Mailman 3 March 2004 - SciPy-Dev

value+error type (long)
by Gary Ruben March 16, 2004

March 16, 2004

I recently became fed up with performing error calculations on experimental data and decided to make a Python data type which I could use with Numeric. Now I can enter data with error along with the errors as in the following example and all the error calculations are automatically carried through for me. I thought there might be some interest amongst others for inclusion of this in the scipy distribution, although you might prefer it to be in C. I provide it as food for thought, but let me know if there is interest in including it as is and I can look at making it robust by adding testcases etc. and some nicer helper functions for constructors with relative errors etc. Note, the helper functions for extracting the limits would be better implemented as properties of an array type subclassed from the Numeric array type. I gather Numarray would allow this, but I couldn't think of a way to do it in Numeric and I wanted to maintain compatibility. Similarly, I couldn't think of a nicer way to apply Ufuncs across the prime value and error extrema. It would be nice to not have to call ApplyUfuncToErr() to do this. Here's a sample of usage of the class, followed by the class itself. Note I've used Gnuplot.py in this but you'll get the idea by looking at the code: -- R_AB.py: from Numeric import * import Gnuplot, Gnuplot.funcutils from ErrorVal import * from scipy.interpolate import splrep,splev # manometer readings [mmHg] upperPressure = ArrayOfErr([909., 802., 677., 585., 560., 548.], 1.0) lowerPressure = ArrayOfErr([144., 246., 378., 469., 493., 505.], 1.0) pressureDiff = upperPressure - lowerPressure # Temperatures & Pressures from lookup table lowerTablePressures = array([760. , 540. , 290. , 110. , 60. , 40. ]) # [mmHg] lowerTableTemps = array([4.210, 3.867, 3.332, 2.685, 2.373, 2.194]) # [K] upperTablePressures = array([780. , 560. , 300. , 120. , 70. , 50. ]) # [mmHg] upperTableTemps = array([4.238, 3.902, 3.358, 2.735, 2.447, 2.290]) # [K] # Linearly interpolate table values to produce temperatures temps = ( lowerTableTemps + (pressureDiff - lowerTablePressures) * (upperTableTemps - lowerTableTemps) / (upperTablePressures - lowerTablePressures) ) # Voltages across R_AB [V] V_RStandard = ArrayOfErr([2.016, 2.016, 2.020, 2.017, 2.021, 2.019], 0.001) R = 100.2 # standard resistor value [Ohm] I = V_RStandard / R # current [A] # Voltages across Germanium resistor [V] V_RAB = array([Err(6.167, 0.002), Err(6.168, 0.002), Err(6.170, 0.002), Err(6.160, 0.002), Err(6.153, 0.02), Err(5.894, 0.01)], PyObject) R_AB = V_RAB / I logRAB = ApplyUfuncToErr(R_AB, log10) # This means log10(R_AB) sqrtLogROnT = (logRAB/temps)**0.5 g = Gnuplot.Gnuplot(debug=1) g.title('Allen-Bradley model log(R)=A+B[log(R)/T]^1/2') g.ylabel('log(R)') g.xlabel('[log(R)/T]^1/2') g('set bar 1') # set bar end length g('set grid') # spline fit x1 = PrimeVals(sqrtLogROnT)[0] x2 = PrimeVals(sqrtLogROnT)[5] splineX = arange(x1,x2+.005,.01) exactSpline = splrep(PrimeVals(sqrtLogROnT), PrimeVals(logRAB), s=0) exactSplineY = splev(splineX, exactSpline) g.plot(\ Gnuplot.Data(PrimeVals(sqrtLogROnT), PrimeVals(logRAB), inline=0, with='linesp lt 1 pt 0'), Gnuplot.Data(splineX, exactSplineY, inline=0, with='linesp lt 2 pt 0'), # exact spline Gnuplot.Data(PrimeVals(sqrtLogROnT), # x-points PrimeVals(logRAB), # y-points MinVals(sqrtLogROnT), MaxVals(sqrtLogROnT), # x-axis error bars MinVals(logRAB), MaxVals(logRAB), # y-axis error bars inline=0, with='xyerrorbars -1 0'), ) raw_input('Gary says copy to clipboard now\n') -- ErrorVal.py: from Numeric import * class Err: def __init__(self, value, posErr=0., negErr=None): self.value = float(value) self.posErr = float(posErr) if negErr: self.negErr = float(negErr) else: self.negErr = float(posErr) def __repr__(self): return "Err(%s,%s,%s)" % (self.value, self.posErr, self.negErr) def __str__(self): return "%s +%s/-%s" % (self.value, self.posErr, self.negErr) def __abs__(self): value = abs(self.value) if value == self.value: posErr = self.posErr negErr = self.negErr else: negErr = self.posErr posErr = self.negErr return Err(value, posErr, negErr) def __neg__(self): return Err(-self.value, self.negErr, self.posErr) def __pos__(self): return Err(self.value, self.posErr, self.negErr) def __add__(self, other): value = self.value + other.value posErr = self.posErr + other.posErr negErr = self.negErr + other.negErr