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Data
Analysis
by
Bernd Klein
bodenseo
© 2021 Bernd Klein
All rights reserved. No portion of this book may be reproduced or used in any
manner without written permission from the copyright owner.
www.python-course.eu
Python Course
Data Analysis With
Python by Bernd
Klein
Numpy Tutorial ..........................................................................................................................8
Numpy Tutorial: Creating Arrays.............................................................................................17
Data Type Objects, dtype..........................................................................................................36
Numerical Operations on Numpy Arrays.................................................................................48
Numpy Arrays: Concatenating, Flattening and Adding Dimensions .......................................68
Python, Random Numbers and Probability ..............................................................................79
Weighted Probabilities..............................................................................................................90
Synthetical Test Data With Python.........................................................................................119
Numpy: Boolean Indexing......................................................................................................136
Matrix Multiplicaion, Dot and Cross Product ........................................................................143
Reading and Writing Data Files .............................................................................................149
Overview of Matplotlib ..........................................................................................................157
Format Plots............................................................................................................................168
Matplotlib Tutorial..................................................................................................................172
Shading Regions with fill_between() .....................................................................................183
Matplotlib Tutorial: Spines and Ticks ....................................................................................186
Matplotlib Tutorial, Adding Legends and Annotations..........................................................197
Matplotlib Tutorial: Subplots .................................................................................................212
Exercise ....................................................................................................................................44
Exercise ....................................................................................................................................44
Matplotlib Tutorial: Gridspec .................................................................................................239
GridSpec using SubplotSpec ..................................................................................................244
Matplotlib Tutorial: Histograms and Bar Plots ......................................................................248
Matplotlib Tutorial: Contour Plots .........................................................................................268
Introduction into Pandas.........................................................................................................303
Data Structures .......................................................................................................................305
Accessing and Changing values of DataFrames.....................................................................343
Pandas: groupby .....................................................................................................................361
Reading and Writing Data ......................................................................................................380
Dealing with NaN...................................................................................................................394
Binning in Python and Pandas................................................................................................404
Expenses and Income Example ..............................................................................................465
Net Income Method Example.................................................................................................478
3
NUMERICAL PROGRAMMING WITH
PYTHON
Numerical Computing defines an area of computer science and mathematics dealing with algorithms for
numerical approximations of problems from mathematical or numerical analysis, in other words: Algorithms
solving problems involving continuous variables. Numerical analysis is used to solve science and engineering
problems.
Data science is an interdisciplinary subject which includes for example statistics and computer science,
especially programming and problem solving skills. Data Science includes everything which is necessary to
create and prepare data, to manipulate, filter and clense data and to analyse data. Data can be both structured
and unstructured. We could also say Data Science includes all the techniques needed to extract and gain
information and insight from data.
Data Science is an umpbrella term which incorporates data analysis, statistics, machine learning and other
related scientific fields in order to understand and analyze data.
Another term occuring quite often in this context is "Big Data". Big Data is for sure one of the most often used
buzzwords in the software-related marketing world. Marketing managers have found out that using this term
can boost the sales of their products, regardless of the fact if they are really dealing with big data or not. The
term is often used in fuzzy ways.
Big data is data which is too large and complex, so that it is hard for data-processing application software to
deal with them. The problems include capturing and collecting data, data storage, search the data, visualization
of the data, querying, and so on.
• volume:
the sheer amount of data, whether it will be giga-, tera-, peta- or exabytes
• velocity:
the speed of arrival and processing of data
• veracity:
4
uncertainty or imprecision of data
• variety:
the many sources and types of data both structured and unstructured
The big question is how useful Python is for these purposes. If we would only use Python without any special
modules, this language could only poorly perform on the previously mentioned tasks. We will describe the
necessary tools in the following chapter.
5
Numpy is a module which provides the basic data structures,
implementing multi-dimensional arrays and matrices. Besides
that the module supplies the necessary functionalities to create
and manipulate these data structures. SciPy is based on top of
Numpy, i.e. it uses the data structures provided by NumPy. It
extends the capabilities of NumPy with further useful functions
for minimization, regression, Fourier-transformation and many
others.
