Scatter Plots - Python Matplotlib Tutorial #3

In this Python tutorial, you will learn everything you need to know about scatter plots using Matplotlib library. Scatter plots are great in showing the relationship between variables in our dataset, eventually revealing a correlation.

This is a complete tutorial on scatter plots including Bubble plots and an additional variable mapped to the marker’s color (you will also learn how to add colorbar and choose the best colormap to your case). We will discuss how to change the marker of your scatter plot using two different methods: 1. Symbols from Matplotlib and 2. Symbols from Latex. As usual, I will share several tips and tricks to save your time when customizing your graph.

We will cover from the very basic to more advanced aspects in 15 minutes. I hope you enjoy this tutorial.

Playlist: Matplotlib Course | Video #3
Access the code here: https://github.com/rscorrea1/youtube.git

Learn how to use Jupyter Notebooks: https://www.youtube.com/watch?v=gGYaFfAvYtg

Additional Courses:
Beginner Python Tutorials: https://www.youtube.com/watch?v=HG_E6EaKY90&list=PLJgwF35R54crXsGuSKR_MtUG2ABU_BFAq
Intermediate Python Tutorials: https://www.youtube.com/watch?v=oNwaOFZDAWo&list=PLJgwF35R54coNbQXGNJyawp-_3CC6I1B4
NumPy Tutorials: https://www.youtube.com/watch?v=YRes9M71_Ts&list=PLJgwF35R54cqqbFFHdArwQuBUUUoLKJ4V

#matplotlib #python #python matplotlib tutorial #scatter plots

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A Pure PHP Implementation Of The MessagePack Serialization Format

msgpack.php

A pure PHP implementation of the MessagePack serialization format.

Features

• Fully compliant with the latest MessagePack specification
• Supports streaming unpacking
• Supports unsigned 64-bit integers handling
• Supports object serialization
• Fully tested
• Relatively fast

Installation

The recommended way to install the library is through Composer:

composer require rybakit/msgpack

Usage

Packing

To pack values you can either use an instance of a Packer:

$packer = new Packer();
$packed = $packer->pack($value);

or call a static method on the MessagePack class:

$packed = MessagePack::pack($value);

In the examples above, the method pack automatically packs a value depending on its type. However, not all PHP types can be uniquely translated to MessagePack types. For example, the MessagePack format defines map and array types, which are represented by a single array type in PHP. By default, the packer will pack a PHP array as a MessagePack array if it has sequential numeric keys, starting from 0 and as a MessagePack map otherwise:

$mpArr1 = $packer->pack([1, 2]);               // MP array [1, 2]
$mpArr2 = $packer->pack([0 => 1, 1 => 2]);     // MP array [1, 2]
$mpMap1 = $packer->pack([0 => 1, 2 => 3]);     // MP map {0: 1, 2: 3}
$mpMap2 = $packer->pack([1 => 2, 2 => 3]);     // MP map {1: 2, 2: 3}
$mpMap3 = $packer->pack(['a' => 1, 'b' => 2]); // MP map {a: 1, b: 2}

However, sometimes you need to pack a sequential array as a MessagePack map. To do this, use the packMap method:

$mpMap = $packer->packMap([1, 2]); // {0: 1, 1: 2}

Here is a list of type-specific packing methods:

$packer->packNil();           // MP nil
$packer->packBool(true);      // MP bool
$packer->packInt(42);         // MP int
$packer->packFloat(M_PI);     // MP float (32 or 64)
$packer->packFloat32(M_PI);   // MP float 32
$packer->packFloat64(M_PI);   // MP float 64
$packer->packStr('foo');      // MP str
$packer->packBin("\x80");     // MP bin
$packer->packArray([1, 2]);   // MP array
$packer->packMap(['a' => 1]); // MP map
$packer->packExt(1, "\xaa");  // MP ext

Check the "Custom types" section below on how to pack custom types.

