[SciPy-user] histogramdd once more

David Huard david.huard@gmail....
Fri Feb 15 10:25:22 CST 2008


Chris,

Thanks again for the bug report.

I implemented a solution where you need only one axes-swapping pass, no
matter what.

I just submitted the fix into SVN and the test you sent me passes. Maybe
check the fix  does the appropriate thing for you too.

Cheers,

David


2008/2/15, Chris Lee <c.j.lee@tnw.utwente.nl>:
>
> Hi All,
>
> I didn't strip all of the debug print comments from the earlier snippet.
> I think this is clean
>
> def histogramdd(sample, bins=10, range=None, normed=False, weights=None):
>     """histogramdd(sample, bins=10, range=None, normed=False,
> weights=None)
>
>     Return the N-dimensional histogram of the sample.
>
>     Parameters:
>
>         sample : sequence or array
>             A sequence containing N arrays or an NxM array. Input data.
>
>         bins : sequence or scalar
>             A sequence of edge arrays, a sequence of bin counts, or a
> scalar
>             which is the bin count for all dimensions. Default is 10.
>
>         range : sequence
>             A sequence of lower and upper bin edges. Default is [min,
> max].
>
>         normed : boolean
>             If False, return the number of samples in each bin, if True,
>             returns the density.
>
>         weights : array
>             Array of weights.  The weights are normed only if normed is
> True.
>             Should the sum of the weights not equal N, the total bin
> count will
>             not be equal to the number of samples.
>
>     Returns:
>
>         hist : array
>             Histogram array.
>
>         edges : list
>             List of arrays defining the lower bin edges.
>
>     SeeAlso:
>
>         histogram
>
>     Example
>
>         >>> x = random.randn(100,3)
>         >>> hist3d, edges = histogramdd(x, bins = (5, 6, 7))
>
>     """
>
>     try:
>         # Sample is an ND-array.
>         N, D = sample.shape
>     except (AttributeError, ValueError):
>         # Sample is a sequence of 1D arrays.
>         sample = atleast_2d(sample).T
>         N, D = sample.shape
>     nbin = empty(D, int)
>     edges = D*[None]
>     dedges = D*[None]
>     if weights is not None:
>         weights = asarray(weights)
>
>     try:
>         M = len(bins)
>         if M != D:
>             raise AttributeError, 'The dimension of bins must be a equal
> to the dimension of the sample x.'
>     except TypeError:
>         bins = D*[bins]
>
>     # Select range for each dimension
>     # Used only if number of bins is given.
>     if range is None:
>         smin = atleast_1d(array(sample.min(0), float))
>         smax = atleast_1d(array(sample.max(0), float))
>     else:
>         smin = zeros(D)
>         smax = zeros(D)
>         for i in arange(D):
>             smin[i], smax[i] = range[i]
>
>     # Make sure the bins have a finite width.
>     for i in arange(len(smin)):
>         if smin[i] == smax[i]:
>             smin[i] = smin[i] - .5
>             smax[i] = smax[i] + .5
>
>     # Create edge arrays
>     for i in arange(D):
>         if isscalar(bins[i]):
>             nbin[i] = bins[i] + 2 # +2 for outlier bins
>             edges[i] = linspace(smin[i], smax[i], nbin[i]-1)
>         else:
>             edges[i] = asarray(bins[i], float)
>             nbin[i] = len(edges[i])+1  # +1 for outlier bins
>         dedges[i] = diff(edges[i])
>
>     nbin =  asarray(nbin)
>
>     # Compute the bin number each sample falls into.
>     Ncount = {}
>     for i in arange(D):
>         Ncount[i] = digitize(sample[:,i], edges[i])
>
>     # Using digitize, values that fall on an edge are put in the right
> bin.
>     # For the rightmost bin, we want values equal to the right
>     # edge to be counted in the last bin, and not as an outlier.
>     outliers = zeros(N, int)
>     for i in arange(D):
>         # Rounding precision
>         decimal = int(-log10(dedges[i].min())) +6
>         # Find which points are on the rightmost edge.
>         on_edge = where(around(sample[:,i], decimal) ==
> around(edges[i][-1], decimal))[0]
>         # Shift these points one bin to the left.
>         Ncount[i][on_edge] -= 1
>
>     # Flattened histogram matrix (1D)
>     hist = zeros(nbin.prod(), int)
>
>     # Compute the sample indices in the flattened histogram matrix.
>     ni = nbin.argsort()
>     shape = []
>     xy = zeros(N, int)
>     for i in arange(0, D-1):
>         xy += Ncount[ni[i]] * nbin[ni[i+1:]].prod()
>     xy += Ncount[ni[-1]]
>
>     # Compute the number of repetitions in xy and assign it to the
> flattened histmat.
>     if len(xy) == 0:
>         return zeros(nbin-2, int), edges
>
>     flatcount = bincount(xy, weights)
>     a = arange(len(flatcount))
>     hist[a] = flatcount
>     # Shape into a proper matrix
>     hist = hist.reshape(sort(nbin))
>     mustPermute = True
>     while mustPermute:
>         nothingChanged = True
>         for i in arange(nbin.size):
>             j = ni[i]
>             if j != i:
>                 nothingChanged = False
>             hist = hist.swapaxes(i,j)
>             ni[i],ni[j] = ni[j],ni[i]
>         if nothingChanged:
>             mustPermute = False
>     #print "THis is after swapping the axis ", hist.shape
>     # Remove outliers (indices 0 and -1 for each dimension).
>     core = D*[slice(1,-1)]
>     hist = hist[core]
>
>     # Normalize if normed is True
>     if normed:
>         s = hist.sum()
>         for i in arange(D):
>             shape = ones(D, int)
>             shape[i] = nbin[i]-2
>             hist = hist / dedges[i].reshape(shape)
>         hist /= s
>
>     return hist, edges
>
> --
> **********************************************
> *  Chris Lee                                 *
> *  Laser physics and nonlinear optics group  *
> *  MESA+ Institute                           *
> *  University of Twente                      *
> *  Phone: ++31 (0)53 489 3968                *
> *  fax: ++31 (0) 53 489 1102                 *
> **********************************************
>
> _______________________________________________
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> SciPy-user@scipy.org
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>
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