Mailman 3 January 2010 - NumPy-Discussion

wrong casting of augmented assignment statements
by Sebastian Walter 14 Jan '10

14 Jan '10

Hello, I have a question about the augmented assignment statements *=, +=, etc. Apparently, the casting of types is not working correctly. Is this known resp. intended behavior of numpy? (I'm using numpy.__version__ = '1.4.0.dev7039' on this machine but I remember a recent checkout of numpy yielded the same result). The problem is best explained at some examples: wrong casting from float to int:: In [1]: import numpy In [2]: x = numpy.ones(2,dtype=int) In [3]: y = 1.3 * numpy.ones(2,dtype=float) In [4]: z = x * y In [5]: z Out[5]: array([ 1.3, 1.3]) In [6]: x *= y In [7]: x Out[7]: array([1, 1]) In [8]: x.dtype Out[8]: dtype('int32') wrong casting from float to object:: In [1]: import numpy In [2]: import adolc In [3]: x = adolc.adouble(numpy.array([1,2,3],dtype=float)) In [4]: y = numpy.array([4,5,6],dtype=float) In [5]: x Out[5]: array([1(a), 2(a), 3(a)], dtype=object) In [6]: y Out[6]: array([ 4., 5., 6.]) In [7]: x * y Out[7]: array([4(a), 10(a), 18(a)], dtype=object) In [8]: y *= x In [9]: y Out[9]: array([ 4., 5., 6.]) It is inconsistent to the Python behavior:: In [9]: a = 1 In [10]: b = 1.3 In [11]: c = a * b In [12]: c Out[12]: 1.3 In [13]: a *= b In [14]: a Out[14]: 1.3 I would expect that numpy should at least raise an exception in the case of casting object to float. Any thoughts? regards, Sebastian

4 7

Getting Callbacks with arrays to work
by Jon Moore 14 Jan '10

14 Jan '10

Hi, I'm trying to build a differential equation integrator and later a stochastic differential equation integrator. I'm having trouble getting f2py to work where the callback itself receives an array from the Fortran routine does some work on it and then passes an array back. For the stoachastic integrator I'll need 2 callbacks both dealing with arrays. The idea is the code that never changes (ie the integrator) will be in Fortran and the code that changes (ie the callbacks defining differential equations) will be different for each problem. To test the idea I've written basic code which should pass an array back and forth between Python and Fortran if it works right. Here is some code which doesn't work properly:- SUBROUTINE CallbackTest(dv,v0,Vout,N) !IMPLICIT NONE cF2PY intent( hide ):: N INTEGER:: N, ic EXTERNAL:: dv DOUBLE PRECISION, DIMENSION( N ), INTENT(IN):: v0 DOUBLE PRECISION, DIMENSION( N ), INTENT(OUT):: Vout DOUBLE PRECISION, DIMENSION( N ):: Vnow DOUBLE PRECISION, DIMENSION( N ):: temp Vnow = v0 temp = dv(Vnow, N) DO ic = 1, N Vout( ic ) = temp(ic) END DO END SUBROUTINE CallbackTest When I test it with this python code I find the code just replicates the first term of the array! from numpy import * import callback as c def dV(v): print 'in Python dV: V is: ',v return v.copy() arr = array([2.0, 4.0, 6.0, 8.0]) print 'Arr is: ', arr output = c.CallbackTest(dV, arr) print 'Out is: ', output Arr is: [ 2. 4. 6. 8.] in Python dV: V is: [ 2. 4. 6. 8.] Out is: [ 2. 2. 2. 2.] Any ideas how I should do this, and also how do I get the code to work with implicit none not commented out? Thanks Jon

