Open clegaard opened 4 years ago
It seems the standardize function adds a significant amount of reads to the underlying dataset. Calling the function on a dataset containing a single element seemingly causes 7 reads to be carried out.
ds_one = ds.take(1) def foo(): ds_center = ds_one.standardize(0, axis=1) s = ds_center[0] def bar(): from sklearn.preprocessing import StandardScaler scaler = StandardScaler() s = ds[0] scaler.fit(s.data) scaled = scaler.transform(s.data) mu = np.mean(scaled) std = np.std(scaled) def do_profile(func): print(f"######### PROFILING {func.__name__} #########") pr = cProfile.Profile(subcalls=False) pr.enable() func() pr.disable() s = io.StringIO() sortby = SortKey.TIME ps = pstats.Stats(pr, stream=s).sort_stats(sortby) ps.print_stats() # return s.getvalue() print(f"{s.getvalue()}\n") do_profile(foo) do_profile(bar)
######### PROFILING foo ######### 40119 function calls (39755 primitive calls) in 18.561 seconds Ordered by: internal time ncalls tottime percall cumtime percall filename:lineno(function) 7 17.962 2.566 18.073 2.582 {method 'read' of 'pandas._libs.parsers.TextReader' objects} 94/65 0.102 0.001 0.283 0.004 {built-in method numpy.core._multiarray_umath.implement_array_function} 7 0.098 0.014 0.098 0.014 C:\ProgramData\Miniconda3\lib\site-packages\numpy\lib\arraypad.py:86(_pad_simple) 7 0.097 0.014 0.098 0.014 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\managers.py:1828(_stack_arrays) 217 0.085 0.000 0.085 0.000 {built-in method numpy.array} 36 0.036 0.001 0.036 0.001 {method 'reduce' of 'numpy.ufunc' objects} 7 0.022 0.003 0.023 0.003 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:1864(__init__) 7 0.018 0.003 18.256 2.608 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:416(_read) 7 0.018 0.003 18.377 2.625 c:\users\clega\desktop\datasetops\src\datasetops\loaders.py:491(get_data) 1 0.009 0.009 0.039 0.039 C:\ProgramData\Miniconda3\lib\site-packages\numpy\lib\nanfunctions.py:1421(nanvar) 2 0.007 0.003 0.036 0.018 C:\ProgramData\Miniconda3\lib\site-packages\numpy\lib\nanfunctions.py:68(_replace_nan) 1 0.006 0.006 0.025 0.025 C:\ProgramData\Miniconda3\lib\site-packages\sklearn\preprocessing\_data.py:780(transform) 1 0.006 0.006 0.076 0.076 C:\ProgramData\Miniconda3\lib\site-packages\sklearn\utils\extmath.py:710(_incremental_mean_and_var) 7847 0.005 0.000 0.011 0.000 {built-in method builtins.isinstance} 4018 0.005 0.000 0.006 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\generic.py:10(_check) 1 0.005 0.005 5.368 5.368 c:\users\clega\desktop\datasetops\src\datasetops\dataset.py:238(item_stats) 1 0.005 0.005 8.000 8.000 c:\users\clega\desktop\datasetops\src\datasetops\dataset.py:1385(make_fn) 7 0.004 0.001 0.004 0.001 {method 'close' of 'pandas._libs.parsers.TextReader' objects} 1148 0.003 0.000 0.005 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1708(_is_dtype_type) 15/7 0.003 0.000 18.405 2.629 c:\users\clega\desktop\datasetops\src\datasetops\dataset.py:235(__getitem__) 1 0.003 0.003 2.729 2.729 c:\users\clega\desktop\datasetops\src\datasetops\scaler.py:62(fit) 1 0.003 0.003 13.269 13.269 c:\users\clega\desktop\datasetops\src\datasetops\dataset.py:648(transform) 1 0.003 0.003 10.639 10.639 c:\users\clega\desktop\datasetops\src\datasetops\dataset.py:1088(wrapped) 1 0.003 0.003 15.911 15.911 c:\users\clega\desktop\datasetops\src\datasetops\dataset.py:854(standardize) 1 0.002 0.002 0.017 0.017 c:\users\clega\desktop\datasetops\src\datasetops\dataset.py:1194(fn) 812 0.002 0.000 0.004 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1565(is_extension_array_dtype) 665 0.002 0.000 0.009 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:542(is_categorical_dtype) 1106 0.002 0.000 0.011 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\base.py:247(is_dtype) 455 0.002 0.000 0.004 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:775(is_integer_dtype) 49/21 0.002 0.000 0.012 0.001 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\indexes\base.py:276(__new__) 819 0.002 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\dtypes.py:75(find) 273 0.001 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1401(is_float_dtype) 56 0.001 0.000 0.001 0.000 {built-in method numpy.empty} 539 0.001 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:216(<lambda>) 609 0.001 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:208(<lambda>) 609 0.001 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:206(classes) 539 0.001 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:211(classes_and_not_datetimelike) 