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Python Data
Visualization Cookbook
Igor Milovanović
BIRMINGHAM - MUMBAI
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Python Data Visualization Cookbook
All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or
transmitted in any form or by any means, without the prior written permission of the publisher,
except in the case of brief quotations embedded in critical articles or reviews.
Every effort has been made in the preparation of this book to ensure the accuracy of the
information presented. However, the information contained in this book is sold without
warranty, either express or implied. Neither the author, nor Packt Publishing, and its dealers
and distributors will be held liable for any damages caused or alleged to be caused directly or
indirectly by this book.
Packt Publishing has endeavored to provide trademark information about all of the companies
and products mentioned in this book by the appropriate use of capitals. However, Packt
Publishing cannot guarantee the accuracy of this information.
ISBN 978-1-78216-336-7
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Credits
Reviewers Proofreaders
Tarek Amr Amy Johnson
Simeone Franklin Lindsey Thomas
Jayesh K. Gupta
Indexer
Kostiantyn Kucher
Mariammal Chettiyar
Kenneth Emeka Odoh
Graphics
Acquisition Editor Abhinash Sahu
James Jones
Production Coordinator
Lead Technical Editor Shantanu Zagade
Ankita Shashi
Cover Work
Technical Editors Shantanu Zagade
Pratik More
Amit Ramadas
Ritika Singh
Copy Editors
Brandt D'Mello
Janbal Dharmaraj
Deepa Nambiar
Kirti Pai
Laxmi Subramanian
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About the Author
He is an Evangelist for high-quality systems design who holds strong interests in software
architecture and development methodologies. He is always persistent on advocating
methodologies that promote high-quality software, such as test-driven development,
one-step builds, and continuous integration.
He also possesses solid knowledge of product development. Having field experience and
official training, he is capable of transferring knowledge and communication flow from
business to developers and vice versa.
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About the Reviewers
Tarek Amr achieved his postgraduate degree in Data Mining and Information Retrieval from
the University of East Anglia. He has about 10 years' experience in Software Development.
He has been volunteering in Global Voices Online (GVO) since 2007, and currently he is the
local ambassador of the Open Knowledge Foundation (OKFN) in Egypt. Words such as Open
Data, Government 2.0, Data Visualisation, Data Journalism, Machine Learning, and Natural
Language Processing are like music to his ears.
Jayesh K. Gupta is the Lead Developer of Matlab Toolbox for Biclustering Analysis (MTBA).
He is currently an undergraduate student and researcher at IIT Kanpur. His interests lie in the
field of pattern recognition. His interests also lie in basic sciences, recognizing them as the
means of analyzing patterns in nature. Coming to IIT, he realized how this analysis is being
augmented by Machine Learning algorithms with various diverse applications. He believes
that augmenting human thought with machine intelligence is one of the best ways to advance
human knowledge. He is a long time technophile and a free-software Evangelist. He usually
goes by the handle, rejuvyesh online. He is also an avid reader and his books can be checked
out at Goodreads. Checkout his projects at Bitbucket and GitHub. For all links visit http://
home.iitk.ac.in/~jayeshkg/. He can be contacted at [email protected].
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Kostiantyn Kucher was born in Odessa, Ukraine. He received his Master's degree in
Computer Science from Odessa National Polytechnic University in 2012. He used Python
as well as Matplotlib and PIL for Machine Learning and Image Recognition purposes.
Kenneth Emeka Odoh performs research on state of the art Data Visualization
techniques. His research interest includes exploratory search where the users are
guided to their search results using visual clues.
When Kenneth is not writing source codes, you can find him singing at the Campion College
chant choir.