2 2

numpy1.4 dtype issues: scipy.stats & pytables
by Tim Michelsen 14 Jan '10

14 Jan '10

Hello, I experienced the following issue with numpy 1.4: scipy.stats: Python 2.6.2 (r262:71605, Apr 14 2009, 22:40:02) [MSC v.1500 32 bit (Intel)] on win32 import scipy.stats as st Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Python26\lib\site-packages\scipy\stats\__init__.py", line 7, in <module> from stats import * File "C:\Python26\lib\site-packages\scipy\stats\stats.py", line 203, in <module> from morestats import find_repeats #is only reference to scipy.stats File "C:\Python26\lib\site-packages\scipy\stats\morestats.py", line 7, in <module> import distributions File "C:\Python26\lib\site-packages\scipy\stats\distributions.py", line 27, in <module> import vonmises_cython File "numpy.pxd", line 30, in scipy.stats.vonmises_cython (scipy\stats\vonmises_cython.c:2939) ValueError: numpy.dtype does not appear to be the correct type object pytables: import tables Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Python26\lib\site-packages\tables\__init__.py", line 56, in <module> from tables.utilsExtension import getPyTablesVersion, getHDF5Version File "definitions.pxd", line 138, in tables.utilsExtension ValueError: numpy.dtype does not appear to be the correct type object Is this an error in numpy or no the other packages require update in the code? Thanks, Timmie

6 8

numpy sum table by category
by ms＠TheBrookhavenGroup.com 13 Jan '10

13 Jan '10

I have a csv file like this: Account, Symbol, Quantity, Price One,SPY,5,119.00 One,SPY,3,120.00 One,SPY,-2,125.00 One,GE,... One,GE,... Two,SPY, ... Three,GE, ... ... The data is much larger, could be 10,000 records. I can load it into a numpy array using matplotlib.mlab.csv2rec(). I learned several useful numpy functions and have been reading lots of documentation. However, I have not found a way to create a unique list of symbols and the Sum of their respective Quantity values. I want do various calculations on the data like pull out all the records for a given Account. The actual data has lots more columns and sometimes I may want to sum(Quantity*Price) by Account and Symbol. I'm attracted to numpy for speed but would welcome alternative suggestions. I tried unsuccessfully to install PyTables on my Ubuntu system and abandoned that avenue. Can anyone provide some examples on how to do this or point me to documentation? Much appreciated. _________________________________________________________ Marc Schwarzschild The Brookhaven Group, LLC 1-212-580-1175 Analytics for Hedge Fund Investors Risk it, carefully!

3 2

sphinx numpydoc fails due to no __init__ for class SignedType
by Peter Caldwell 12 Jan '10