Packing options

The Packer object supports a number of bitmask-based options for fine-tuning the packing process (defaults are in bold):

Name	Description
FORCE_STR	Forces PHP strings to be packed as MessagePack UTF-8 strings
FORCE_BIN	Forces PHP strings to be packed as MessagePack binary data
DETECT_STR_BIN	Detects MessagePack str/bin type automatically
FORCE_ARR	Forces PHP arrays to be packed as MessagePack arrays
FORCE_MAP	Forces PHP arrays to be packed as MessagePack maps
DETECT_ARR_MAP	Detects MessagePack array/map type automatically
FORCE_FLOAT32	Forces PHP floats to be packed as 32-bits MessagePack floats
FORCE_FLOAT64	Forces PHP floats to be packed as 64-bits MessagePack floats

The type detection mode (DETECT_STR_BIN/DETECT_ARR_MAP) adds some overhead which can be noticed when you pack large (16- and 32-bit) arrays or strings. However, if you know the value type in advance (for example, you only work with UTF-8 strings or/and associative arrays), you can eliminate this overhead by forcing the packer to use the appropriate type, which will save it from running the auto-detection routine. Another option is to explicitly specify the value type. The library provides 2 auxiliary classes for this, Map and Bin. Check the "Custom types" section below for details.

Examples:

// detect str/bin type and pack PHP 64-bit floats (doubles) to MP 32-bit floats
$packer = new Packer(PackOptions::DETECT_STR_BIN | PackOptions::FORCE_FLOAT32);

// these will throw MessagePack\Exception\InvalidOptionException
$packer = new Packer(PackOptions::FORCE_STR | PackOptions::FORCE_BIN);
$packer = new Packer(PackOptions::FORCE_FLOAT32 | PackOptions::FORCE_FLOAT64);

Unpacking

To unpack data you can either use an instance of a BufferUnpacker:

$unpacker = new BufferUnpacker();

$unpacker->reset($packed);
$value = $unpacker->unpack();

or call a static method on the MessagePack class:

$value = MessagePack::unpack($packed);

If the packed data is received in chunks (e.g. when reading from a stream), use the tryUnpack method, which attempts to unpack data and returns an array of unpacked messages (if any) instead of throwing an InsufficientDataException:

while ($chunk = ...) {
    $unpacker->append($chunk);
    if ($messages = $unpacker->tryUnpack()) {
        return $messages;
    }
}

If you want to unpack from a specific position in a buffer, use seek:

$unpacker->seek(42); // set position equal to 42 bytes
$unpacker->seek(-8); // set position to 8 bytes before the end of the buffer

To skip bytes from the current position, use skip:

$unpacker->skip(10); // set position to 10 bytes ahead of the current position

To get the number of remaining (unread) bytes in the buffer:

$unreadBytesCount = $unpacker->getRemainingCount();

To check whether the buffer has unread data:

$hasUnreadBytes = $unpacker->hasRemaining();

If needed, you can remove already read data from the buffer by calling:

$releasedBytesCount = $unpacker->release();

With the read method you can read raw (packed) data:

$packedData = $unpacker->read(2); // read 2 bytes

Besides the above methods BufferUnpacker provides type-specific unpacking methods, namely:

$unpacker->unpackNil();   // PHP null
$unpacker->unpackBool();  // PHP bool
$unpacker->unpackInt();   // PHP int
$unpacker->unpackFloat(); // PHP float
$unpacker->unpackStr();   // PHP UTF-8 string
$unpacker->unpackBin();   // PHP binary string
$unpacker->unpackArray(); // PHP sequential array
$unpacker->unpackMap();   // PHP associative array
$unpacker->unpackExt();   // PHP MessagePack\Type\Ext object

Unpacking options

The BufferUnpacker object supports a number of bitmask-based options for fine-tuning the unpacking process (defaults are in bold):

Name	Description
BIGINT_AS_STR	Converts overflowed integers to strings [1]
BIGINT_AS_GMP	Converts overflowed integers to GMP objects [2]
BIGINT_AS_DEC	Converts overflowed integers to Decimal\Decimal objects [3]

1. The binary MessagePack format has unsigned 64-bit as its largest integer data type, but PHP does not support such integers, which means that an overflow can occur during unpacking.

