Im using trunk. You shouldn't need it though. What was the secondary error? On Feb 17, 2012 10:39 PM, "wang yunbo" <[email protected]> wrote:
> Hi Dr. Wheeler, > > We updated the cython and had an other error. > > Traceback (most recent call last): > File "circle.py", line 7, in <module> > m = Grid2D(nx=N, ny=N, Lx=L, Ly=L) > TypeError: Grid2D() got an unexpected keyword argument 'Lx' > > When we replace them with the standard dx and dy, then circle.py fails > further down in the script. Which fipy version are you using? > > Thanks. > > Yunbo > > On Feb 17, 2012, at 4:12 PM, Daniel Wheeler wrote: > > 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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