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Table of Contents
Preface 1
Chapter 1: Preparing Your Working Environment 5
Introduction 5
Installing matplotlib, NumPy, and SciPy 6
Installing virtualenv and virtualenvwrapper 8
Installing matplotlib on Mac OS X 10
Installing matplotlib on Windows 11
Installing Python Imaging Library (PIL) for image processing 12
Installing a requests module 14
Customizing matplotlib's parameters in code 14
Customizing matplotlib's parameters per project 16
Chapter 2: Knowing Your Data 19
Introduction 19
Importing data from CSV 20
Importing data from Microsoft Excel files 22
Importing data from fixed-width datafiles 25
Importing data from tab-delimited files 27
Importing data from a JSON resource 28
Exporting data to JSON, CSV, and Excel 31
Importing data from a database 36
Cleaning up data from outliers 40
Reading files in chunks 46
Reading streaming data sources 48
Importing image data into NumPy arrays 50
Generating controlled random datasets 56
Smoothing the noise in real-world data 64
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Table of Contents
Chapter 3: Drawing Your First Plots and Customizing Them 71
Introduction 72
Defining plot types – bar, line, and stacked charts 72
Drawing a simple sine and cosine plot 78
Defining axis lengths and limits 81
Defining plot line styles, properties, and format strings 84
Setting ticks, labels, and grids 89
Adding a legend and annotations 92
Moving spines to the center 95
Making histograms 96
Making bar charts with error bars 99
Making pie charts count 101
Plotting with filled areas 103
Drawing scatter plots with colored markers 105
Chapter 4: More Plots and Customizations 109
Introduction 109
Setting the transparency and size of axis labels 110
Adding a shadow to the chart line 113
Adding a data table to the figure 116
Using subplots 118
Customizing grids 121
Creating contour plots 125
Filling an under-plot area 128
Drawing polar plots 131
Visualizing the filesystem tree using a polar bar 134
Chapter 5: Making 3D Visualizations 139
Introduction 139
Creating 3D bars 139
Creating 3D histograms 143
Animating in matplotlib 146
Animating with OpenGL 150
ii
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Table of Contents
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Table of Contents
iv
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Preface
The best data is the data that we can see and understand. As developers, we want to
create and build the most comprehensive and understandable visualizations. It is not always
simple; we need to find the data, read it, clean it, massage it, and then use the right tool to
visualize it. This book explains the process of how to read, clean, and visualize the data into
information with straight and simple (and not so simple) recipes.
How to read local data, remote data, CSV, JSON, and data from relational databases are all
explained in this book.
Some simple plots can be plotted with a simple one-liner in Python using matplotlib, but
doing more advanced charting requires knowledge of more than just Python. We need to
understand the information theory and human perception aesthetics to produce the most
appealing visualizations.
This book will explain some practices behind plotting with matplotlib in Python, statistics used,
and usage examples for different charting features we should use in an optimal way.
This book is written and the code is developed on Ubuntu 12.03 using Python 2.7,
IPython 0.13.2, virtualenv 1.9.1, matplotlib 1.2.1, NumPy 1.7.1, and SciPy 0.11.0.
Chapter 2, Knowing Your Data, introduces you to common data formats and how to read and
write them, be it CSV, JSON, XSL, or relational databases.
Chapter 3, Drawing Your First Plots and Customizing Them, starts with drawing simple plots
and covers some of the customization.
Chapter 4, More Plots and Customizations, follows up from previous chapter and covers more
advanced charts and grid customization.
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Preface
Chapter 6, Plotting Charts with Images and Maps, covers image processing, projecting data
onto maps, and creating CAPTCHA test images.
Chapter 7, Using Right Plots to Understand Data, covers explanations and recipes on some
more advanced plotting techniques such as spectrograms and correlations.
Chapter 8, More on matplotlib Gems, covers a set of charts such as Gantt charts, box plots,
and whisker plots, and also explains how to use LaTeX for rendering text in matplotlib.
Other software packages used in this book are IPython, which is an interactive Python
environment that is very powerful, and flexible. This can be installed using package
managers for Linux-based OSes or prepared installers for Windows and Mac OSes.
If you are new to Python installation and software installation in general, it is very much
recommended to use prepackaged scientific Python distributions such as Anaconda,
Enthought Python Distribution, or Python(X,Y).
Other required software mainly comprises of Python packages that are all installed using
the Python installation manager, pip, which itself is installed using Python's easy_install
setup tool.
You will need to know some general programming concepts, and any kind of programming
experience will be helpful. However, the code in this book is explained almost line by line. You
don't need math for this book; every concept that is introduced is thoroughly explained in plain
English, and references are available for further interest in the topic.