The principal disadvantage of MATLAB against Python are the costs. Python with NumPy, SciPy, Matplotlib
and Pandas is completely free, whereas MATLAB can be very expensive. "Free" means both "free" as in "free
beer" and "free" as in "freedom"! Even though MATLAB has a huge number of additional toolboxes available,
Python has the advantage that it is a more modern and complete programming language. Python is continually
becoming more powerful by a rapidly growing number of specialized modules.
Python in combination with Numpy, Scipy, Matplotlib and Pandas can be used as a complete replacement for
MATLAB.
6
7
NUMPY TUTORIAL
INTRODUCTION
NumPy is a module for Python. The name is an acronym for
"Numeric Python" or "Numerical Python". It is pronounced
/ˈnʌmpaɪ/ (NUM-py) or less often /ˈnʌmpi (NUM-pee)). It is an
extension module for Python, mostly written in C. This makes
sure that the precompiled mathematical and numerical functions
and functionalities of Numpy guarantee great execution speed.
SciPy (Scientific Python) is often mentioned in the same breath with NumPy. SciPy needs Numpy, as it is
based on the data structures of Numpy and furthermore its basic creation and manipulation functions. It
extends the capabilities of NumPy with further useful functions for minimization, regression, Fourier-
transformation and many others.
Both NumPy and SciPy are not part of a basic Python installation. They have to be installed after the Python
installation. NumPy has to be installed before installing SciPy.
(Comment: The diagram of the image on the right side is the graphical visualisation of a matrix with 14 rows
and 20 columns. It's a so-called Hinton diagram. The size of a square within this diagram corresponds to the
size of the value of the depicted matrix. The colour determines, if the value is positive or negative. In our
example: the colour red denotes negative values and the colour green denotes positive values.)
NumPy is based on two earlier Python modules dealing with arrays. One of these is Numeric. Numeric is like
NumPy a Python module for high-performance, numeric computing, but it is obsolete nowadays. Another
predecessor of NumPy is Numarray, which is a complete rewrite of Numeric but is deprecated as well. NumPy
is a merger of those two, i.e. it is build on the code of Numeric and the features of Numarray.
8
When we say "Core Python", we mean Python without any special modules, i.e. especially without NumPy.
import numpy
But you will hardly ever see this. Numpy is usually renamed to np:
import numpy as np
Our first simple Numpy example deals with temperatures. Given is a list with values, e.g. temperatures in
Celsius:
cvalues = [20.1, 20.8, 21.9, 22.5, 22.7, 22.3, 21.8, 21.2, 20.9, 2
0.1]
C = np.array(cvalues)
print(C)
[20.1 20.8 21.9 22.5 22.7 22.3 21.8 21.2 20.9 20.1]
Let's assume, we want to turn the values into degrees Fahrenheit. This is very easy to accomplish with a
numpy array. The solution to our problem can be achieved by simple scalar multiplication:
print(C * 9 / 5 + 32)
[68.18 69.44 71.42 72.5 72.86 72.14 71.24 70.16 69.62 68.18]
9
The array C has not been changed by this expression:
print(C)
[20.1 20.8 21.9 22.5 22.7 22.3 21.8 21.2 20.9 20.1]
Compared to this, the solution for our Python list looks awkward:
So far, we referred to C as an array. The internal type is "ndarray" or to be even more precise "C is an instance
of the class numpy.ndarray":
type(C)
Output: numpy.ndarray
In the following, we will use the terms "array" and "ndarray" in most cases synonymously.
If you use the jupyter notebook, you might be well advised to include the following line of code to prevent an
external window to pop up and to have your diagram included in the notebook:
%matplotlib inline
The code to generate a plot for our values looks like this:
plt.plot(C)
plt.show()
10
The function plot uses the values of the array C for the values of the ordinate, i.e. the y-axis. The indices of the
array C are taken as values for the abscissa, i.e. the x-axis.
11
To calculate the memory consumption of the list from the above picture, we will use the function getsizeof
from the module sys.
The size of a Python list consists of the general list information, the size needed for the references to the
elements and the size of all the elements of the list. If we apply sys.getsizeof to a list, we get only the size
without the size of the elements. In the previous example, we made the assumption that all the integer
elements of our list have the same size. Of course, this is not valid in general, because memory consumption
will be higher for larger integers.