2. Make sure the GMP extension is enabled.

3. Make sure the Decimal extension is enabled.

Examples:

$packedUint64 = "\xcf"."\xff\xff\xff\xff"."\xff\xff\xff\xff";

$unpacker = new BufferUnpacker($packedUint64);
var_dump($unpacker->unpack()); // string(20) "18446744073709551615"

$unpacker = new BufferUnpacker($packedUint64, UnpackOptions::BIGINT_AS_GMP);
var_dump($unpacker->unpack()); // object(GMP) {...}

$unpacker = new BufferUnpacker($packedUint64, UnpackOptions::BIGINT_AS_DEC);
var_dump($unpacker->unpack()); // object(Decimal\Decimal) {...}

Custom types

In addition to the basic types, the library provides functionality to serialize and deserialize arbitrary types. This can be done in several ways, depending on your use case. Let's take a look at them.

Type objects

If you need to serialize an instance of one of your classes into one of the basic MessagePack types, the best way to do this is to implement the CanBePacked interface in the class. A good example of such a class is the Map type class that comes with the library. This type is useful when you want to explicitly specify that a given PHP array should be packed as a MessagePack map without triggering an automatic type detection routine:

$packer = new Packer();

$packedMap = $packer->pack(new Map([1, 2, 3]));
$packedArray = $packer->pack([1, 2, 3]);

More type examples can be found in the src/Type directory.

Type transformers

As with type objects, type transformers are only responsible for serializing values. They should be used when you need to serialize a value that does not implement the CanBePacked interface. Examples of such values could be instances of built-in or third-party classes that you don't own, or non-objects such as resources.

A transformer class must implement the CanPack interface. To use a transformer, it must first be registered in the packer. Here is an example of how to serialize PHP streams into the MessagePack bin format type using one of the supplied transformers, StreamTransformer:

$packer = new Packer(null, [new StreamTransformer()]);

$packedBin = $packer->pack(fopen('/path/to/file', 'r+'));

More type transformer examples can be found in the src/TypeTransformer directory.

Extensions

In contrast to the cases described above, extensions are intended to handle extension types and are responsible for both serialization and deserialization of values (types).

An extension class must implement the Extension interface. To use an extension, it must first be registered in the packer and the unpacker.

The MessagePack specification divides extension types into two groups: predefined and application-specific. Currently, there is only one predefined type in the specification, Timestamp.

Timestamp

The Timestamp extension type is a predefined type. Support for this type in the library is done through the TimestampExtension class. This class is responsible for handling Timestamp objects, which represent the number of seconds and optional adjustment in nanoseconds:

$timestampExtension = new TimestampExtension();

$packer = new Packer();
$packer = $packer->extendWith($timestampExtension);

$unpacker = new BufferUnpacker();
$unpacker = $unpacker->extendWith($timestampExtension);

$packedTimestamp = $packer->pack(Timestamp::now());
$timestamp = $unpacker->reset($packedTimestamp)->unpack();

$seconds = $timestamp->getSeconds();
$nanoseconds = $timestamp->getNanoseconds();

When using the MessagePack class, the Timestamp extension is already registered:

$packedTimestamp = MessagePack::pack(Timestamp::now());
$timestamp = MessagePack::unpack($packedTimestamp);

Application-specific extensions

In addition, the format can be extended with your own types. For example, to make the built-in PHP DateTime objects first-class citizens in your code, you can create a corresponding extension, as shown in the example. Please note, that custom extensions have to be registered with a unique extension ID (an integer from 0 to 127).

More extension examples can be found in the examples/MessagePack directory.