Conventions
In this book, you will find a number of styles of text that distinguish between different kinds of
information. Here are some examples of these styles, and an explanation of their meaning.
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Another Random Scribd Document
with Unrelated Content
CHAPTER XXX
WHEN GREEK MEETS GREEK
It was Westy who spoke first. Just the same as it had been Westy
to speak for the others at the stricken home of this child whom
Emerson Skybrow had rescued. And what impelled Westy to break
the silence was the sight of Pee-wee gone to pieces, all his
boisterous enthusiasm ebbed away. A pitiable sight he was as he
stood there, trying bravely not to show his feelings. Of all the
botches he had ever made (and he had made many) this was the
worst. Within twenty-four hours the local paper of Bridgeboro would
have the name of Emerson Skybrow in glaring headlines. And he had
lost him. A deed worthy of the scout gold cross had been done by
this boy to whom a little girl and a noble dog paid the tribute of their
trust and love.
As by a miracle, the boy who had “treated him fine” in the city
was transformed into a rugged hero before his eyes. No wonder he
saw that scarred and ragged figure as through a haze! No wonder
the irrepressible Roy Blakeley kept his mouth shut. No wonder
Westy, always kind and thoughtful, had to speak for the “boss” of
the Raven Patrol. There is dignity in a boy’s last name and Westy
paid Emerson this tribute in addressing him.
“Some searching party,” he said, quoting Emerson’s own phrase.
“Some scouts, I’ll say! Skybrow, I’ll be hanged if I wouldn’t hide my
little old face in shame, if it wasn’t that I like to look at you. Give us
your hand, will you?”
“I’ll be very glad to,” said Emerson. “It’s pretty muddy, I’m afraid.
Is this a new member of your troop, Harris? I’ve often seen you with
the dog,” he added, addressing Toby. “They were lucky to find you.”
“What do you mean, new member?” Toby demanded. “Don’t pick
on me, I’m out of it. Put me on the waiting list if you want to.
There’s your scout, right there. Bob picked him out for you. You’ll
find me up at Hamburger Mike’s any time you want me. If I’m not
there, I’ll be talking to the girl over in the station.”
“That’s the talk,” said Westy. “Now we know you’re a scout and
you’ll get tagged before long. Before we go any further, let’s get this
thing settled. I hear a car coming, and I want to try to stop it and
see if they’ll take us back to Bridgeboro. You’re wished onto the
raving Ravens, you understand that, don’t you?” Westy asked
Emerson.
“Why—eh, I promised in a way——”
“Yes, well, you’re going to keep your word, aren’t you?” Westy
insisted. “If you’re willing to tie up with a bunch of simps like us.
What do you say, Skybrow? We can talk it all over afterward, but
just say the word now—on account of the kid.”
“I kept—I kept my—promise to you,” said Pee-wee, speaking with
difficulty. “Gee whiz, I should think you’d be willing to join us
because anyway, we’re not such terrible simps and anyway, maybe
you can sort of teach us, kind of.” The sound of an auto was heard
in the distance.
“Come on, Em, say the word,” said Connie.
“You’re very kind,” said Emerson.
“Is it yes?” demanded Artie.
“Why if, I’m sure——”
“Say yop,” said Pee-wee.
“Yop,” said Emerson Skybrow.
“Now to stop the auto,” said Westy. “Seems to be coming along
pretty fast; I bet he doesn’t pay any attention——”
“Leave it to me! Leave it to me!” Pee-wee thundered. “I know a
way to stop it! Leave it to me. Gee whiz, didn’t I even stop a circus
parade?”
“Oh, absolutely, positively,” laughed Roy.
“And don’t forget Queen Tut,” said Dorry Benton.
“Oh, posilutely not,” laughed Roy again.
“Don’t worry about the auto,” said Connie.
“Leave it to Pee-wee,” laughed several voices in chorus.
“Safe in the hands of the fixer,” shouted Roy joyously. “Goooood
niiiiiiight.”
CHAPTER XXXII
THE NEW SCOUT
The latter part of the evening was given over to the radio, and the
two sat listening in with the receivers on their ears.