We will check now, how the memory usage changes, if we add another integer element to the list. We also
look at an empty list:
lst = []
print("Emtpy list size: ", size(lst))
12
Size without the size of the elements: 104
Size of all the elements: 112
Total size of list, including elements: 216
Emtpy list size: 72
We can conclude from this that for every new element, we need another eight bytes for the reference to the
new object. The new integer object itself consumes 28 bytes. The size of a list "lst" without the size of the
elements can be calculated with:
64 + 8 * len(lst)
To get the complete size of an arbitrary list of integers, we have to add the sum of all the sizes of the integers.
We will examine now the memory consumption of a numpy.array. To this purpose, we will have a look at the
implementation in the following picture:
We will create the numpy array of the previous diagram and calculate the memory usage:
We get the memory usage for the general array information by creating an empty array:
e = np.array([])
print(size(e))
96
13
Other documents randomly have
different content
PRUNUS INSITITIA
The yellow plums of the Roman poets, Ovid and Vergil, are probably
the Bullaces or Mirabelles of this species. Indeed, its cultivation was
probably prehistoric, for Heer[67] has illustrated and described
stones of a plum found in the lake-dwellings of Robenhausen which
can be no other than those of Insititia.
The authentic written history of this plum may be said to have
begun with or a little before the Christian Era. The records of the
cultivation and development through the early centuries of the
present chronology and the Middle Ages to our own day may be
found in the herbals, botanies, pomologies, agricultural and general
literature of the past two thousand years.
Prunus insititia now grows wild in nearly all temperate parts of
Europe and western Asia—from the Mediterranean northward into
Norway, Sweden and Russia. The botanists of Europe very generally
agree that its original habitat was in southern and southeastern
Europe and the adjoining parts of Asia, and that elsewhere it is an
escape from cultivation. Hooker[68] says that Prunus insititia grows
in western temperate Himalaya, cultivated and indigenous, from
Gurwhal to Kashmir, the type being that of the “common yellow-
fruited Bullace.” A few botanical writers hold that it is truly wild in
the parts of Europe where now found growing. There are also not a
few botanists who, as has been stated in the discussion of the
Domestica plums, unite the Insititias with the Domesticas, and
others who combine these two with the Spinosa plums in one
species, Prunus communis.[69]
It is possible that the species is occasionally found naturalized in
eastern United States; several botanists so give it.
Wherever the habitat of the Insititia plums may have been,
practically all writers from the Greeks and Romans who first mention
this fruit to those of the present time, connect the cultivated
varieties in one way or another with the old Semite city, Damascus.
It is almost certain that the Syrians or Persians were the first to
cultivate these plums, and that they were unknown in Europe as
domesticated varieties until the Greeks first and the Romans
afterward came in intimate contact with the people of the Orient.
Thus it is often stated in the old pomologies that Alexander the
Great brought these plums from the Orient after his expedition of
conquest and that some centuries later Pompey, returning from his
invasion of the eastern countries, brought plums to the Roman
Empire.
The history of the Insititia plums in America has been given in the
main in the discussion of the Domestica plums, for the varieties of
the two species have never been kept separate by plum-growers, all
being grouped together as European plums. It is probable, however,
that the Damson plums of this species were earlier introduced and
more generally grown than any other of the European plums by the
English settlers of America, as the references to plum-growing
before the Revolution are largely to the Damsons. The reasons for
this early preference for these plums are that they come true to seed
while most varieties of the Domestica do not; and trees and cions
were not readily transportable in colonial times; and, too, the
Damsons have always been favorite plums with the English.
When the first American fruit books were published at the
beginning of the Nineteenth Century the Damsons and Bullaces were
widely grown, for all writers give a relatively large number of
varieties of these plums and speak well of them. Thus McMahon,[70]
in his list of thirty plums gives six that belong here, ending his list
with “Common Damson, etc.,” as if there were still more than those
he enumerates. Prince, in his Pomological Manual, in 1832, gives at
least eighteen sorts that may be referred to Insititia with the
statement that one of them, the Early Damson “appears to have
been brought to this country by the early Dutch settlers, or by the
French who settled here at the time of the revocation of the Edict of
Nantes,” adding, “It is much disseminated throughout this section of
the country.” At the end of the Eighteenth Century Deane’s[71] New
England Farmer or Georgical Dictionary, in a discussion of plums in
general says: “The most common plum in this country is the
Damascene plum, an excellent fruit for preserving, which is said to
have been brought from Damasam, hence the name.”
