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@llimllib /jenks2.py
Last active Apr 12, 2016

import json
from pprint import pprint as pp
def jenks_matrices_init(data, n_classes):
#fill the matrices with data+1 arrays of n_classes 0s
lower_class_limits = []
variance_combinations = []
for i in xrange(0, len(data)+1):
temp1 = []
temp2 = []
for j in xrange(0, n_classes+1):
temp1.append(0.)
temp2.append(0.)
lower_class_limits.append(temp1)
variance_combinations.append(temp2)
inf = float('inf')
for i in xrange(1, n_classes+1):
lower_class_limits[1][i] = 1.
variance_combinations[1][i] = 0.
for j in xrange(2, len(data)+1):
variance_combinations[j][i] = inf
return lower_class_limits, variance_combinations
def jenks_matrices(data, n_classes):
lower_class_limits, variance_combinations = jenks_matrices_init(data, n_classes)
variance = 0.0
for l in xrange(2, len(data)+1):
sum = 0.0
sum_squares = 0.0
w = 0.0
for m in xrange(1, l+1):
# `III` originally
lower_class_limit = l - m + 1
val = data[lower_class_limit-1]
# here we're estimating variance for each potential classing
# of the data, for each potential number of classes. `w`
# is the number of data points considered so far.
w += 1
# increase the current sum and sum-of-squares
sum += val
sum_squares += val * val
# the variance at this point in the sequence is the difference
# between the sum of squares and the total x 2, over the number
# of samples.
variance = sum_squares - (sum * sum) / w
i4 = lower_class_limit - 1
if i4 != 0:
for j in xrange(2, n_classes+1):
if variance_combinations[l][j] >= (variance + variance_combinations[i4][j - 1]):
lower_class_limits[l][j] = lower_class_limit
variance_combinations[l][j] = variance + variance_combinations[i4][j - 1]
lower_class_limits[l][1] = 1.
variance_combinations[l][1] = variance
return lower_class_limits, variance_combinations
def get_jenks_breaks(data, lower_class_limits, n_classes):
k = len(data) - 1
kclass = [0.] * (n_classes+1)
countNum = n_classes
kclass[n_classes] = data[len(data) - 1]
kclass[0] = data[0]
while countNum > 1:
elt = int(lower_class_limits[k][countNum] - 2)
kclass[countNum - 1] = data[elt]
k = int(lower_class_limits[k][countNum] - 1)
countNum -= 1
return kclass
def jenks(data, n_classes):
if n_classes > len(data): return
data.sort()
lower_class_limits, _ = jenks_matrices(data, n_classes)
return get_jenks_breaks(data, lower_class_limits, n_classes)
def main():
pp(jenks(json.load(open('test.json')), 5))
if __name__ == "__main__":
main()
$ python -mcProfile -scumulative jenks2.py
[0.0028109620325267315,
2.0935479691252112,
4.205495140049607,
6.178148351609707,
8.09175917180255,
9.997982932254672]
30199 function calls (30116 primitive calls) in 4.253 seconds
Ordered by: cumulative time
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.001 0.001 4.253 4.253 jenks2.py:1(<module>)