To learn more about how extension types can be useful, check out this article.

Exceptions

If an error occurs during packing/unpacking, a PackingFailedException or an UnpackingFailedException will be thrown, respectively. In addition, an InsufficientDataException can be thrown during unpacking.

An InvalidOptionException will be thrown in case an invalid option (or a combination of mutually exclusive options) is used.

Tests

Run tests as follows:

vendor/bin/phpunit

Also, if you already have Docker installed, you can run the tests in a docker container. First, create a container:

./dockerfile.sh | docker build -t msgpack -

The command above will create a container named msgpack with PHP 8.1 runtime. You may change the default runtime by defining the PHP_IMAGE environment variable:

PHP_IMAGE='php:8.0-cli' ./dockerfile.sh | docker build -t msgpack -

See a list of various images here.

Then run the unit tests:

docker run --rm -v $PWD:/msgpack -w /msgpack msgpack

Fuzzing

To ensure that the unpacking works correctly with malformed/semi-malformed data, you can use a testing technique called Fuzzing. The library ships with a help file (target) for PHP-Fuzzer and can be used as follows:

php-fuzzer fuzz tests/fuzz_buffer_unpacker.php

Performance

To check performance, run:

php -n -dzend_extension=opcache.so \
-dpcre.jit=1 -dopcache.enable=1 -dopcache.enable_cli=1 \
tests/bench.php

