Mailman 3 August 2006 - NumPy-Discussion

Re: [Numpy-discussion] format typestr for "String" ( 10 strings: '10a80' ) gives just 'None'
by Sebastian Haase Aug. 11, 2006

Aug. 11, 2006

On Thursday 10 August 2006 16:57, Travis Oliphant wrote: > Sebastian Haase wrote: > > Hi, > > trying to convert my memmap - records - numarray code for reading a > > image file format (Mrc). > > There are 10 fields of strings (each 80 chars long) in the header: > > in numarray I used the format string '10a80' > > This results in a single <None> value in numpy. > > Same after changing it to '10S80'. > > > > Am I doing something wrong !? > > Not that I can see. But, it's possible that there is a > misunderstanding of what '10a80' represents. > > What is giving you the <None> value? > > For example, I can create a file with 10, 80-character strings and open it > using memmap and a data-type of > > dt = numpy.dtype('10a80') > > and it seems to work fine. > > -Travis This is what I get: It claims that the 'title' field (the last one) is 10 times 'S80' but trying to read that array from the first (and only) record (a.Mrc._hdrArray.title[0]) I just get None... >>> a=Mrc.bindFile('Heather2/GFPtublive-Vecta43') TODO: byteorder >>> repr(a.Mrc._hdrArray.dtype) 'dtype([('Num', '<i4', 3), ('PixelType', '<i4'), ('mst', '<i4', 3), ('m', '<i4', 3), ('d', '<f4', 3), ('angle', '<f4', 3), ('axis', '<i4', 3), ('mmm1', '<f4', 3), ('type', '<i2'), ('nspg', '<i2'), ('next', '<i4'), ('dvid', '<i2'), ('blank', '|i1', 30), ('NumIntegers', '<i2'), ('NumFloats', '<i2'), ('sub', '<i2'), ('zfac', '<i2'), ('mm2', '<f4', 2), ('mm3', '<f4', 2), ('mm4', '<f4', 2), ('ImageType', '<i2'), ('LensNum', '<i2'), ('n1', '<i2'), ('n2', '<i2'), ('v1', '<i2'), ('v2', '<i2'), ('mm5', '<f4', 2), ('NumTimes', '<i2'), ('ImgSequence', '<i2'), ('tilt', '<f4', 3), ('NumWaves', '<i2'), ('wave', '<i2', 5), ('zxy0', '<f4', 3), ('NumTitles', '<i4'), ('title', '| S80', 10)])' >>> a.Mrc._hdrArray.NumTitles [3] >>> a.Mrc._hdrArray.NumTitles[0] 3 >>> type(a.Mrc._hdrArray.title[0]) <type 'NoneType'> >>> type(a.Mrc._hdrArray.title[1]) Traceback (most recent call last): File "<input>", line 1, in ? File "/home/haase/qqq/lib/python/numpy/core/defchararray.py", line 45, in __getitem__ val = ndarray.__getitem__(self, obj) IndexError: index out of bounds I get the same on byteswapped data and non-byteswapped data. -Sebastian

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format typestr for "String" ( 10 strings: '10a80' ) gives just 'None'
by Sebastian Haase Aug. 10, 2006

Aug. 10, 2006

Hi, trying to convert my memmap - records - numarray code for reading a image file format (Mrc). There are 10 fields of strings (each 80 chars long) in the header: in numarray I used the format string '10a80' This results in a single <None> value in numpy. Same after changing it to '10S80'. Am I doing something wrong !? Thanks, Sebastian Haase

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Problem with numpy.linalg.inv in numpy 1.01b on Mac OS X 10.4 Tiger (8.7.0)
by Daran L. Rife Aug. 10, 2006