1 0.000 0.000 4.250 4.250 jenks2.py:93(main)
1 0.000 0.000 4.248 4.248 jenks2.py:82(jenks)
1 4.239 4.239 4.248 4.248 jenks2.py:26(jenks_matrices)
1 0.006 0.006 0.009 0.009 jenks2.py:4(jenks_matrices_init)
1 0.000 0.000 0.003 0.003 __init__.py:99(<module>)
28392 0.002 0.000 0.002 0.000 {method 'append' of 'list' objects}
1 0.000 0.000 0.002 0.002 decoder.py:2(<module>)
6 0.000 0.000 0.002 0.000 re.py:188(compile)
6 0.000 0.000 0.002 0.000 re.py:226(_compile)
6 0.000 0.000 0.002 0.000 sre_compile.py:495(compile)
6 0.000 0.000 0.001 0.000 sre_compile.py:480(_code)
1 0.000 0.000 0.001 0.001 scanner.py:2(<module>)
1 0.000 0.000 0.001 0.001 __init__.py:245(load)
1 0.000 0.000 0.001 0.001 encoder.py:2(<module>)
1 0.000 0.000 0.001 0.001 __init__.py:281(loads)
1 0.000 0.000 0.001 0.001 decoder.py:361(decode)
1 0.001 0.001 0.001 0.001 decoder.py:372(raw_decode)
26/6 0.000 0.000 0.001 0.000 sre_compile.py:32(_compile)
6 0.000 0.000 0.001 0.000 sre_parse.py:663(parse)
13/6 0.000 0.000 0.001 0.000 sre_parse.py:301(_parse_sub)
14 0.000 0.000 0.001 0.000 sre_compile.py:178(_compile_charset)
15/6 0.000 0.000 0.001 0.000 sre_parse.py:379(_parse)
14 0.000 0.000 0.001 0.000 sre_compile.py:207(_optimize_charset)
1 0.000 0.000 0.001 0.001 decoder.py:17(_floatconstants)
1 0.000 0.000 0.000 0.000 {method 'decode' of 'str' objects}
1 0.000 0.000 0.000 0.000 __init__.py:71(search_function)
1 0.000 0.000 0.000 0.000 {__import__}
1 0.000 0.000 0.000 0.000 {method 'sort' of 'list' objects}
1 0.000 0.000 0.000 0.000 hex_codec.py:8(<module>)
6 0.000 0.000 0.000 0.000 sre_compile.py:361(_compile_info)
1 0.000 0.000 0.000 0.000 pprint.py:35(<module>)
1 0.000 0.000 0.000 0.000 pprint.py:52(pprint)
1 0.000 0.000 0.000 0.000 pprint.py:113(pprint)
7/1 0.000 0.000 0.000 0.000 pprint.py:129(_format)
4 0.000 0.000 0.000 0.000 sre_compile.py:258(_mk_bitmap)
94 0.000 0.000 0.000 0.000 sre_parse.py:201(get)
118 0.000 0.000 0.000 0.000 sre_parse.py:182(__next)
35/15 0.000 0.000 0.000 0.000 sre_parse.py:140(getwidth)
7 0.000 0.000 0.000 0.000 pprint.py:228(_repr)
7 0.000 0.000 0.000 0.000 pprint.py:237(format)
13/7 0.000 0.000 0.000 0.000 pprint.py:247(_safe_repr)
91 0.000 0.000 0.000 0.000 sre_parse.py:130(__getitem__)
18 0.000 0.000 0.000 0.000 sre_parse.py:225(_class_escape)
453/438 0.000 0.000 0.000 0.000 {len}
80 0.000 0.000 0.000 0.000 sre_parse.py:195(match)
111 0.000 0.000 0.000 0.000 {isinstance}
14 0.000 0.000 0.000 0.000 {method 'write' of 'file' objects}
1 0.000 0.000 0.000 0.000 {method 'read' of 'file' objects}
73 0.000 0.000 0.000 0.000 {issubclass}
12 0.000 0.000 0.000 0.000 {repr}
50 0.000 0.000 0.000 0.000 sre_parse.py:126(__len__)
9 0.000 0.000 0.000 0.000 sre_compile.py:354(_simple)
32 0.000 0.000 0.000 0.000 {method 'format' of 'str' objects}
6 0.000 0.000 0.000 0.000 sre_parse.py:178(__init__)