6128 0.001 0.000 0.001 0.000 {built-in method builtins.getattr} 63 0.001 0.000 0.005 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\blocks.py:2981(get_block_type) 21/14 0.001 0.000 0.018 0.001 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\series.py:183(__init__) 56 0.001 0.000 0.005 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\construction.py:388(sanitize_array) 91 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\numpy\core\_dtype.py:321(_name_get) 817/642 0.000 0.000 0.001 0.000 {built-in method builtins.len} 234 0.000 0.000 0.001 0.000 <frozen importlib._bootstrap>:1009(_handle_fromlist) 154 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\dtypes.py:1124(is_dtype) 182 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:506(is_interval_dtype) 154 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\dtypes.py:917(is_dtype) 182 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:472(is_period_dtype) 7 0.000 0.000 0.104 0.015 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\managers.py:1700(form_blocks) 876 0.000 0.000 0.000 0.000 {built-in method builtins.hasattr} 119 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:441(is_timedelta64_dtype) 217 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1844(pandas_dtype) 105 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:222(is_object_dtype) 7 0.000 0.000 0.100 0.014 C:\ProgramData\Miniconda3\lib\site-packages\numpy\lib\arraypad.py:532(pad) 14 0.000 0.000 0.001 0.000 {pandas._libs.lib.clean_index_list} 161 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:403(is_datetime64tz_dtype) 105 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:372(is_datetime64_dtype) 7 0.000 0.000 18.359 2.623 c:\users\clega\desktop\datasetops\src\datasetops\loaders.py:448(read_single_csv) 2827 0.000 0.000 0.000 0.000 {built-in method builtins.issubclass} 7 0.000 0.000 18.074 2.582 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:2035(read) 69/14 0.000 0.000 0.000 0.000 {built-in method _abc._abc_subclasscheck} 7 0.000 0.000 0.102 0.015 c:\Users\clega\Desktop\vibration\sandbox.py:25(func_csv) 98 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:987(is_datetime64_any_dtype) 84 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\indexes\base.py:5393(maybe_extract_name) 49 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\cast.py:1088(maybe_castable) 56 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1435(is_bool_dtype) 42 0.000 0.000 0.096 0.002 <__array_function__ internals>:2(concatenate) 157 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\numpy\core\_asarray.py:14(asarray) 56 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\construction.py:506(_try_cast) 63 0.000 0.000 0.013 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\indexes\base.py:5293(ensure_index) 7 0.000 0.000 18.209 2.601 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:1131(read) 91 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\numpy\core\_dtype.py:307(_name_includes_bit_suffix) 54 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\numpy\core\numerictypes.py:360(issubdtype) 63 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:252(is_sparse) 63/56 0.000 0.000 0.002 0.000 {built-in method builtins.all} 84 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1672(_get_dtype) 49 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\common.py:219(asarray_tuplesafe) 7 0.000 0.000 0.134 0.019 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\construction.py:213(init_dict) 21 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\urllib\parse.py:361(urlparse) 35 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\generic.py:5276(__setattr__) 21 0.000 0.000 0.003 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\blocks.py:3027(make_block) 7 0.000 0.000 0.100 0.014 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\managers.py:1811(_multi_blockify) 4 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\sre_parse.py:469(_parse) 108 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\numpy\core\numerictypes.py:286(issubclass_) 21 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\blocks.py:118(__init__) 7 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\indexes\range.py:83(__new__) 3 0.000 0.000 0.027 0.009 C:\ProgramData\Miniconda3\lib\site-packages\sklearn\utils\validation.py:350(check_array) 131 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\abc.py:137(__instancecheck__) 119 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\inference.py:358(is_hashable) 