O.U.J. was furnishing a varied program that evening. Pee-wee
liked O.U.J. for the performers were a happy, bantering set, seeming
to make the distant listener one of their own merry party. Moreover,
O.U.J. was a night owl pursuing its wanton course of song and
laughter after other stations had said good night and gone to bed.
Evidently Plarry Blythe who sang songs and jollied the silver-tongued
announcer had no home; at least he never went to it.
Emerson had never listened to a radio and he found it novel and
entertaining. The ear pieces did double duty for they not only
transmitted the voices of the night to Emerson but they effectually
shut off Pee-wee’s voice as well. He talked but Emerson did not hear
him.
It must have been nearly midnight and time for all respectable
broadcasting stations to be home and in bed. Certainly it was time
for Pee-wee to be in bed. But O.U.J. kept it up, and as the hour
grew later they sang the latest songs. Lateness was their middle
name. At last the Jamboree Jazz Band struck up. This outlandish and
earsplitting group, compared with which the noises of a boiler
factory were like a gentle zephyr, usually heralded the conclusion of
the program. Pee-wee liked the Jamboree Jazz Band. Emerson,
educated to good music, listened with rueful amusement.
Suddenly, in the very midst of the Jumping Jiminy One Step, the
Jamboree Jazz Band ceased to play. For a few moments a holy calm
seemed to have fallen upon the still night. Then came a series of
weird squeaks and plaintive wails as if the spirits of the air were
uniting in an uncanny chorus. One of these spirits seemed to have
gone completely out of its head, shrieking uncontrollably.
Schooled to such a contingency, Pee-wee’s hand sought the little
knob by which the unseen performers might be lured back to their
duties.
But the weird voices only screamed the more discordantly. Then
they ceased altogether. With both hands Pee-wee tried desperately
to find the music but his frantic efforts were of no avail. The
Jamboree Jazz Band was as silent as the grave. The Jumping Jiminy
One Step had stepped away altogether.
“What’s the matter?” Emerson asked.
“Wait a minute,” Pee-wee said, frantically preoccupied with the
mechanism.
But the Jumping Jiminy One Step had evidently jumped too far
and he could not overtake it.
“They stopped right in the middle,” said Emerson.
Then suddenly Pee-wee caught the friendly, ingratiating voice of
the announcer at O.U.J. Nothing could ruffle that gentlemanly tone.
He would have announced the end of the world in a voice of soft
composure.
“Listen!” said Pee-wee, “he’s saying something.”
He was certainly saying something. He had evidently begun
saying it before Pee-wee had succeeded in arresting that soft voice.
From the rather startling nature of his announcement (or such of it
as our listeners-in heard) it seemed likely that the Jamboree Jazz
Band had been summarily silenced in the interest of this important
matter. The boys listened attentively, Pee-wee spellbound as the
voice continued:
“... and the police department of New York will be glad of any
information that might be helpful in running down this car.”
“Listen!” Pee-wee gasped in a tragic whisper. “He’s finished, we
missed it,” said Emerson. But the announcer continued, hesitating
now and then, as if putting into his own words a request made from
some other source, “Every effort is being made to head off this car
in Westchester County in this state but it is thought not unlikely that
the thieves may have crossed one of the Jersey ferries with it,
probably an uptown ferry, and be heading through northern New
Jersey. If the car was stolen by gypsies, as is suspected——”
Here the announcer’s voice was drowned in a riot of irrelevant
sounds characteristic of Pee-wee’s radio set, and when our hero
succeeded in catching the voice again, the announcer was
concluding his thrilling appeal to listeners—in New Jersey. “The car
was a Hunkajunk six touring car thought to be occupied by gypsies,
the license number is 642-987 N.Y. but the number may have been
obscured to prevent identification. Any information concerning this
car should be telephoned at once to the police authorities where the
car was seen. This is station O.U.J., New York City. Please stand by
for continuation of our regular program.”
CHAPTER XXXIV
THE SHORT CUT
But Pee-wee did not “stand by” for continuation of the regular
program. The Jamboree Jazz Band had no more charms for him.
