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# llimllib/jenks2.py

Last active Aug 3, 2017
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 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()
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 \$ 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() 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() 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() 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() 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() 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() 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() 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} 7 0.000 0.000 0.000 0.000 {method 'copy' of 'dict' objects}
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### kootenpv commented Mar 24, 2016

Seems wrong?

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