knowyourdata.kyd

Complexity

Total Complexity

29

Size/Duplication

Total Lines	306
Duplicated Lines	0 %

Importance

Changes

0

8 Methods

Rating	Name	Duplication	Size	Complexity
B	KYD.get_basic_stats()	0	25	2
A	KYD.clear_memory()	0	4	1
A	KYD.check_struct()	0	8	1
A	KYD.__init__()	0	13	2
A	KYD.display_struct()	0	55	1
B	KYD.display_basic_stats_new()	0	65	5
B	KYD.check_finite()	0	20	5
C	KYD.display()	0	38	7

"""
KnowYourData
============

A rapid and lightweight module to describe the statistics and structure of
data arrays for interactive use.

The most simple use case to display data is if you have a numpy array 'x':

    >>> from knowyourdata import kyd
    >>> kyd(x)

"""

import sys
import numpy as np


class KYD(object):

The variable __class__ seems to be unused.

Too many instance attributes (25/7)

    """The Central Class for KYD"""

    # Variable for Data Vector
    data = None

    # Initial Flags
    f_allfinite = False
    f_allnonfinite = False
    f_hasnan = False
    f_hasinf = False

    # Initialized Numbers
    num_nan = 0
    num_inf = 0

    # Display Settings
    col_width = 10
    precision = 4

    def check_finite(self):
        """Checking to see if all elements are finite and setting flags"""
        if np.all(np.isfinite(self.data)):
            self.filt_data = self.data
            self.f_allfinite = True
        else:
            finite_inds = np.where(np.isfinite(self.data))

            self.filt_data = self.data[finite_inds]

            if self.filt_data.size == 0:
                self.f_allnonfinite = True

            if np.any(np.isnan(self.data)):
                self.f_hasnan = True
                self.num_nan = np.sum(np.isnan(self.data))

            if np.any(np.isinf(self.data)):
                self.f_hasinf = True
                self.num_inf = np.sum(np.isinf(self.data))

    def check_struct(self):
        """Determining the Structure of the Numpy Array"""
        self.dtype = self.data.dtype
        self.ndim = self.data.ndim
        self.shape = self.data.shape
        self.size = self.data.size
        self.memsize = sys.getsizeof(self.data)
        self.human_memsize = sizeof_fmt(self.memsize)

    def get_basic_stats(self):
        """Get basic statistics about array"""

        if self.f_allnonfinite:
            self.min = self.max = self.range = np.nan
            self.mean = self.std = self.median = np.nan
            self.firstquartile = self.thirdquartile = np.nan
            self.ci_68 = self.ci_95 = self.ci_99 = np.array([np.nan, np.nan])

            return

        self.min = np.float_(np.min(self.filt_data))
        self.max = np.float_(np.max(self.filt_data))
        self.range = self.max - self.min
        self.mean = np.mean(self.filt_data)
        self.std = np.std(self.filt_data)
        self.median = np.float_(np.median(self.filt_data))
        self.firstquartile = np.float_(np.percentile(self.filt_data, 25))
        self.thirdquartile = np.float_(np.percentile(self.filt_data, 75))
        self.ci_99 = np.float_(
            np.percentile(self.filt_data, np.array([0.5, 99.5])))
        self.ci_95 = np.float_(
            np.percentile(self.filt_data, np.array([2.5, 97.5])))
        self.ci_68 = np.float_(
            np.percentile(self.filt_data, np.array([16.0, 84.0])))

    def display_basic_stats_new(self):
        """Display Basic Statistics"""
        pstr_list = []

        pstr_struct_header1 = "Basic Statistics  "
        pstr_struct_header2 = ''

        pstr_list.append(pstr_struct_header1)
        pstr_list.append(pstr_struct_header2)

        template_str = (
            " {0:^10} "
            " {1:>8} "
            " {2:<10} "
            " {3:>8} "
            " {4:<10} "
        )

        tmp_data = [
            [
                "Mean:", "{self.mean:.{self.precision}}".format(self=self),
                "",
                "Std Dev:", "{self.std:.{self.precision}}".format(self=self)
            ],
            ["Min:", "1Q:", "Median:", "3Q:", "Max:"],
            [
                "{self.min: .{self.precision}}".format(self=self),
                "{self.firstquartile: .{self.precision}}".format(self=self),
                "{self.median: .{self.precision}}".format(self=self),
                "{self.thirdquartile: .{self.precision}}".format(self=self),
                "{self.max: .{self.precision}}".format(self=self),
            ],
            ['-99 CI:', '-95 CI:', '-68 CI:', '+68 CI:', '+95 CI:', '+99 CI:'],
            [
                "{self.ci_99[0]: .{self.precision}}".format(self=self),
                "{self.ci_95[0]: .{self.precision}}".format(self=self),
                "{self.ci_68[0]: .{self.precision}}".format(self=self),
                "{self.ci_68[1]: .{self.precision}}".format(self=self),
                "{self.ci_95[1]: .{self.precision}}".format(self=self),
                "{self.ci_99[1]: .{self.precision}}".format(self=self),
            ],
        ]

        n_tmp_data = len(tmp_data)

        num_rows_in_cols = [len(i) for i in tmp_data]
        num_rows = np.max(num_rows_in_cols)

        for i in range(n_tmp_data):
            tmp_col = tmp_data[i]
            for j in range(num_rows_in_cols[i], num_rows):