He had heard and read of startling announcements being made
over the radio, of interruptions in deference to appalling S.O.S. calls,
of appeals for cooperation and assistance from the constituted
authorities here and there. But never in his wildest dreams (and his
dreams were the wildest) had he, Walter Harris, ever been asked,
directly and indirectly to cooperate in the apprehension of a fugitive
criminal. He felt now that in a way he had been appointed a member
of the great metropolitan police force and that a terrible
responsibility had been placed upon him.
“That’s very interesting,” said Emerson, unmoved by the dramatic
character of the announcement.
“Interesting?” roared Pee-wee. “Do you call it interesting if—if—if
a lot of gypsies steal a car and we have to be on the lookout for
them? Do you call it interesting, just kind of, if we have to hurry out
of here to circumspect thieves?”
“Do you mean circumvent?” Emerson asked.
“I mean foil!” Pee-wee shouted. “Come ahead, we have to catch
them, hurry up, where did I leave my cap?”
“I don’t know,” said Emerson, arising dutifully but reluctantly. “You
said scouts always know where they leave things.”
“In the woods I said,” roared Pee-wee. “If a scout hides
something in the woods he can always find it. Caps are different,” he
added, instituting a frantic search for his ever elusive cap.
“I should think the best place to keep it would be on your head,”
Emerson commented, “then you’d always know where to find it.
Mine’s downstairs on the hat rack.”
Pee-wee presently apprehended his cap on the top of the
bookcase and then hurried downstairs intent on apprehending the
fugitives from New York. Emerson followed with a calmness quite
disproportionate to the dramatic character of their errand. He had
just begun thoroughly to enjoy the broadcasting and was listening in
with quiet interest when suddenly he found himself launched again
upon the sea of adventure.
Having accustomed himself to the clamor and turmoil of the
Jamboree Jazz Band and begun to enjoy the novelty of the distant,
unseen entertainment, he would have preferred to let well enough
alone. But he was beginning to learn that one who followed Pee-wee
must be prepared for anything or must be willing to do anything
whether he is prepared or not.
“What are we going to do?” Emerson asked as they hurried along
the dark street.
“We’re going to take a short-cut to the state road,” Pee-wee
answered, “because that’ll surely be the road they’ll take.”
“Why will it?” the reasonable Emerson asked.
“Because it will be. We’re going to lie in ambush along the road
just where it leaves town where we can see every car that comes
along. Do you know where Lanky Betts keeps his frankfurter stand in
the summer? We’re going to hang out there. That little shack is
open,” Pee-wee panted as they ran, “and we can wait inside of it
because the door is broken and we can get in and it’ll be all right
because I know Lanky because I buy lots of frankfurters from him
when the shack is open and root beer too—you get great big ice
cream cones there.”
Emerson was not too hopeful of a triumphant sequel to their
midnight excursion into the detective field; he felt that it was a long
call between the rather unconclusive information of the broadcaster
and the actual halting of the criminals in this neighborhood. But the
mention of frankfurters touched a responsive chord in his nature, for
the night was chill and raw and even the lowly frankfurter appealed
to him.
“It’s a pity we can’t get something to eat there now,” he observed.
“We’re not supposed to be thinking of eats now,” panted our hero.
This was rather odd, coming from Pee-wee.
CHAPTER XXXV
“DANGER”
“I didn’t tell you all I’m going to do,” said Pee-wee darkly. “I didn’t
tell you all the plans I have.”
This rather startling pronouncement prompted Emerson to say,
“You’d better tell me the worst.”
“You’ll see,” said Pee-wee.
On arriving at Lanky Betts’ deserted shack, Emerson was
somewhat caught by the spirit of their adventure. Pee-wee had at
least brought him to a good waiting place. The rough, little
refreshment stand had that forlorn look which all such roadside
dispensaries have during the closed season. But the spirit of the
frankfurter haunted it and it soon became evident to the patient
Emerson that here Pee-wee was on familiar ground.
“Maybe you didn’t know I was here last Saturday,” said Pee-wee.
“I was here with Lanky when he brought his stove and a lot of
things and I helped him to bring them. Do you see that can? That’s
got red paint in it so as he can paint his signs. Do you know why he
uses red paint?”
“So he can paint his signs,” said Emerson.
“He paints ’em in red so everybody’ll know the frankfurters are
hot; gee whiz, he knows how to make you hungry, that feller does.”