Example output

Filter: MessagePack\Tests\Perf\Filter\ListFilter
Rounds: 3
Iterations: 100000

=============================================
Test/Target            Packer  BufferUnpacker
---------------------------------------------
nil .................. 0.0030 ........ 0.0139
false ................ 0.0037 ........ 0.0144
true ................. 0.0040 ........ 0.0137
7-bit uint #1 ........ 0.0052 ........ 0.0120
7-bit uint #2 ........ 0.0059 ........ 0.0114
7-bit uint #3 ........ 0.0061 ........ 0.0119
5-bit sint #1 ........ 0.0067 ........ 0.0126
5-bit sint #2 ........ 0.0064 ........ 0.0132
5-bit sint #3 ........ 0.0066 ........ 0.0135
8-bit uint #1 ........ 0.0078 ........ 0.0200
8-bit uint #2 ........ 0.0077 ........ 0.0212
8-bit uint #3 ........ 0.0086 ........ 0.0203
16-bit uint #1 ....... 0.0111 ........ 0.0271
16-bit uint #2 ....... 0.0115 ........ 0.0260
16-bit uint #3 ....... 0.0103 ........ 0.0273
32-bit uint #1 ....... 0.0116 ........ 0.0326
32-bit uint #2 ....... 0.0118 ........ 0.0332
32-bit uint #3 ....... 0.0127 ........ 0.0325
64-bit uint #1 ....... 0.0140 ........ 0.0277
64-bit uint #2 ....... 0.0134 ........ 0.0294
64-bit uint #3 ....... 0.0134 ........ 0.0281
8-bit int #1 ......... 0.0086 ........ 0.0241
8-bit int #2 ......... 0.0089 ........ 0.0225
8-bit int #3 ......... 0.0085 ........ 0.0229
16-bit int #1 ........ 0.0118 ........ 0.0280
16-bit int #2 ........ 0.0121 ........ 0.0270
16-bit int #3 ........ 0.0109 ........ 0.0274
32-bit int #1 ........ 0.0128 ........ 0.0346
32-bit int #2 ........ 0.0118 ........ 0.0339
32-bit int #3 ........ 0.0135 ........ 0.0368
64-bit int #1 ........ 0.0138 ........ 0.0276
64-bit int #2 ........ 0.0132 ........ 0.0286
64-bit int #3 ........ 0.0137 ........ 0.0274
64-bit int #4 ........ 0.0180 ........ 0.0285
64-bit float #1 ...... 0.0134 ........ 0.0284
64-bit float #2 ...... 0.0125 ........ 0.0275
64-bit float #3 ...... 0.0126 ........ 0.0283
fix string #1 ........ 0.0035 ........ 0.0133
fix string #2 ........ 0.0094 ........ 0.0216
fix string #3 ........ 0.0094 ........ 0.0222
fix string #4 ........ 0.0091 ........ 0.0241
8-bit string #1 ...... 0.0122 ........ 0.0301
8-bit string #2 ...... 0.0118 ........ 0.0304
8-bit string #3 ...... 0.0119 ........ 0.0315
16-bit string #1 ..... 0.0150 ........ 0.0388
16-bit string #2 ..... 0.1545 ........ 0.1665
32-bit string ........ 0.1570 ........ 0.1756
wide char string #1 .. 0.0091 ........ 0.0236
wide char string #2 .. 0.0122 ........ 0.0313
8-bit binary #1 ...... 0.0100 ........ 0.0302
8-bit binary #2 ...... 0.0123 ........ 0.0324
8-bit binary #3 ...... 0.0126 ........ 0.0327
16-bit binary ........ 0.0168 ........ 0.0372
32-bit binary ........ 0.1588 ........ 0.1754
fix array #1 ......... 0.0042 ........ 0.0131
fix array #2 ......... 0.0294 ........ 0.0367
fix array #3 ......... 0.0412 ........ 0.0472
16-bit array #1 ...... 0.1378 ........ 0.1596
16-bit array #2 ........... S ............. S
32-bit array .............. S ............. S
complex array ........ 0.1865 ........ 0.2283
fix map #1 ........... 0.0725 ........ 0.1048
fix map #2 ........... 0.0319 ........ 0.0405
fix map #3 ........... 0.0356 ........ 0.0665
fix map #4 ........... 0.0465 ........ 0.0497
16-bit map #1 ........ 0.2540 ........ 0.3028
16-bit map #2 ............. S ............. S
32-bit map ................ S ............. S
complex map .......... 0.2372 ........ 0.2710
fixext 1 ............. 0.0283 ........ 0.0358
fixext 2 ............. 0.0291 ........ 0.0371
fixext 4 ............. 0.0302 ........ 0.0355
fixext 8 ............. 0.0288 ........ 0.0384
fixext 16 ............ 0.0293 ........ 0.0359
8-bit ext ............ 0.0302 ........ 0.0439
16-bit ext ........... 0.0334 ........ 0.0499
32-bit ext ........... 0.1845 ........ 0.1888
32-bit timestamp #1 .. 0.0337 ........ 0.0547
32-bit timestamp #2 .. 0.0335 ........ 0.0560
64-bit timestamp #1 .. 0.0371 ........ 0.0575
64-bit timestamp #2 .. 0.0374 ........ 0.0542
64-bit timestamp #3 .. 0.0356 ........ 0.0533
96-bit timestamp #1 .. 0.0362 ........ 0.0699
96-bit timestamp #2 .. 0.0381 ........ 0.0701
96-bit timestamp #3 .. 0.0367 ........ 0.0687
=============================================
Total                  2.7618          4.0820
Skipped                     4               4
Failed                      0               0
Ignored                     0               0

With JIT:

php -n -dzend_extension=opcache.so \
-dpcre.jit=1 -dopcache.jit_buffer_size=64M -dopcache.jit=tracing -dopcache.enable=1 -dopcache.enable_cli=1 \
tests/bench.php

