What version of cython are you using? I'm using 0.15.1. On Fri, Feb 17, 2012 at 3:09 PM, wang yunbo <[email protected]> wrote:
> Hi Dr. Wheeler, > > I installed lsmlib from its official site and then manually grab the > entire pylsmlib folder from your link. My platform is ubuntu 10.04.4 LTS > with Python 2.6.5 and GCC 4.4.3. > > Then I attempted to run circle.py. Here is the error I got: > > pysparse > Traceback (most recent call last): > File "circle.py", line 2, in <module> > from pylsmlib import computeExtensionFields2d > File "/home/wang1320/lsmlib/lsmlib-1.0.1/pylsmlib/pylsmlib.py", line 6, > in <module> > 'include_dirs' : np.get_include() > TypeError: install() got an unexpected keyword argument 'setup_args' > > > I checked pysparse, it was OK. > > Type "help", "copyright", "credits" or "license" for more information. > >>> import pysparse > >>> from pylsmlib import computeExtensionFields2D > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "pylsmlib.py", line 6, in <module> > 'include_dirs' : np.get_include() > TypeError: install() got an unexpected keyword argument 'setup_args' > > > It seems the wrappers don't work here, how can I make it work? Is your > version of lsmlib modified? > Thanks. > > Best, > > Yunbo > > > > On Feb 10, 2012, at 3:40 PM, Daniel Wheeler wrote: > > Yunbo, > > The entire lsmlib code in in my research repository > > <http://matforge.org/wd15/browser/trunk/lsmlib> > > It's not been modified apart from for debug reasons. The pylsmlib section > is in > > <http://matforge.org/wd15/browser/trunk/lsmlib/pylsmlib> > > The three cython wrapper functions are here > > <http://matforge.org/wd15/browser/trunk/lsmlib/pylsmlib/lsmlib.pyx> > > Good luck! > > On Fri, Feb 10, 2012 at 2:20 PM, wang yunbo <[email protected]> wrote: > >> Thanks so much. That'll be great. I'm really looking forwards to trying >> lsmlib with your cython wrappers. >> >> Regards, >> >> Yunbo >> On Feb 10, 2012, at 11:18 AM, Daniel Wheeler wrote: >> >> On Thu, Feb 9, 2012 at 4:56 PM, wang yunbo <[email protected]> wrote: >> >>> Hi, >>> >>> 1. when I look at the 'data' file and checked some point which suppose >>> to be at the surface e.g (50, 25), (62, 71), the results are like 0.0 or >>> 0.7 (not 0.04 as expected). That's where I get confused. How can I reach >>> my expectation? >>> >> >> I don't think you can with the current implementation in FiPy. The >> calcDistanceFunction method is only first order accurate I believe and >> hence the difficulties calculating the curvature accurately. The >> applications in FiPy don't use higher derivatives so get away with first >> order accuracy. The curvature calculation is second order accurate, but the >> underlying calculation of the distance function is not. Hence the issues. >> Basically, FiPy as it stands is not accurate enough for this. >> >> >>> 2. The shape of my plot is quite wavy with many wiggles, not concentric >>> rings as expected. >>> >> >> I'm moving towards using lsmlib < >> http://ktchu.serendipityresearch.org/software/lsmlib/index.html>, which >> I believe has second order accuracy for the distance function calculation >> and is also way faster than FiPy. At the moment I have cython wrappers for >> calcDistanceFunction2d, calcEikonalEquation2d and calcExtensionFields2d, >> which seem to work though I haven't tested extensively. My hope is to >> replace all the level set functionality in FiPy with the cython lsmlib >> calls. I'm happy to share the cython wrappers with you if you wish. >> >> In short I recommend that you give lsmlib a shot and then use the my >> cython wrappers to integrate with python. >> >> Cheers. >> >> -- >> Daniel Wheeler >> _______________________________________________ >> fipy mailing list >> [email protected] >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> >> >> >> _______________________________________________ >> fipy mailing list >> [email protected] >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> >> > > > -- > Daniel Wheeler > _______________________________________________ > fipy mailing list > [email protected] > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > -- Daniel Wheeler
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