The hardiness, thriftiness and productiveness of all of the varieties
of this species commend them to those who cannot give the care
required to grow the less easily grown Domesticas, and in America,
as in Europe, these plums are to be found in almost every orchard
and in many communities half-wild, thriving with little or no care.
The fact that they are easily propagated, growing readily from
suckers and coming true to seed is an added reason for their general
distribution.
The Insititia plums do not seem to hybridize freely with other
species—at least there are no recorded offspring of such hybrids,
though Koch believes the Reine Claudes to be a hybrid group
between this species and the Domesticas and there is much
evidence in the fruit to show that the French Damson is part
Domestica. The tree-characters of the Insititia plums are such,
especially as regards vigor, hardiness, productiveness and freedom
from disease, as to seemingly make hybrids with them very
desirable. That this species can be hybridized with Domestica, at
least, is certain from work done at this Station where we have made
a number of crosses between them.
Four groups of plums, the Damsons, Bullaces, Mirabelles and St.
Juliens, in all eighty-six varieties mentioned in The Plums of New
York, may be referred to this species. There are so few real
differences between these divisions, however, that it is hardly
possible, logically, to sub-divide Insititia plums into more than two
groups. But since the groups of plums given above are so often
referred to in pomological works it is necessary to discuss them.
The Damsons.—The description given the species fits this division
of it closely, the differentiating character for the fruit, if any, being
oval fruits, while the Bullaces, most nearly like these, are round. The
origin of the Damsons, as we have seen, was in Syria and near the
ancient city, Damascus, their written history dating back several
centuries before Christ. This plum has escaped from cultivation in
nearly all the temperate parts of Europe and more or less in the
eastern United States, the wild forms often passing under other
names, as the Wild, Wheat, Spilling, Donkey, Ass, Hog and Horse
plums. The true Damsons have a fine spicy taste, which makes them
especially desirable for cooking and preserving, but a very decided
astringency of the skin makes most of the varieties of Damsons
undesirable to eat out of the hand; this astringency largely
disappears with cooking or after a light frost. Nearly all Damsons are
sour, though a few sweet Insititias are placed in this group.
Since the seeds grow readily and the sprouts are very
manageable, the Damsons, with the other Insititias, are much used
as stocks upon which to work other plums, especially the less hardy
and less thrifty Domesticas. Although less used now than formerly
for stocks it is a question if these plums, or some of their near kin,
do not make the best obtainable stocks. There seems to be much
difference in the varieties of Insititia in their capacity to send up
sprouts. The forms which send up the fewest sprouts are much the
best for use as stocks.
Curiously enough, the Damsons are highly esteemed now only by
the Americans and English, being grown much less at present in
Continental Europe than a century or two ago. Late pomological
works and nurserymen’s catalogs from others than the English or
Americans barely mention these plums.
The Bullaces.—It is impossible to distinguish between the tree-
characters of the Damsons and the Bullaces, and pomologists are far
from agreeing as to what differences in the fruit throw a variety into
one group or the other. Some writers call a sour variety of Insititia a
Damson, and a sweet one a Bullace; others make color the
differentiating character, calling the purple plums Damsons and the
light colored ones Bullaces; still others call oval Insititias Damsons
and round ones Bullaces. If a distinction is to be made, shape seems
to be the character upon which it should be based. The name
Bullace applies to the round shape of the fruit, but when first used
or by whom given it is impossible to say. It is commonly used in the
old herbals and pomologies of both England and Continental Europe,
there being many variations of the name, of which bullis and bulloes
are most common with the word bullum in frequent use for the fruit
of the Bullace tree. The varieties of Bullaces are few in number, and
are not largely grown, being known for most part only in fruit
collections, the Damsons serving all the purposes for which the
Bullaces would be worth growing, and to better advantage.
