

Prof Brian Ripley wrote:

> On Thu, 17 Mar 2005, Oleg Sklyar wrote:
>
>> Dear Simon,
>>
>>> you gave us only a fragment of your code, so I can only guess what the
>>
>> problem is:
>>
>>> What is imgSize? The behavior you describe seems as if you re-using the
>>
>> imgSize SEXP in all elements.
>>
>>> AFAIR in your case setAttrib doesn't copy the value, so you need to
>>> do so
>>
>> yourself (or alloc new dim array
>>
>>> for each element).
>>
>>
>> Sorry, it is always a tradeoff - either to explain or put a
>> relatively large code, which also uses non-standard libraries making
>> the code difficult to read. imgSize values are reset in between: see
>> the full code below. The SEXP pointer imgSize stays in tact, that's
>> true, but its values are changed (the problem is, they are always the
>> last in the row). I.e. if I have 3 images 40x20, 200x100 and 150x75 I
>> will get three matrices of 150x75, but if I omit setAtrib and return
>> vectors I get vectors of different length.
>
>
> So, as Simon says, you need to create separate objects for the
> dimensions of each matrix, not share the object. It is the object
> pointed to by imgSize you have attached as the dimensions, not the
> values.
>
> BTW, setAttrib(element, R_DimSymbol, imgSize) just calls
> dimgets(element, imgSize), so I would have used the latter directly.
>
> I believe you do not have three matrices of 150x75, rather a vector of
> length 40*20 with an inconsistent dim attribute of c(150, 75), etc.
>
>>
>> Oleg
>>
>> SEXP load2DImages(SEXP fileNames) {
>> int nFiles = LENGTH(fileNames);
>> std::cout << "Loading " << nFiles << " files..." << std::endl;
>> // SEXP result = allocList(nFiles);
>> SEXP result = allocVector(VECSXP, nFiles);
>> PROTECT(result);
>> SEXP imgSize = allocVector(INTSXP, 2);
>> PROTECT(imgSize);
>> TRGB2DImage::Pointer image;
>> TRGB2DReader::Pointer reader = TRGB2DReader::New();
>> TRGB2DImage::SizeType size; TRGB2DImage::IndexType pixIndex;
>> for (int i = 0; i < nFiles; i++) {
>> try {
>> char *filename = CHAR(asChar(VECTOR_ELT(fileNames, i)));
>> std::cout << std::endl << "Loading image file " << filename
>> << "... ";
>> reader->SetFileName(filename);
>> reader->Update();
>> image = reader->GetOutput();
>> } catch(...) {
>> std::cout << "failed!";
>> continue;
>> }
>> std::cout << std::endl;
>> size = image->GetLargestPossibleRegion().GetSize();
>> INTEGER(imgSize)[0] = size[1];
>> INTEGER(imgSize)[1] = size[0];
>> std::cout << size[0] << " x " << size[1] << std::endl;
>> SET_VECTOR_ELT(result, i, allocVector(INTSXP, size[0] * size[1]));
>> SEXP element = VECTOR_ELT(result, i);
>> for (int ix = 0; ix < size[0]; ix++) {
>> pixIndex[0] = ix;
>> for (int iy = 0; iy < size[1]; iy++) {
>> pixIndex[1] = iy;
>> INTEGER(element)[size[1] * ix + iy] =
>> getIntRGBColour(image->GetPixel(pixIndex));
>> }
>> }
>> setAttrib(element, R_DimSymbol, imgSize);
>> }
>> UNPROTECT(2);
>> if (nFiles == 1)
>> return VECTOR_ELT(result, 0);
>> else
>> return result;
>> }
>>
>> Dr Oleg Sklyar
>> European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge, CB10 1SD
>> England
>> phone/fax +44(0)1223 49 4478/4468
>> e-mail osklyar@ebi.ac.uk
>>
>>
>>
>> Simon Urbanek wrote:
>>
>>> Oleg,
>>>
>>> you gave us only a fragment of your code, so I can only guess what
>>> the problem is:
>>>
>>> On Mar 16, 2005, at 12:40 PM, Oleg Sklyar wrote:
>>>
>>>> // converting element into a matrix
>>>> setAttrib(element, R_DimSymbol, imgSize);
>>>
>>>
>>>
>>> What is imgSize? The behavior you describe seems as if you re-using
>>> the imgSize SEXP in all elements. AFAIR in your case setAttrib
>>> doesn't copy the value, so you need to do so yourself (or alloc new
>>> dim array for each element).
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>
>>
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>> R-devel@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>



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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri Mar 18 02:19:43 2005

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