Example output

Filter: MessagePack\Tests\Perf\Filter\ListFilter
Rounds: 3
Iterations: 100000

=============================================
Test/Target            Packer  BufferUnpacker
---------------------------------------------
nil .................. 0.0005 ........ 0.0054
false ................ 0.0004 ........ 0.0059
true ................. 0.0004 ........ 0.0059
7-bit uint #1 ........ 0.0010 ........ 0.0047
7-bit uint #2 ........ 0.0010 ........ 0.0046
7-bit uint #3 ........ 0.0010 ........ 0.0046
5-bit sint #1 ........ 0.0025 ........ 0.0046
5-bit sint #2 ........ 0.0023 ........ 0.0046
5-bit sint #3 ........ 0.0024 ........ 0.0045
8-bit uint #1 ........ 0.0043 ........ 0.0081
8-bit uint #2 ........ 0.0043 ........ 0.0079
8-bit uint #3 ........ 0.0041 ........ 0.0080
16-bit uint #1 ....... 0.0064 ........ 0.0095
16-bit uint #2 ....... 0.0064 ........ 0.0091
16-bit uint #3 ....... 0.0064 ........ 0.0094
32-bit uint #1 ....... 0.0085 ........ 0.0114
32-bit uint #2 ....... 0.0077 ........ 0.0122
32-bit uint #3 ....... 0.0077 ........ 0.0120
64-bit uint #1 ....... 0.0085 ........ 0.0159
64-bit uint #2 ....... 0.0086 ........ 0.0157
64-bit uint #3 ....... 0.0086 ........ 0.0158
8-bit int #1 ......... 0.0042 ........ 0.0080
8-bit int #2 ......... 0.0042 ........ 0.0080
8-bit int #3 ......... 0.0042 ........ 0.0081
16-bit int #1 ........ 0.0065 ........ 0.0095
16-bit int #2 ........ 0.0065 ........ 0.0090
16-bit int #3 ........ 0.0056 ........ 0.0085
32-bit int #1 ........ 0.0067 ........ 0.0107
32-bit int #2 ........ 0.0066 ........ 0.0106
32-bit int #3 ........ 0.0063 ........ 0.0104
64-bit int #1 ........ 0.0072 ........ 0.0162
64-bit int #2 ........ 0.0073 ........ 0.0174
64-bit int #3 ........ 0.0072 ........ 0.0164
64-bit int #4 ........ 0.0077 ........ 0.0161
64-bit float #1 ...... 0.0053 ........ 0.0135
64-bit float #2 ...... 0.0053 ........ 0.0135
64-bit float #3 ...... 0.0052 ........ 0.0135
fix string #1 ....... -0.0002 ........ 0.0044
fix string #2 ........ 0.0035 ........ 0.0067
fix string #3 ........ 0.0035 ........ 0.0077
fix string #4 ........ 0.0033 ........ 0.0078
8-bit string #1 ...... 0.0059 ........ 0.0110
8-bit string #2 ...... 0.0063 ........ 0.0121
8-bit string #3 ...... 0.0064 ........ 0.0124
16-bit string #1 ..... 0.0099 ........ 0.0146
16-bit string #2 ..... 0.1522 ........ 0.1474
32-bit string ........ 0.1511 ........ 0.1483
wide char string #1 .. 0.0039 ........ 0.0084
wide char string #2 .. 0.0073 ........ 0.0123
8-bit binary #1 ...... 0.0040 ........ 0.0112
8-bit binary #2 ...... 0.0075 ........ 0.0123
8-bit binary #3 ...... 0.0077 ........ 0.0129
16-bit binary ........ 0.0096 ........ 0.0145
32-bit binary ........ 0.1535 ........ 0.1479
fix array #1 ......... 0.0008 ........ 0.0061
fix array #2 ......... 0.0121 ........ 0.0165
fix array #3 ......... 0.0193 ........ 0.0222
16-bit array #1 ...... 0.0607 ........ 0.0479
16-bit array #2 ........... S ............. S
32-bit array .............. S ............. S
complex array ........ 0.0749 ........ 0.0824
fix map #1 ........... 0.0329 ........ 0.0431
fix map #2 ........... 0.0161 ........ 0.0189
fix map #3 ........... 0.0205 ........ 0.0262
fix map #4 ........... 0.0252 ........ 0.0205
16-bit map #1 ........ 0.1016 ........ 0.0927
16-bit map #2 ............. S ............. S
32-bit map ................ S ............. S
complex map .......... 0.1096 ........ 0.1030
fixext 1 ............. 0.0157 ........ 0.0161
fixext 2 ............. 0.0175 ........ 0.0183
fixext 4 ............. 0.0156 ........ 0.0185
fixext 8 ............. 0.0163 ........ 0.0184
fixext 16 ............ 0.0164 ........ 0.0182
8-bit ext ............ 0.0158 ........ 0.0207
16-bit ext ........... 0.0203 ........ 0.0219
32-bit ext ........... 0.1614 ........ 0.1539
32-bit timestamp #1 .. 0.0195 ........ 0.0249
32-bit timestamp #2 .. 0.0188 ........ 0.0260
64-bit timestamp #1 .. 0.0207 ........ 0.0281
64-bit timestamp #2 .. 0.0212 ........ 0.0291
64-bit timestamp #3 .. 0.0207 ........ 0.0295
96-bit timestamp #1 .. 0.0222 ........ 0.0358
96-bit timestamp #2 .. 0.0228 ........ 0.0353
96-bit timestamp #3 .. 0.0210 ........ 0.0319
=============================================
Total                  1.6432          1.9674
Skipped                     4               4
Failed                      0               0
Ignored                     0               0