The Mirabelles.—The Mirabelles are round, yellowish or golden,
freestone Insititias, ranging from half an inch to an inch in diameter,
very slightly sub-acid or sweet. The trees do not differ from the type
of the species unless it be in even greater productiveness than the
other groups of Insititia, all of which bear very abundant crops. The
fruits represent the highest quality to be found in the varieties of this
species, approaching the Reine Claudes of Prunus domestica in
richness of flavor. Indeed, the Mirabelles may almost be said to be
diminutive Reine Claudes, resembling them not only in quality but in
color and in shape, and so closely as to lend color to Koch’s[72]
supposition that the Reine Claudes are hybrids between Prunus
domestica and Prunus insititia.
In France the Mirabelles are accorded second if not first place
among plums, being superseded in popularity, if at all, only by the
Reine Claudes. They are used in the fresh state and as prunes, and
are freely made into conserves, preserves, jellies and jams, being
found in the markets in some of these forms the year round. They
are much used for pastry, their size being such that one layer of fruit
suffices and is none too deep for a good pie or tart. The fermented
juice of these plums is somewhat largely used in the making of a
distilled liquor, a sort of plum brandy. The dozen or more varieties of
Mirabelles differ chiefly in size of fruit and in time of maturity. The
range in size is from half an inch to an inch in diameter and in time
of ripening in France from the first of August to the first of October.
The Red Mirabelle frequently referred to in pomological works is
Prunus cerasifera, and the name is wrongly so used, for if not first
applied to the several varieties of Insititia it now by almost universal
usage belongs to these plums. The origin of the word, as now
commonly used, dates back over two centuries, being found in the
pomological treatises of the Seventeenth Century. The assumption is
that Mirabelle is derived from mirable meaning wonderful, and the
name was first so used by the French.
Unfortunately the Mirabelles are hardly known in America. These
plums have so many good qualities of tree and fruit that American
pomology would be greatly enriched if the best Mirabelle varieties
were grown in both home and commercial orchards. They should be
used in cookery much as are the Damsons, which they surpass for
some purposes.
St. Juliens.—The St. Julien that the writer has seen in American
and European nurseries is unmistakably an Insititia. At one time St.
Julien stocks were used almost exclusively in New York nurseries,
and few large plum orchards are free from trees which have through
accident to the cion grown from the stock. Such trees bear fruit so
like the Damson that one is warranted in saying that the two are
identical, and that St. Julien is but a name used for a Damson when
the latter is employed as a stock. The fruit is sweetish with a taste
identical with that of the sweet Damsons.
Plum-growers who have had experience with plums on several
stocks are almost united in the opinion that the St. Julien is the best
of all for the Domesticas, at least. St. Julien stocks were formerly
imported in great numbers from France, where it is still largely
grown for European use. The name seems to have come in use in
France more than a century ago, but why given or to what particular
Insititia applied does not appear. There is, however, a distinct variety
or type of Insititia used by the French in producing stocks, for
French pomologists advise careful selection of mother-plants for the
production of the young trees by suckers or layers, and caution
growers of stocks in no case to use seeds which bring twiggy, spiny
and crooked stocks.[73] St. Julien plums are seemingly nowhere
grown at present for their fruits.
There are several ornamental forms of plums which are given
specific names by European horticulturists, mentioned in the last
paragraph in the discussion of the Domestica plums, which some
writers place, in part at least, with the Insititias. These plums are not
found in America and it is impossible to place them with certainty in
either of the two species upon the contradictory evidence of the
Europeans.
The few herbarium specimens that the writer has seen of this
species from southeastern Europe strongly resemble Prunus spinosa
but Schneider in the above reference describing it from living
specimens says that it differs from the species last named as
follows: “Lower growth, about one-half as high, spreading squarrose
ramification, much less thorniness; leaves more like domestica, when
young hairy on both sides, later above nearly and underneath more
or less glabrous; petiole shorter, not exceeding one cm.; blooms
later, nearly with the leaves, white, about twenty-two mm. in
diameter, borne almost always single in this species; pedicel finely
pilose, in Prunus spinosa almost glabrous; stamens fewer, about
twenty; fruit blue black, stem longer, exceeding twelve mm.”
So far as appears from the few and scant European references to
the species it has no horticultural value.