The variable j seems to be unused.

                tmp_col.append("")

        for i in range(num_rows):
            pstr_list.append(
                template_str.format(
                    tmp_data[0][i],
                    tmp_data[1][i],
                    tmp_data[2][i],
                    tmp_data[3][i],
                    tmp_data[4][i],
                )
            )

        return pstr_list

    def display_struct(self):
        """Display information about array structure"""

        pstr_list = []

        # pstr_struct_header0 = "................."
        # Commenting out Ansi Coloured Version
        # pstr_struct_header1 = '\033[1m' + "Array Structure  " + '\033[0m'
        pstr_struct_header1 = "Array Structure  "
        pstr_struct_header2 = "                 "

        # pstr_list.append(pstr_struct_header0)
        pstr_list.append(pstr_struct_header1)
        pstr_list.append(pstr_struct_header2)

        pstr_n_dim = (
            "Number of Dimensions:\t"
            "{self.ndim}").format(
                self=self)
        pstr_list.append(pstr_n_dim)

        pstr_shape = (
            "Shape of Dimensions:\t"
            "{self.shape}").format(
                self=self)
        pstr_list.append(pstr_shape)

        pstr_dtype = (
            "Array Data Type:\t"
            "{self.dtype}").format(
                self=self)
        pstr_list.append(pstr_dtype)

        pstr_memsize = (
            "Memory Size:\t\t"
            "{self.human_memsize}").format(
                self=self)
        pstr_list.append(pstr_memsize)

        pstr_spacer = ("")
        pstr_list.append(pstr_spacer)

        pstr_numnan = (
            "Number of NaN:\t"
            "{self.num_nan}").format(
                self=self)
        pstr_list.append(pstr_numnan)

        pstr_numinf = (
            "Number of Inf:\t"
            "{self.num_inf}").format(
                self=self)
        pstr_list.append(pstr_numinf)

        return pstr_list

    def display(self, short=False):
        """Displaying all relevant statistics"""

        if short:
            pass

        print("")
        pstr_basic = self.display_basic_stats_new()
        pstr_struct = self.display_struct()
        n_basic = len(pstr_basic)
        n_struct = len(pstr_struct)

        l_colwidth = max([len(x) for x in pstr_basic]) + 1

        r_colwidth = max([len(x) for x in pstr_struct]) + 2

        # new_colwidth = self.col_width + 20

        # Finding the longest string
        len_list = max([n_basic, n_struct])

        for i in range(len_list):
            tmp_str = '| '
            if i < n_basic:
                tmp_str += (pstr_basic[i].ljust(l_colwidth))
            else:
                tmp_str += ''.ljust(l_colwidth)
            tmp_str += ' | '

            if i < n_struct:
                tmp_str += (pstr_struct[i].expandtabs().ljust(r_colwidth))
            else:
                tmp_str += ''.ljust(r_colwidth)
            tmp_str += '\t|'

            print(tmp_str)

        print("")

    def clear_memory(self):
        """Ensuring the Numpy Array does not exist in memory"""
        del self.data
        del self.filt_data

    def __init__(self, data):
        super(KYD, self).__init__()

        # Ensuring that the array is a numpy array
        if not isinstance(data, np.ndarray):
            data = np.array(data)

        self.data = data

        self.check_finite()
        self.check_struct()
        self.get_basic_stats()
        self.clear_memory()


def sizeof_fmt(num, suffix='B'):
    """Return human readable version of in-memory size.
    Code from Fred Cirera from Stack Overflow:
    https://stackoverflow.com/questions/1094841/reusable-library-to-get-human-readable-version-of-file-size
    """
    for unit in ['', 'Ki', 'Mi', 'Gi', 'Ti', 'Pi', 'Ei', 'Zi']:
        if abs(num) < 1024.0:
            return "%3.1f%s%s" % (num, unit, suffix)
        num /= 1024.0
    return "%.1f%s%s" % (num, 'Yi', suffix)


def kyd(data, full_statistics=False):
    """Print statistics of any numpy array

    data -- Numpy Array of Data

    Keyword arguments:
    full_statistics -- printing all detailed statistics of the sources
    (Currently Not Implemented)

    """

    data_kyd = KYD(data)
    if full_statistics:
        data_kyd.display()
    else:
        data_kyd.display(short=True)

    return data_kyd