Eric Firing wrote:
Robert Cimrman wrote:
Eric Firing wrote:
Robert and any other spy users:
I have committed to svn a new axes method, spy3, that combines a modification of the functionality of both spy and spy2. I hope you can check it out. If it looks OK, then I would like to simply replace spy and spy2 with this combined version. In that case the pylab interface, which now gives access to spy and spy2, would have a single spy function which would access the new version. My suspicion is that spy is used almost entirely in interactive mode, and probably not by very many people, so that this changeover can be made quickly with little disruption to present users.
Attached is a script illustrating the difference in the way spy3 displays a matrix (it matches the way it is printed: first index is row number, second is column number, row number increases down) versus what spy and spy2 do (first index is X, second index is Y).
Also attached is the diff for spy3.
Users may want to comment in particular on the default for the "aspect" kwarg. Presently it is set to "equal" so that the shape of the plot is the shape of the array with square cells. This differs from spy and spy2. The rationale is that it gives the best picture of what the array looks like, including its shape.
Thumbs up :), just add the sparse-full matrix switch to the imshow branch too, if possible. But I am happy with it as it is.
The sparse-full difference only works with the plot mode; for an image there is no alternative to providing a value for every pixel, so I don't know of any way to optimize it for the case of sparse storage. A polygon collection could be used to achieve the same result in this case. I'm not sure it is a good idea, though, because there would be an advantage of not converting to a regular array only in the case where the array is so large that such a conversion would use a big chunk of memory, and in that case the polygons probably would be less than single-pixel size anyway, so one would be better off using the present symbol-plotting mode.
Yeah, I have tried to write it myself before I posted this message but found that it probably would not work well - nevertheless I asked :).
What could be done, though, is to raise an exception explaining that sparse matrices and the image mode don't like each other; as it is, the function spy3 just dies on asarray (should be st. like asarray( Z.todense() ))
In :import numpy as nm
In :import scipy.sparse as sp
In :a = nm.array( [[0, 1], [0,1], [2,3]] )
In :b = sp.csr_matrix( a )
In :gca().spy3( b )
exceptions.TypeError Traceback (most recent call last)
/usr/lib/python2.4/site-packages/matplotlib/axes.py in spy3(self, Z, precision, marker, markersize, aspect, **kwargs)
4378 if marker is None and markersize is None:
-> 4379 Z = asarray(Z)
4380 if precision is None: mask = Z!=0.
4381 else: mask = absolute(Z)>precision
/usr/lib/python2.4/site-packages/numarray/numarraycore.py in asarray(seq, type, typecode, dtype)
432 if isinstance(seq, _gen.NDArray) and type is None and typecode is None:
433 return seq
--> 434 return array(seq, type=type, typecode=typecode, copy=0, dtype=dtype)
436 inputarray = asarray # Obsolete synonym
/usr/lib/python2.4/site-packages/numarray/numarraycore.py in array(sequence, typecode, copy, savespace, type, shape, dtype)
415 if (hasattr(sequence,'__getitem__')
416 and hasattr(sequence,'__len__')):
--> 417 return fromlist(sequence,type,shape)
419 ##SEQUENCE is a scalar or unhandleable
/usr/lib/python2.4/site-packages/numarray/numarraycore.py in fromlist(seq, type, shape, check_overflow, typecode, dtype)
246 return arr
--> 248 if not len(seq) and type is None:
249 type = _nt.Long
/home/share/software/usr/lib/python2.4/site-packages/scipy/sparse/sparse.py in __len__(self)
163 def __len__(self):
164 # return self.getnnz()
--> 165 raise TypeError, "sparse matrix length is ambiguous; use getnnz()" \
166 " or shape"
Anyway, I'm glad it works for you. Thanks for checking.
Thanks for your fast help!