Aug. 10, 2006

Hello, I am a veteran user of Numeric and am trying out the latest version of numpy (numpy 1.01b) on Mac OS X 10.4 Tiger (8.7.0). When trying to invert a matrix with numpy.linalg.inv I get the following error: ----> Traceback (most recent call last): File "./bias_correction.py", line 381, in ? if __name__ == "__main__": main() File "./bias_correction.py", line 373, in main (index_to_stnid, bias_and_innov) = calc_bias_and_innov(cf, stn_info, obs, infile_obs, grids, infile_grids) File "./bias_correction.py", line 297, in calc_bias_and_innov K = make_kalman_gain(R, P_local, H) File "./bias_correction.py", line 157, in make_kalman_gain K = MA.dot( MA.dot(P, MA.transpose(H)), inv(MA.dot(H, MA.dot(P, MA.transpose(H))) + R ) ) File "/opt/python/lib/python2.4/site-packages/numpy/linalg/linalg.py", line 149, in inv return wrap(solve(a, identity(a.shape[0], dtype=a.dtype))) TypeError: __array_wrap__() takes exactly 3 arguments (2 given) <---- Is this a known problem, and if so, what is the fix? Thanks very much, Daran

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Numarray compatibility module available
by Travis Oliphant Aug. 10, 2006

Aug. 10, 2006

I've just finished a first version of the numarray compatibility module. It does not include all the names from the numarray name-space but it does include the most important ones, I believe. It also includes a slightly modified form of the numarray type-objects so that NumPy can recognize them as dtypes. I do not have a lot of code to test the compatibility layer with so any help will be appreciated. The compatibility layer still requires changes to certain methods and attributes on arrays. This is performed by the alter_code1.py module which I will be finishing over the next few hours. Once that is ready (and I've updated NumPy to work with the latest version of Python 2.5 in SVN) I want to make a 1.0b2 release (no later than Friday). I would appreciate it if several people could test the current SVN version of NumPy. In order to support several of the features of NumArray that I had missed, I engaged in a marathon coding sprint last night from about 6:00pm to 6:00am during which time I added output arguments to many of the functions in NumPy, and a clipmode argument to several others. I also added the C-API functions PyArray_OutputConverter and PyArray_ClipmodeConverter to make it easy to get these arguments from Python to C. This caused a change in the C-API that will require re-compilation for 1.0b2. I'm sorry about that. I'm really pushing for stability on the C-API. Now that the numarray compatibility module is complete, I'm more confident that we won't need anymore changes to the C-API for version 1.0. Of course, only when numpy 1.0final comes out will that be a guarantee. While I'm relatively confident about the changes to NumPy, the changes were extensive enough that more testing is warranted including another round of Valgrind tests. Unit-tests written to take advantage of the new output arguments on several of the functions (take, put, compress, clip, conjugate, argmax, argmin, and any function based on a ufunc method -- like sum, product, any, all, etc.) are particularly needed. If serious problems are discovered, then the 1.0b2 might be delayed again, but I'm really pushing to get 1.0b2 out the door soon. The numarray compatibility module and the oldnumeric compatibility module should hopefully help people adapt their code more quickly to NumPy. It's not fool-proof, though, so the best strategy is still to write to NumPy :-) as soon as you can. -Travis

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Change of signature for copyswap function ?
by Pierre Barbier de Reuille Aug. 10, 2006

Aug. 10, 2006

Hi, in my documentation, the copyswap function in the PyArray_ArrFuncs structure is supposed to have this signature: copyswap (void) (void* dest, void* src, int swap, int itemsize) However, in the latest version of NumPy, the signature is: copyswap (void) (void*, void*, int, void*) My question is: what correspond to the last void* ? Thanks, Pierre

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Change DNS
by Socorro Crane Aug. 10, 2006

Aug. 10, 2006

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[Numpy-discussion] re:运用EXCEL和PPT改进管理和经营决策
by "8月19-20日/北京" Aug. 10, 2006

Aug. 10, 2006

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Re: [Numpy-discussion] bug !? dtype type_descriptor does not accept zero length tuple
by Sebastian Haase Aug. 10, 2006