return Err(value, posErr, negErr) def __radd__(self, other): value = self.value + other.value posErr = self.posErr + other.posErr negErr = self.negErr + other.negErr return Err(value, posErr, negErr) def __sub__(self, other): value = self.value - other.value posErr = self.posErr + other.negErr negErr = self.negErr + other.posErr return Err(value, posErr, negErr) def __rsub__(self, other): value = other.value - self.value posErr = other.posErr + self.negErr negErr = other.negErr + self.posErr return Err(value, posErr, negErr) def __mul__(self, other): value = self.value * other.value posErr = value * ((self.posErr/self.value) + (other.posErr/other.value)) negErr = value * ((self.negErr/self.value) + (other.negErr/other.value)) return Err(value, posErr, negErr) def __rmul__(self, other): value = self.value * other.value posErr = value * ((self.posErr/self.value) + (other.posErr/other.value)) negErr = value * ((self.negErr/self.value) + (other.negErr/other.value)) return Err(value, posErr, negErr) def __div__(self, other): value = self.value / other.value posErr = value * ((self.posErr/self.value) + (other.posErr/other.value)) negErr = value * ((self.negErr/self.value) + (other.negErr/other.value)) return Err(value, posErr, negErr) def __rdiv__(self, other): value = other.value / self.value posErr = value * ((self.posErr/self.value) + (other.posErr/other.value)) negErr = value * ((self.negErr/self.value) + (other.negErr/other.value)) return Err(value, posErr, negErr) def __pow__(self, y): value = self.value**y.value posErr = (self.value + self.posErr)**(y.value + y.posErr) - value negErr = value - (self.value - self.negErr)**(y.value - y.negErr) return Err(value, posErr, negErr) def __rpow__(self, y): value = y.value**self.value posErr = (y.value + y.posErr)**(self.value + self.posErr) - value negErr = value - (y.value - y.negErr)**(self.value - self.negErr) return Err(value, posErr, negErr) def __coerce__(self, other): if isinstance(other, Err): return self, other try: return self, Err(float(other)) except ValueError: pass def ApplyFunc(self, func): value = func(self.value) posErr = func(self.value + self.posErr) - value negErr = value - func(self.value - self.negErr) return Err(value, posErr, negErr) def ArrayOfErr(errArray, posErr=0., negErr=None): ''' Builds a Numeric array of Err() objects given an array and a +ve or both a +ve and -ve errorval Example: egErr = ArrayOfErr([909., 802., 677., 585., 560., 548.], 1.0) eg2Err = ArrayOfErr([909., 802., 677., 585., 560., 548.], 1.0, 1.5) ''' valArray = asarray(errArray) arrayLength = valArray.shape[0] errs = repeat(array([Err(0.0, posErr, negErr)], PyObject), arrayLength) return valArray + errs def PrimeVals(errArray): ''' Extract a Numeric array with just the prime value of the Err() objects ''' li = [] for i in errArray: li.append(i.value) return asarray(li) def PosErrs(errArray): ''' Return a Numeric array with the posErr values of the Err() objects ''' li = [] for i in errArray: li.append(i.posErr) return asarray(li) def MaxVals(errArray): ''' Return a Numeric array with the prime+posErr values of the Err() objects ''' li = [] for i in errArray: li.append(i.value + i.posErr) return asarray(li) def NegErrs(errArray): ''' Return a Numeric array with the negErr values of the Err() objects ''' li = [] for i in errArray: li.append(i.negErr) return asarray(li) def MinVals(errArray): ''' Return a Numeric array with the prime-negArr values of the Err() objects ''' li = [] for i in errArray: li.append(i.value - i.negErr) return asarray(li) def ErrToFloatArrays(errArray): ''' Return a Numeric array with 3 rows: row 1: the prime value of the Err() objects row 2: the prime+posErr values of the Err() objects row 3: the prime-negErr values of the Err() objects ''' r1 = PrimeVals(errArray) r2 = MaxVals(errArray) r3 = MinVals(errArray) return array([r1, r2, r3]) def FloatToErrArrays(floatArray): ''' Convert a Numeric array of the form produced by ErrToFloatArrays, which contains 3 rows, to an errArray ''' r1 = floatArray[0] r2 = floatArray[1]-r1 r3 = r1-floatArray[2] return asarray(map(Err,r1,r2,r3), PyObject) def ApplyUfuncToErr(errArray, func): ''' Example: a = ArrayOfErr([99., 82., 67., 58., 50., 54.], 1.0) b = ApplyUfuncToErr(a, log) # This means log(a) ''' a = ErrToFloatArrays(errArray) b = func(a) c = FloatToErrArrays(b) return c -- -- ___________________________________________________________ Sign-up for Ads Free at Mail.com http://promo.mail.com/adsfreejump.htm

