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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