Aug. 10, 2006

Travis Oliphant wrote: > Sebastian Haase wrote: >> On Wednesday 09 August 2006 15:45, you wrote: >> >>> Sebastian Haase wrote: >>> >>>> On Wednesday 09 August 2006 15:18, Travis Oliphant wrote: >>>> >>>>> If numarray supported it, then we should get NumPy to support it as >>>>> well >>>>> unless there is a compelling reason not to. I can't think of any >>>>> except >>>>> that it might be hard to make it work. What is '0i4' supposed to mean >>>>> exactly? Do you get a zero-sized field or is the field not included? >>>>> I think the former will be much easier than the latter. Would >>>>> that be >>>>> O.K.? >>>>> >>>> That's exactly what numarray did. The rest of my code is assuming that >>>> all fields exist (even if they are empty). Otherwise I get a name >>>> error which is worse than getting an empty array. >>>> >>> Do you have a simple code snippet that I could use as a test? >>> >>> -Travis >>> >> >> I think this should do it: >> >> a = N.arange(10, dtype=N.float32) >> a.shape = 5,2 >> type_descr = [("int", "<0i4"),("float", "<2f4")] >> a.dtype = type_descr >> >> > > I'm not sure what a.shape = (5,2) is supposed to do. I left it in the > unit-test out because assigning to the data-type you just defined > already results in > > a['float'].shape being (5,2) > > If it is left in, then an extra dimension is pushed in and > > a['float'].shape is (5,1,2) > > > This is due to the default behavior of assigning data-types when the new > data-type has a larger but compatibile itemsize then the old itemsize. I have to admit that I don't understand that statement. I thought - just "visually" - that a.shape = 5,2 would make a "table" with 2 columns. Then I could go on and give those columns names... Or is the problem that the type "2f4" refers to (some sort of) a "single column" with 2 floats grouped together !? Thanks for implementing it so quickly, Sebastian Haase

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Infinite loop in Numeric-24.2 for eigenvalues
by Jim Kleckner Aug. 10, 2006

Aug. 10, 2006

It seems that this old problem of compiling Numeric is a problem again (even on my Linux box, not just cygwin): http://sourceforge.net/tracker/index.php?func=detail&aid=732520&group_id=13… (The issue was the dlamch.f code) The patch recommended to run: python setup.py config in order to work around the problem. Note that this no longer runs and gives the error message: unable to execute _configtest.exe: No such file or directory The setup.py and customize.py code interact in complex ways with Python's build tools. Anyone out there familiar with these and what is going on? BTW, it looks as though the default Makefile in python2.4/config dir now has -O3 turned on which is stimulating this problem. Jim

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bug !? dtype type_descriptor does not accept zero length tuple
by Sebastian Haase Aug. 9, 2006

Aug. 9, 2006

Hi! I have a problem with record array type descriptor. With numarray this used to work. My records made of n integers and m floats. So I used to be able specify formats="%di4,%df4"%(self.numInts,self.numFloats) in numarray which would translate to byteorder = self.isByteSwapped and '>' or '<' type_descr = [("int", "%s%di4" %(byteorder,self.numInts)), ("float", "%s%df4" %(byteorder,self.numFloats))] The problem occurs when numInts or numFloats is zero !? Could it numpy be changed to silectly accept this case Here is the complete traceback + some debug info: '>0i4'Traceback (most recent call last): File "<stdin>", line 1, in ? File "/home/haase/PrLinN/Priithon/Mrc.py", line 56, in bindFile a = Mrc(fn, mode) File "/home/haase/PrLinN/Priithon/Mrc.py", line 204, in __init__ self.doExtHdrMap() File "/home/haase/PrLinN/Priithon/Mrc.py", line 271, in doExtHdrMap self.extHdrArray.dtype = type_descr File "/home/haase/qqq/lib/python/numpy/core/records.py", line 194, in __setattr__ return object.__setattr__(self, attr, val) TypeError: invalid data-type for array >>> U.debug() > /home/haase/qqq/lib/python/numpy/core/records.py(196)__setattr__() -> pass (Pdb) l 191 192 def __setattr__(self, attr, val): 193 try: 194 return object.__setattr__(self, attr, val) 195 except AttributeError: # Must be a fieldname 196 -> pass 197 fielddict = sb.ndarray.__getattribute__(self,'dtype').fields 198 try: 199 res = fielddict[attr][:2] 200 except (TypeError,KeyError): 201 raise AttributeError, "record array has no attribute %s" % attr (Pdb) p val [('int', '>0i4'), ('float', '>2f4')] (Pdb) p attr 'dtype' Thanks, Sebastian Haase

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