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problem building scipy on win32
by Alexandre Gillet March 11, 2004

March 11, 2004

Hi, I am trying to build SciPy-0.2.0_alpha_200.4161. I did follow the note from Pearu Peterson (http://cens.ioc.ee/~pearu/scipy/BUILD_WIN32.html) I am not using the cvs version, but I did use the cvs version of scipy_core for installing it. Then I cd in SciPy-0.2.0_alpha_200.4161 and type msys.py python setup.py build. I am now getting the following error: /building 'scipy_base.fastumath' extension Traceback (most recent call last): File "setup.py", line 111, in ? setup_package() File "setup.py", line 101, in setup_package url = "http://www.scipy.org", File "scipy_core\scipy_distutils\core.py", line 42, in setup return old_setup(**new_attr) File "c:\Python23\lib\distutils\core.py", line 149, in setup dist.run_commands() File "c:\Python23\lib\distutils\dist.py", line 907, in run_commands self.run_command(cmd) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "c:\Python23\lib\distutils\command\build.py", line 107, in run self.run_command(cmd_name) File "c:\Python23\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "c:\Python23\lib\distutils\command\build_ext.py", line 269, in run self.build_extensions() File "c:\Python23\lib\distutils\command\build_ext.py", line 395, in build_extensions self.build_extension(ext) File "scipy_core\scipy_distutils\command\build_ext.py", line 116, in build_extension res = old_build_ext.build_extension(self,ext) File "c:\Python23\lib\distutils\command\build_ext.py", line 492, in build_extension target_lang=language) File "c:\Python23\lib\distutils\ccompiler.py", line 843, in link_shared_object extra_preargs, extra_postargs, build_temp, target_lang) TypeError: link() takes exactly 13 arguments (14 given) Any Idea. I need to use that version of Scipy as the GA module seems not to work on later version, that version was installed on Linux and works fine for us. Thanks Alex /-- o Alexandre Gillet email: gillet(a)scripps.edu / The Scripps Research Institute, o Dept. Molecular Biology, MB-5, \ 10550 North Torrey Pines Road, o La Jolla, CA 92037-1000, USA. / tel: (858) 784-2053 o fax: (858) 784-2860 / /

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latest scipy CVS fails to build with python-2.1
by José Fonseca March 5, 2004