7 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\series.py:3857(_reduce) 7 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\managers.py:212(_rebuild_blknos_and_blklocs) 7 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\numpy\lib\arraypad.py:457(_as_pairs) 7 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\common.py:144(get_filepath_or_buffer) 42 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\indexes\base.py:3911(__getitem__) 7 0.000 0.000 0.023 0.003 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:792(__init__) 84 0.000 0.000 0.001 0.000 {pandas._libs.lib.is_list_like} 7 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:939(_clean_options) 63 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:339(is_categorical) 42 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\managers.py:1831(_asarray_compat) 21 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\blocks.py:251(mgr_locs) 7 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\numpy\lib\stride_tricks.py:114(_broadcast_to) 21 0.000 0.000 0.000 0.000 {pandas._libs.lib.infer_dtype} 7 0.000 0.000 0.003 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\construction.py:300(_homogenize) 7 0.000 0.000 0.003 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\missing.py:225(_isna_ndarraylike) 42 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:830(is_signed_integer_dtype) 7 0.000 0.000 18.256 2.608 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:530(parser_f) 14 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\cast.py:1209(maybe_cast_to_datetime) 7 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\nanops.py:234(_get_values) 7 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\common.py:40(is_url) 7 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\internals\managers.py:122(__init__) 42 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:887(is_unsigned_integer_dtype) 7 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:885(_get_options_with_defaults) 91 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\numpy\core\_dtype.py:24(_kind_name) 14 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\indexes\base.py:4046(equals) 21 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\urllib\parse.py:412(urlsplit) 21 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\series.py:376(_set_axis) 7 0.000 0.000 0.000 ######### PROFILING bar ######### 5890 function calls (5849 primitive calls) in 2.768 seconds Ordered by: internal time ncalls tottime percall cumtime percall filename:lineno(function) 1 2.570 2.570 2.586 2.586 {method 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C:\ProgramData\Miniconda3\lib\site-packages\sklearn\preprocessing\_data.py:780(transform) 1 0.004 0.004 0.004 0.004 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:1864(__init__) 1 0.003 0.003 2.613 2.613 C:\ProgramData\Miniconda3\lib\site-packages\pandas\io\parsers.py:416(_read) 1 0.003 0.003 2.631 2.631 c:\users\clega\desktop\datasetops\src\datasetops\loaders.py:491(get_data) 1 0.003 0.003 0.028 0.028 C:\ProgramData\Miniconda3\lib\site-packages\numpy\core\_methods.py:232(_std) 1141 0.001 0.000 0.002 0.000 {built-in method builtins.isinstance} 574 0.001 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\generic.py:10(_check) 1 0.001 0.001 0.001 0.001 {method 'close' of 'pandas._libs.parsers.TextReader' objects} 164 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1708(_is_dtype_type) 116 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1565(is_extension_array_dtype) 158 0.000 0.000 0.002 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\base.py:247(is_dtype) 95 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:542(is_categorical_dtype) 65 0.000 0.000 0.001 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:775(is_integer_dtype) 117 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\dtypes.py:75(find) 7/3 0.000 0.000 0.002 0.001 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\indexes\base.py:276(__new__) 1 0.000 0.000 2.768 2.768 c:\Users\clega\Desktop\vibration\sandbox.py:80(bar) 8 0.000 0.000 0.000 0.000 {built-in method numpy.empty} 39 0.000 0.000 0.000 0.000 C:\ProgramData\Miniconda3\lib\site-packages\pandas\core\dtypes\common.py:1401(is_float_dtype) 87 0.000 0.000 0.000 0.000 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It seems the standardize function adds a significant amount of reads to the underlying dataset. Calling the function on a dataset containing a single element seemingly causes 7 reads to be carried out.