On Monday August 9 2010 04:42:51 Anders Logg wrote: > On Fri, Aug 06, 2010 at 01:37:12PM -0700, Johan Hake wrote: > > On Friday August 6 2010 12:10:34 Anders Logg wrote: > > > On Fri, Aug 06, 2010 at 07:57:52PM +0100, Garth N. Wells wrote: > > > > On Fri, 2010-08-06 at 11:55 -0700, Johan Hake wrote: > > > > > On Friday August 6 2010 11:48:37 Anders Logg wrote: > > > > > > On Wed, Aug 04, 2010 at 05:06:57PM -0700, Johan Hake wrote: > > > > > > > On Wednesday August 4 2010 13:09:47 Riesen Patrick wrote: > > > > > > > > -----Original Message----- > > > > > > > > From: Garth N. Wells [mailto:gn...@cam.ac.uk] > > > > > > > > Sent: Wed 04.08.2010 19:07 > > > > > > > > To: johan.h...@gmail.com > > > > > > > > Cc: Riesen Patrick; dolfin@lists.launchpad.net > > > > > > > > Subject: Re: [Dolfin] python: xml read for vector / > > > > > > > > std::vector > > > > > > > > > > > > > > > > On Wed, 2010-08-04 at 10:03 -0700, Johan Hake wrote: > > > > > > > > > On Wednesday August 4 2010 09:28:22 Patrick Riesen wrote: > > > > > > > > > > Patrick Riesen wrote: > > > > > > > > > > > Johan Hake wrote: > > > > > > > > > > >> Patrick! > > > > > > > > > > >> > > > > > > > > > > >> On Wednesday August 4 2010 09:13:24 Patrick Riesen wrote: > > > > > > > > > > >>> hello dolfin developers > > > > > > > > > > >>> > > > > > > > > > > >>> I write out a std::vector in XML file format from > > > > > > > > > > >>> cpp. Can I read the XML file in again in python and > > > > > > > > > > >>> construct a numpy array? I know how to do it with a > > > > > > > > > > >>> dolfin Vector, but is it possible with a > > > > > > > > > > >>> std::vector<double>? I could not figure out the > > > > > > > > > > >>> syntax, i tried > > > > > > > > > > >>> > > > > > > > > > > >>> # this is ok > > > > > > > > > > >>> fn = File("data/norm.xml") > > > > > > > > > > >>> div_vec = d.Vector() > > > > > > > > > > >>> a = n.array((11,1)) > > > > > > > > > > >>> > > > > > > > > > > >>> # fails > > > > > > > > > > >>> fn >> a > > > > > > > > > > >>> # fails > > > > > > > > > > >>> fn >> div_vec.array() > > > > > > > > > > >> > > > > > > > > > > >> Have you tried: > > > > > > > > > > >> fn >> div_vec > > > > > > > > > > >> a = div_vec.array() > > > > > > > > > > > > > > > > > > > > > > yes, that gives the error: > > > > > > > > > > > *** Error: Handler stack not empty. Something is wrong! > > > > > > > > > > > > > > > > > > The format is then different for the Vector XML file and > > > > > > > > > the std::vector file? > > > > > > > > > > > > > > > > > > > if i write out a dolfin::Vector in xml, it's all fine > > > > > > > > > > with: > > > > > > > > > > > > > > > > > > > > fn = File("data/norm.xml") > > > > > > > > > > div_vec = d.Vector() > > > > > > > > > > fn >> div_vec > > > > > > > > > > a = div_vec.array() > > > > > > > > > > > > > > > > > > > > but if i write out a std::vector<double> in xml, I can't > > > > > > > > > > read it in. > > > > > > > > > > > > > > > > > > Silly question from a Python user: > > > > > > > > > How do you write the std::vector to a XML file? > > > > > > > > > > > > > > > > You don't ;); > > > > > > > > > > > > > > > > DOLFIN does. It's overloaded in the XMLFile class. > > > > > > > > Well, anyway, i thought if dolfin can write out a std::vector > > > > > > > > to xml via File/XMLFile, pydolfin can also read it in, but > > > > > > > > obviously not. > > > > > > > > > > > > > > I think you stumble across some unused code there. I am not > > > > > > > sure but I think Ola implemented this for some debugging of > > > > > > > the parallel interface. But I am not sure actually. > > > > > > > > > > > > > > If we had a typemap for std::vector <-> numpy array (which we > > > > > > > could have, but > > > > > > > > > > > > > > desided we did not want...) we sould be able to do: > > > > > > > somefile >> array > > > > > > > somefile << array > > > > > > > > > > > > > > Where somefile will be file generated by XMLArray, which > > > > > > > probably define a different XML interfaces than XMLVector. > > > > > > > > > > > > Input/output is implemented for the Array class so it would be > > > > > > appropriate to use that. It was implemented to handle > > > > > > input/output for parallel mesh data (stored in the data section > > > > > > of a mesh as MeshFunctions, Arrays and maps). > > > > > > > > > > Ok > > > > > > > > > > > Can someone remind me of why we don't have a typemap for > > > > > > numpy.array and dolfin::Array? Or what am I missing here? > > > > > > > > > > We have that, but the XMLArray read and writes std::vector, which > > > > > typemaps we decided to ditch. > > > > > > > > The best solution is to use dolfin::Array in XMLArray. It will also > > > > simplify io of dolfin::Vector. > > > > > > Aha. I missed that. I suggest we support input/output for both > > > dolfin::Array and std::vector. It should be possible to implement > > > with a good deal of code reuse. > > > > Another thing, is it anything that prevent us to harmonize the xml format > > of an XMLArray and an XMLVector? Any potential issues during parallel? > > If so one should be able to do what Patrick did in the first place. > > > > > Speaking of which, would it be possible to add a constructor to > > > dolfin::Array that takes a std::vector? > > > > > > std::vector<int> x(10); > > > > > > dolfin::Array<int> xx(x); > > > > > > ? > > > > > > I have been missing that on a few occasions. > > > > That should be possible with copying of data of course. > > I meant without copying. Isn't that one of the main points with the > Array class that it is flexible in terms of ownership?
Yes you are probably right there. We then need to wrap a shared_array around the pointer to the first element of the std::vector in a constructor. The vector can then of course not go out of scope. We do have a problem if a user resize the std::vector though. Johan Johan _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : dolfin@lists.launchpad.net Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