March 5, 2004

When trying to rebuild debian packages for lates CVS I noticed it fails to build with python-2.1. When "byte compiling" scipy_core python complains: ---- /usr/lib/python2.1/site-packages/scipy_distutils/system_info.py:770: SyntaxWarning: local name 'magic' in 'get_atlas_version' shadows use of 'magic' as global in nested scope 'atlas_version_c' def get_atlas_version(**config): ---- And when trying to build scipy it fails with: ---- building extension "atlas_version" sources creating build creating build/src global name 'magic' is not defined FOUND: include_dirs = ['/usr/include'] language = c library_dirs = ['/usr/lib'] libraries = ['f77blas', 'cblas', 'atlas'] define_macros = [('NO_ATLAS_INFO', 2)] Traceback (most recent call last): File "setup.py", line 125, in ? setup_package(ignore_packages) File "setup.py", line 98, in setup_package parent_path=local_path) File "setup.py", line 59, in get_packages config = setup_module.configuration(*args) File "/home/jfonseca/projects/debian/scipy/SciPy-0.2.1_253.3737/Lib/integrate/setup_integrate.py", line 23, in configuration linpack_lite = ('linpack_lite_src',{'sources':local_glob('linpack_lite','*.f')}) File "/home/jfonseca/projects/debian/scipy/SciPy-0.2.1_253.3737/Lib/integrate/setup_integrate.py", line 17, in local_glob return glob.glob(os.path.join(*((local_path,)+names))) NameError: global name 'local_path' is not defined ---- This must have been caused by some recent change in scipy_distutils which violates python 2.1 syntax. Python 2.2 and 2.3 build fine. Note that if there is no interest to support python 2.1 in scipy, I can drop those packages just as well. BTW, the reason scipy is not yet on debian official repository is that no sponsor replied my request... I'll incorporate some fixes resulting from the user feedback I received and try again. Regards, Jose Fonseca

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distutils, weave dependency of scipy/xplt/Mplot.py
by Arnd Baecker March 5, 2004

March 5, 2004

Hi, while tracking down a problem with scipy on the latest quantian 0.4.9.4 (based on Knoppix) we came across the following: A) weave dependency of scipy/xplt/Mplot.py In scipy/xplt/Mplot.py the function _getdir() uses weave to get a directory that the user has write access to. So commenting out the line weave = ppimport('weave'); _level_docs(weave) in scipy/__init__.py is not enough to remove any dependency on weave. Would it be possible to write a _getdir() which does not make use of weave ? Presumably this is not that critical, but in the quantian case python2.3-dev was not installed which contains distutils. This brings me to my second question: B) It seems that without distutils an `import weave` fails. Are distutils really necessary to _use_ weave ? (At least for scipy itself distutils seems only necessary to run scipy.test()) Best, Arnd

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FW: RFC: Chebychev polynomials
by Chuck Harris March 3, 2004

March 3, 2004

Hi all, I have written a small set of routines for dealing with Chebychev polynomials. I would like suggestions for improvements, extra functions to include etc. I use these functions often myself, and thought they might be useful to include in scipy. Where they might go is an open question. Perhaps a package of polynomial routines that also contained divided differences, Lagrange interpolation, Newton interpolation, a modern root finding routine, a routine for orthogonal polynomials over a given set of sample points, etc. I have written some of these and wonder what the general interest is. A question about power series. There are routines in scipy-base for manipulating power series, but the coefficients are ordered from high degree to low degree. This is okay for polynomials, maybe, but doesn't seem the most natural order when dealing with the initial entries in an infinite series. Is there any settled view on this? My own routine that converts Chebychev series to power series orders the coefficients from low degree to high degree and the Chebychev coefficients themselves are ordered in the same way. I have a few routines that might go into a misc package, specifically routines for equivalence relations, very useful for clustering, and a generator for permutations of a list. Any interest? The contouring functions in xplt have also proved useful as stand alone functions. It might be nice to break these out into their own module. I think it might be nice to have separate functions for various spline operations also : B-splines, splines in tension, not-a-knot end conditions, natural splines, etc. The current single function call is hard to understand in line, and in any case, python it the natural language in which to produce such a monstrosity. I have attached the Chebychev module. Feedback welcome. Chuck

