[Numpy-discussion] OT: A Way to Approximate and Compress a 3D Surface
Francesc Altet
faltet@carabos....
Tue Nov 20 12:43:44 CST 2007
A Tuesday 20 November 2007, Geoffrey Zhu escrigué:
> Hi Everyone,
>
> This is off topic for this mailing list but I don't know where else
> to ask.
>
> I have N tabulated data points { (x_i, y_i, z_i) } that describes a
> 3D surface. The surface is pretty "smooth." However, the number of
> data points is too large to be stored and manipulated efficiently. To
> make it easier to deal with, I am looking for an easy method to
> compress and approximate the data. Maybe the approximation can be
> described by far fewer number of coefficients.
>
> If you can give me some hints about possible numpy or non-numpy
> solutions or let me know where is better to ask this kind of
> question, I would really appreciate it.
First, a good and easy try would be to use PyTables. It does support
on-the-flight compression, that is, allows you to access compressed
dataset slices without decompressing the complete dataset. This, in
combination with a handy 'shuffle' filter (also included), allows for
pretty good compression ratios on numerical data. See [1] [2] for a
discussion on how to use and what you can expect from a
compressor/shuffle process on PyTables.
Also, if you can afford lossy compression, you may want to try
truncation (quantization) before compressing as it does benefit the
compression rate quite a lot. Feel free to experiment with the next
function (Jeffrey Whittaker was the original author):
def _quantize(data,least_significant_digit):
"""quantize data to improve compression.
data is quantized using around(scale*data)/scale,
where scale is 2**bits, and bits is determined from
the least_significant_digit.
For example, if least_significant_digit=1, bits will be 4."""
precision = 10.**-least_significant_digit
exp = math.log(precision,10)
if exp < 0:
exp = int(math.floor(exp))
else:
exp = int(math.ceil(exp))
bits = math.ceil(math.log(10.**-exp,2))
scale = 2.**bits
return numpy.around(scale*data)/scale
[1] http://www.pytables.org/docs/manual/ch05.html#compressionIssues
[2] http://www.pytables.org/docs/manual/ch05.html#ShufflingOptim
Cheers,
--
>0,0< Francesc Altet http://www.carabos.com/
V V Cárabos Coop. V. Enjoy Data
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