“He’s made me hungry already,” said Emerson.
“Are you hungry?”
“I think it makes you hungry being out in the chill air, don’t you?”
“I don’t know,” said Pee-wee; “gee whiz, I’m always hungry. But
don’t you care, because afterwards we’ll get something to eat. Do
you know what I’m going to do? Now you’ll see all the ideas I had.
I’m going to paint the word Danger on a board, good and big, in red
letters. See, I got my flashlight to work by; a scout has to remember
things. So hurry up, you open the can while I get a board.”
There is reality in action. And such desperate action as Pee-wee’s
was bound to be convincing.
Even the quiet Emerson could not fail to be captivated by the
situation, and all of Pee-wee’s frantic preparations for his epoch-
making coup had the true ring of adventure. It was not like sitting
home talking about catching bandits. Here they were in a little,
deserted, rough board shack on the outskirts of town, bordering the
likeliest exit from the metropolitan area. And this within ten or
fifteen minutes of the sensational appeal broadcasted from station
O.U.J., New York.
Surely, Emerson felt bound to acknowledge, it was not at all
unlikely that the gypsies in the stolen car might pass here, and if he
and Pee-wee could but stop them a great triumph would be theirs. A
great triumph was Pee-wee’s already, for his enthusiasm and
concentrated efforts proved contagious. Picking up an old rusty
knife, Emerson proceeded to dig a hole in the top of the can of red
paint while Pee-wee hauled forth an old board which was part of the
detachable architecture of the shack.
“Now while I paint Danger on the board,” said Pee-wee excitedly,
“you take that old chair and stand it in the middle of the road and
then we’ll stand the board against the back of the chair.”
Within five minutes Lanky Betts’ rickety old kitchen chair in which
he was wont to sit tilted back against the shack waiting for trade
was cast in the heroic role of easel for a board on which the
arresting word Danger was painted in huge red letters. So liberally
had the paint been used in Pee-wee’s frantic haste that the letters
had pendants of dripping red below them, imparting an artistic effect
to Pee-wee’s handiwork.
But the whole thing looked like business and the general effect of
something impending was heightened by the appearance of Pee-wee
himself lurking in the doorway of the shack clutching in one hand
the rusty knife, dripping red, with which Emerson had opened the
paint can, and in his other hand another weapon equally dangerous,
which he had rescued from a grocery box under the counter. This
was an ice-pick used in the good old summer-time to reduce the ice
to fragments in the genial freezers containing chocolate, vanilla and
raspberry cream. But now it was to be used for a purpose less
kindly.
“Now I’ll tell you the way we’ll do,” said Pee-wee. “We’ll sit inside
here all quiet like and every car that stops we’ll see if it’s a
Hunkajunk six, and if it is and it’s got gypsies in it, I’m going to
sneak around in back of it and jab this ice-pick into one of the rear
tires and then run. While I’m doing that—do you see that house up
off the road? There’s no light in it but you can see it.”
“I see it,” said Emerson.
“As soon as I sneak around in back of the car you run up to that
house for all you’re worth and ring the bell and bang on the door
and everything and wake them up no matter what and tell them to
’phone down to Chief Shay that we stopped some bandits stealing a
car. I’ll come running up to the house by a roundabout way and I’ll
meet you there. See? They won’t be able to drive the car, not very
fast anyway, and before they could change a tire or drive half a mile
the Bridgeboro police will be here.”
This plan seemed sound and scientific. Nobody whose armament
was limited to an ice-pick could have planned better. There was at
least an even chance that the auto thieves would come this way and
unless they were very near-sighted or very reckless they would
certainly pause before Pee-wee’s flaunted warning. If Emerson had
been skeptical at first he was now convinced that the chances were
at least fair and that the plan of campaign was masterly.
In short there was not the slightest reason why the moon should
have smiled down upon these brave preparations. But the moon did
smile. Pee-wee did not smile, however. He scowled. He scowled the
scowl of a hero as he laid aside the knife dripping with gore, and felt
tenderly the point of the deadly ice-pick.
Perhaps it was a wonder the moon did not laugh out loud.
CHAPTER XXXVI
PEE-WEE TRIUMPHANT
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