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testing
by Chuck Harris March 3, 2004

March 3, 2004

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misprint & system_info.py problem
by Arnd Baecker March 2, 2004

March 2, 2004

Hi, I just checked out the CVS version (scipy.__version__, '0.2.1_253.3734' ) and found two small issues a) >>> help("scipy.xplt") File "/opt/python/lib/python2.3/site-packages/scipy/optimize/optimize.py", line 268 if (c<=0) or (i%3)==2): ^ SyntaxError: invalid syntax Removing the additional bracket fixes the problem. b) python scipy_core/scipy_distutils/system_info.py gives the following error (shortened, full output at the end): python scipy_core/scipy_distutils/system_info.py atlas_blas_info: [...] atlas_blas_threads_info: [...] atlas_info: [...] system_info.atlas_info [...] atlas_threads_info: [...] blas_info: [...] blas_opt_info: Traceback (most recent call last): File "scipy_core/scipy_distutils/system_info.py", line 1190, in ? show_all() File "scipy_core/scipy_distutils/system_info.py", line 1187, in show_all r = c.get_info() File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 279, in get_info self.calc_info() File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 930, in calc_info atlas_version = get_atlas_version(**version_info) File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 771, in get_atlas_version from scipy_distutils.core import Extension, setup ImportError: No module named scipy_distutils.core This happens before doing a scipy installation, i.e. if there are no scipy* in site-packages. After the installation `python scipy_core/scipy_distutils/system_info.py` works fine. This may have been like this for quite a while as normally I don't remove the scipy* directories in site-packages. Many thanks, Arnd Full output: ----------- python scipy_core/scipy_distutils/system_info.py atlas_blas_info: ( library_dirs = /opt/python/lib:/usr/local/lib:/usr/lib ) ( paths: /opt/python/lib/libf77blas.a ) ( paths: /opt/python/lib/libcblas.a ) ( paths: /opt/python/lib/libatlas.a ) system_info.atlas_blas_info ( include_dirs = /usr/local/include:/usr/include:/opt/python/include ) ( paths: /opt/python/lib/cblas.h ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/opt/python/lib'] language = c include_dirs = ['/opt/python/lib'] atlas_blas_threads_info: ( library_dirs = /opt/python/lib:/usr/local/lib:/usr/lib ) ( paths: /opt/python/lib/libatlas.a ) system_info.atlas_blas_threads_info NOT AVAILABLE atlas_info: ( library_dirs = /opt/python/lib:/usr/local/lib:/usr/lib ) ( paths: /opt/python/lib/libf77blas.a ) ( paths: /opt/python/lib/libcblas.a ) ( paths: /opt/python/lib/libatlas.a ) ( paths: /opt/python/lib/liblapack.a ) system_info.atlas_info ( include_dirs = /usr/local/include:/usr/include:/opt/python/include ) ( paths: /opt/python/lib/cblas.h ) FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/opt/python/lib'] language = f77 include_dirs = ['/opt/python/lib'] atlas_threads_info: ( library_dirs = /opt/python/lib:/usr/local/lib:/usr/lib ) ( paths: /opt/python/lib/libatlas.a ) system_info.atlas_threads_info NOT AVAILABLE blas_info: ( library_dirs = /opt/python/lib:/usr/local/lib:/usr/lib ) ( paths: /usr/lib/libblas.so ) FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 blas_opt_info: Traceback (most recent call last): File "scipy_core/scipy_distutils/system_info.py", line 1190, in ? show_all() File "scipy_core/scipy_distutils/system_info.py", line 1187, in show_all r = c.get_info() File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 279, in get_info self.calc_info() File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 930, in calc_info atlas_version = get_atlas_version(**version_info) File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 771, in get_atlas_version from scipy_distutils.core import Extension, setup ImportError: No module named scipy_distutils.core

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