The writer has seen only herbarium specimens of this plant and
has taken the description given from European texts. According to
Schneider the species has been divided into two varieties by the
Italian botanists. Prunus cocomilia typica having oblong-ovate fruit
and Prunus cocomilia brutia having round fruit. Schneider holds also
that Prunus pseudoarmeniaca Heldr. and Sart.[82] from Epirus and
Thessaly is a variety of Prunus cocomilia differing chiefly in having
more pointed leaves and smaller oblong-roundish red plums. The
same author puts in this species still another plum, a hairy-leaved
form from Thessaly which he calls Prunus cocomilia puberula. He
places here also Prunus ursina Kotschy[83] which differs only in
minor respects from the species, chiefly in having violet-red fruit
though Boissier[84] mentions a yellow-fruited plum which he calls
Prunus ursina flava. The last named plums come from Lebanon and
North Syria.
1. Ehrhart Beitr. Nat. 4:17. 1789. 2. Hooker Brit. Fl. 220. 1830. 3. Koch,
K. Dend. 1:97. 1869. 4. Koch, W. Syn. Deut. und Schw. Fl. 1:727. 1892.
5. Bailey Cornell Sta. Bul. 38:66. 1892. 6. Schneider Handb. Laubh.
1:632. 1892. 7. Schwarz Forst. Bot. 339. 1892. 8. Dippel Handb. Laubh.
1:633. 1893.
P. domestica myrobalan. 9. Linnaeus Sp. Pl. 475. 1753. 10. Seringe DC.
Prodr. 2:538. 1825.
P. myrobalan. 11. Loisleur Nouv. Duham. 5:184. 1812. 12. Koehne
Deut. Dend. 316. 1893.
Tree twenty to thirty feet in height, vigorous; trunk six to twelve inches
in diameter, straight; bark thick, rough, numerous corky elevations
especially on the branches, reddish or cinnamon-brown, peach-like;
branches long, upright-spreading, much forked, brash and often splitting
at the forks; branchlets thick, straight, glaucous and glabrous, at first light
red, growing darker the second year; lenticels few or many, usually small
but conspicuous, light in color.
Winter-buds small and obtuse, free or appressed; leaves borne
abundantly, small or of but medium size, oblong-obovate, point acuminate
or abrupt, prominent, base rounded, firm, thin, membranaceous, margins
finely and closely serrated, sometimes in two series, teeth usually
glandular; upper surface bright green, glabrous, lower surface dull,
whitish, glabrous or slightly pubescent on the veins; veins pronounced;
petioles one-half inch in length, stoutish, tinged with red; glands few or
several, usually globose, greenish; stipules lanceolate, very narrow, one-
half inch long, caducous.
Flowers expanding early, before, with or sometimes after the leaves,
first of the plum blossoms to appear, very abundant, three-quarters of an
inch in diameter; usually three springing from each flower-bud, often in
dense clusters on lateral spurs and lateral buds on one-year-old wood;
calyx-tube green, glabrous, campanulate or obconic; calyx-lobes acute to
obtuse glandular-serrate, erect, glabrous or pubescent; petals white, oval,
entire or crenate, with a short claw or tip; stamens about twenty-five,
shorter than the petals; anthers yellow, sometimes tinged with red; pistils
glabrous, longer than the stamens; pedicels one-half inch long, slender.
Fruit varying greatly in season, from very early to late; large, from one
to two inches in diameter, globular, heart-shaped or often somewhat
conical; cavity deep; apex conspicuously pointed; suture usually
prominent; color varies greatly but usually a bright red or yellow, never
blue or purple, lustrous, with little or no bloom; dots small, numerous,
usually conspicuous; skin thin, tough, astringent; stem one-half inch in
length; flesh red or more often yellow, firm, fibrous, juicy; quality variable,
of distinct flavor, usually good; stone clinging tenaciously or nearly free,
small, rough or lightly pitted, oval to ovate, one edge grooved, the other
ridged.
All that is known of the history and habitat of this species is that it
came from China in 1867 having been sent to the Paris Museum of
Natural History by Eugene Simon, a French consul in China. The
spontaneous form has not as yet been found. The general aspect of
the tree is more that of the peach than the plum and the drupes are
as much like apricots or nectarines as plums but when all characters
are considered the fruit can better be classed with the plums than
with any of the other stone-fruits named.