56 0.000 0.000 0.000 0.000 {min}
25 0.000 0.000 0.000 0.000 sre_parse.py:138(append)
1 0.000 0.000 0.000 0.000 hex_codec.py:70(getregentry)
54 0.000 0.000 0.000 0.000 sre_compile.py:24(_identityfunction)
26 0.000 0.000 0.000 0.000 sre_parse.py:90(__init__)
1 0.000 0.000 0.000 0.000 jenks2.py:66(get_jenks_breaks)
1 0.000 0.000 0.000 0.000 {open}
38 0.000 0.000 0.000 0.000 {method 'get' of 'dict' objects}
6 0.000 0.000 0.000 0.000 {_sre.compile}
12 0.000 0.000 0.000 0.000 sre_compile.py:474(isstring)
1 0.000 0.000 0.000 0.000 decoder.py:304(__init__)
1 0.000 0.000 0.000 0.000 {_struct.unpack}
32 0.000 0.000 0.000 0.000 {chr}
8 0.000 0.000 0.000 0.000 {range}
1 0.000 0.000 0.000 0.000 __init__.py:49(normalize_encoding)
1 0.000 0.000 0.000 0.000 codecs.py:77(__new__)
6 0.000 0.000 0.000 0.000 sre_parse.py:72(opengroup)
32 0.000 0.000 0.000 0.000 {method 'setdefault' of 'dict' objects}
1 0.000 0.000 0.000 0.000 hex_codec.py:27(hex_decode)
4 0.000 0.000 0.000 0.000 sre_parse.py:257(_escape)
6 0.000 0.000 0.000 0.000 sre_parse.py:83(closegroup)
12 0.000 0.000 0.000 0.000 {method 'startswith' of 'str' objects}
6 0.000 0.000 0.000 0.000 sre_parse.py:67(__init__)
1 0.000 0.000 0.000 0.000 {binascii.a2b_hex}
1 0.000 0.000 0.000 0.000 pprint.py:82(__init__)
2 0.000 0.000 0.000 0.000 {method 'match' of '_sre.SRE_Pattern' objects}
20 0.000 0.000 0.000 0.000 {getattr}
1 0.000 0.000 0.000 0.000 encoder.py:102(__init__)
9 0.000 0.000 0.000 0.000 sre_parse.py:134(__setitem__)
2 0.000 0.000 0.000 0.000 {method 'end' of '_sre.SRE_Match' objects}
15 0.000 0.000 0.000 0.000 {ord}
4 0.000 0.000 0.000 0.000 {max}
1 0.000 0.000 0.000 0.000 encoder.py:71(JSONEncoder)
2 0.000 0.000 0.000 0.000 {method 'join' of 'str' objects}
1 0.000 0.000 0.000 0.000 {method 'split' of 'str' objects}
4 0.000 0.000 0.000 0.000 {method 'extend' of 'list' objects}
8 0.000 0.000 0.000 0.000 {id}
1 0.000 0.000 0.000 0.000 hex_codec.py:62(StreamWriter)
6 0.000 0.000 0.000 0.000 {method 'items' of 'dict' objects}
1 0.000 0.000 0.000 0.000 decoder.py:274(JSONDecoder)
6 0.000 0.000 0.000 0.000 {method 'remove' of 'list' objects}
1 0.000 0.000 0.000 0.000 pprint.py:81(PrettyPrinter)
1 0.000 0.000 0.000 0.000 {built-in method __new__ of type object at 0x10457d148}
1 0.000 0.000 0.000 0.000 hex_codec.py:65(StreamReader)
1 0.000 0.000 0.000 0.000 {method 'disable' of '_lsprof.Profiler' objects}
1 0.000 0.000 0.000 0.000 hex_codec.py:57(IncrementalDecoder)
1 0.000 0.000 0.000 0.000 hex_codec.py:52(IncrementalEncoder)
1 0.000 0.000 0.000 0.000 hex_codec.py:45(Codec)
1 0.000 0.000 0.000 0.000 {hasattr}
1 0.000 0.000 0.000 0.000 {method 'translate' of 'str' objects}
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@kootenpv

Seems wrong?

jenks(range(10), 2)
[0, 3, 9]
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