12 Jan '10

I'm trying to use sphinx to build documentation for our project (CDAT) that uses numpy. I'm running into an exception due to numpy.numarray.numerictypes.SignedType not having an __init__ attribute, which causes problems with numpydoc. I'm sure there must be a workaround or I'm doing something wrong since the basic numpy documentation is created with sphinx! Suggestions? I'm using sphinx v1.0, numpy v1.3.0, and numpydoc v0.3.1on Redhat Enterprise 5.x. Big thanks, Peter ps - I'm sending this question to both Numpy-discussion and sphinx-dev@googlegroups because the issue lies at the intersection of these groups. Here's the error: ========================================================= Running Sphinx v1.0 loading pickled environment... not found building [html]: targets for 6835 source files that are out of date updating environment: 6835 added, 0 changed, 0 removed /usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/docscrape.py:117: UserWarning: Unknown section Unary Ufuncs: warn("Unknown section %s" % key) /usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/docscrape.py:117: UserWarning: Unknown section Binary Ufuncs: warn("Unknown section %s" % key) /usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/docscrape.py:117: UserWarning: Unknown section Seealso warn("Unknown section %s" % key) reading sources... [ 3%] output/lev0/numpy.numarray Exception occurred: File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/numpydoc.py", line 76, in mangle_signature 'initializes x; see ' in pydoc.getdoc(obj.__init__)): AttributeError: class SignedType has no attribute '__init__' The full traceback has been saved in /tmp/sphinx-err-fprbpu.log, if you want to report the issue to the author. Please also report this if it was a user error, so that a better error message can be provided next time. Send reports to sphinx-dev(a)googlegroups.com. Thanks! make: *** [html] Error 1 ===================================================== Here's the full traceback: ------------------------------------------------------------------------------------------------ # Sphinx version: 1.0 # Docutils version: 0.6 release Traceback (most recent call last): File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/cmdline.py", line 172, in main app.build(all_files, filenames) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/application.py", line 130, in build self.builder.build_update() File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/builders/__init__.py", line 265, in build_update 'out of date' % len(to_build)) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/builders/__init__.py", line 285, in build purple, length): File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/builders/__init__.py", line 131, in status_iterator for item in iterable: File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/environment.py", line 513, in update_generator self.read_doc(docname, app=app) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/environment.py", line 604, in read_doc pub.publish() File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/core.py", line 203, in publish self.settings) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/readers/__init__.py", line 69, in read self.parse() File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/readers/__init__.py", line 75, in parse self.parser.parse(self.input, document) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/__init__.py", line 157, in parse self.statemachine.run(inputlines, document, inliner=self.inliner) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 170, in run input_source=document['source']) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/statemachine.py", line 233, in run context, state, transitions) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/statemachine.py", line 421, in check_line return method(match, context, next_state) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2678, in underline self.section(title, source, style, lineno - 1, messages) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 323, in section self.new_subsection(title, lineno, messages) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 391, in new_subsection node=section_node, match_titles=1) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 278, in nested_parse node=node, match_titles=match_titles) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 195, in run results = StateMachineWS.run(self, input_lines, input_offset) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/statemachine.py", line 233, in run context, state, transitions) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/statemachine.py", line 421, in check_line return method(match, context, next_state) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2258, in explicit_markup nodelist, blank_finish = self.explicit_construct(match) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2270, in explicit_construct return method(self, expmatch) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2013, in directive directive_class, match, type_name, option_presets) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2062, in run_directive result = directive_instance.run() File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/autodoc.py", line 1106, in run nested_parse_with_titles(self.state, self.result, node) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/util/__init__.py", line 298, in nested_parse_with_titles return state.nested_parse(content, 0, node, match_titles=1) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 278, in nested_parse node=node, match_titles=match_titles) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 195, in run results = StateMachineWS.run(self, input_lines, input_offset) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/statemachine.py", line 233, in run context, state, transitions) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/statemachine.py", line 421, in check_line return method(match, context, next_state) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2260, in explicit_markup self.explicit_list(blank_finish) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2289, in explicit_list match_titles=self.state_machine.match_titles) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 315, in nested_list_parse node=node, match_titles=match_titles) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 195, in run results = StateMachineWS.run(self, input_lines, input_offset) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/statemachine.py", line 233, in run context, state, transitions) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/statemachine.py", line 421, in check_line return method(match, context, next_state) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2562, in explicit_markup nodelist, blank_finish = self.explicit_construct(match) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2270, in explicit_construct return method(self, expmatch) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2013, in directive directive_class, match, type_name, option_presets) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/docutils/parsers/rst/states.py", line 2062, in run_directive result = directive_instance.run() File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/autosummary/__init__.py", line 192, in run items = self.get_items(names) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/autosummary/__init__.py", line 265, in get_items sig = documenter.format_signature() File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/autodoc.py", line 879, in format_signature return ModuleLevelDocumenter.format_signature(self) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/autodoc.py", line 384, in format_signature self.object, self.options, args, retann) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/application.py", line 226, in emit_firstresult for result in self.emit(event, *args): File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/application.py", line 222, in emit result.append(callback(self, *args)) File "/usr/local/cdat/release/5.2d/lib/python2.5/site-packages/Sphinx-1.0dev_20091202-py2.5.egg/sphinx/ext/numpydoc.py", line 76, in mangle_signature 'initializes x; see ' in pydoc.getdoc(obj.__init__)): AttributeError: class SignedType has no attribute '__init__' -- Peter Caldwell Program for Climate Model Diagnosis and Intercomparison Lawrence Livermore National Lab PO Box 808, L-103 Livermore, CA 94551-0808 925-422-4197

1 0

TypeError: 'module' object is not callable
by Jankins 12 Jan '10

12 Jan '10

Hello, I want to use scipy.sparse.linalg.eigen function, but it keeps popping out error message: TypeError: 'module' object is not callable "eigen" is a module, but it has "__call__" method. Why couldn't I call scipy.sparse.linalg.eigen(...)? Thanks. Jankins

6 18

savetxt only saves real part of complex
by Neal Becker 11 Jan '10

11 Jan '10

Is this a bug? I think silently discarding the imaginary part is a bug.

1 0

Uninformative Error
by T J 10 Jan '10

10 Jan '10

When passing in a list of longs and asking that the dtype be a float (yes, losing precision), the error message is uninformative whenever the long is larger than the largest float. >>> x = 181626642333486640664316511479918087634811756599984861278481913634852446858952226941059178462566942027148832976486383692715763966132465634039844094073670028044755150133224694791817752891901042496950233943249209777416692569138779593594686170807571874640682826295728116325492852625325418526603207268018328608840 >>> array(x, dtype=float) OverflowError: long int too large to convert to float >>> array([x], dtype=float) ValueError: setting an array element with a sequence. The first error is informative, but the second is not and will occur anytime one tries to convert a python list containing longs which are too long. Is there a way this error message could be made more helpful?

1 0

Behaviour of vdot(array2d, array1d)
by Nikolas Tezak 10 Jan '10

10 Jan '10

Hi, I am new to this list, but I have been using scipy for a couple of months now with great satisfaction. Currently I have a problem: I diagonalize a hermitian complex matrix using the eigh routine from scipy.linalg (this is still a numpy question, see below) This returns the eigenvectors as columns of a 2d array. Now I would like to project a vector onto this new basis. I could either do: inital_state = array(...) #dtype=complex, shape=(dim,) coefficients = zeros( shape=(dim,), dtype=complex) matrix = array(...) #dtype=complex, shape=(dim, dim) eigenvalues, eigenvectors = eigh(matrix) for i in xrange(dim): coefficients[i] = vdot(eigenvalues[:, i], initial_state) But it seems to me after reading the documentation for vdot, that it should also be possible to do this without a loop: initial_state = array(...) #dtype=complex, shape=(dim,) matrix = array(...) #dtype=complex, shape=(dim, dim) eigenvalues, eigenvectors = eigh(matrix) coefficients = vdot( eigenvalues.transpose(), initial_state) However when I do this, vdot raises a ValueError complaining that the "vectors have different lengths". It seems that vdot (as opposed to dot) cannot handle arguments with different shape although the documentation suggests otherwise. I am using numpy version 1.3.0. Is this a bug or am I missing something? Regards, Nikolas

2 1

mvoid test error with svn
by Eric Firing 09 Jan '10

09 Jan '10

Building numpy from svn and then running numpy.test(), I get the following error: ERROR: Test filled w/ mvoid ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.6/dist-packages/numpy/ma/tests/test_core.py", line 506, in test_filled_w_mvoid a = mvoid(np.array((1, 2)), mask=[(0, 1)], dtype=ndtype) File "/usr/local/lib/python2.6/dist-packages/numpy/ma/core.py", line 5453, in __new__ _data = ndarray.__new__(self, (), dtype=dtype, buffer=data.data) TypeError: buffer is too small for requested array ---------------------------------------------------------------------- Ran 2505 tests in 10.478s FAILED (KNOWNFAIL=5, SKIP=4, errors=1) In [6]:numpy.version.version Out[6]:'1.5.0.dev8040' In [7]:!uname -a Linux manini 2.6.31-17-generic #54-Ubuntu SMP Thu Dec 10 16:20:31 UTC 2009 i686 GNU/Linux Eric

2 1