You may change default benchmark settings by defining the following environment variables:

Name	Default
MP_BENCH_TARGETS	pure_p,pure_u, see a list of available targets
MP_BENCH_ITERATIONS	100_000
MP_BENCH_DURATION	not set
MP_BENCH_ROUNDS	3
MP_BENCH_TESTS	-@slow, see a list of available tests

For example:

export MP_BENCH_TARGETS=pure_p
export MP_BENCH_ITERATIONS=1000000
export MP_BENCH_ROUNDS=5
# a comma separated list of test names
export MP_BENCH_TESTS='complex array, complex map'
# or a group name
# export MP_BENCH_TESTS='-@slow' // @pecl_comp
# or a regexp
# export MP_BENCH_TESTS='/complex (array|map)/'

Another example, benchmarking both the library and the PECL extension:

MP_BENCH_TARGETS=pure_p,pure_u,pecl_p,pecl_u \
php -n -dextension=msgpack.so -dzend_extension=opcache.so \
-dpcre.jit=1 -dopcache.enable=1 -dopcache.enable_cli=1 \
tests/bench.php

Example output

Filter: MessagePack\Tests\Perf\Filter\ListFilter
Rounds: 3
Iterations: 100000

===========================================================================
Test/Target            Packer  BufferUnpacker  msgpack_pack  msgpack_unpack
---------------------------------------------------------------------------
nil .................. 0.0031 ........ 0.0141 ...... 0.0055 ........ 0.0064
false ................ 0.0039 ........ 0.0154 ...... 0.0056 ........ 0.0053
true ................. 0.0038 ........ 0.0139 ...... 0.0056 ........ 0.0044
7-bit uint #1 ........ 0.0061 ........ 0.0110 ...... 0.0059 ........ 0.0046
7-bit uint #2 ........ 0.0065 ........ 0.0119 ...... 0.0042 ........ 0.0029
7-bit uint #3 ........ 0.0054 ........ 0.0117 ...... 0.0045 ........ 0.0025
5-bit sint #1 ........ 0.0047 ........ 0.0103 ...... 0.0038 ........ 0.0022
5-bit sint #2 ........ 0.0048 ........ 0.0117 ...... 0.0038 ........ 0.0022
5-bit sint #3 ........ 0.0046 ........ 0.0102 ...... 0.0038 ........ 0.0023
8-bit uint #1 ........ 0.0063 ........ 0.0174 ...... 0.0039 ........ 0.0031
8-bit uint #2 ........ 0.0063 ........ 0.0167 ...... 0.0040 ........ 0.0029
8-bit uint #3 ........ 0.0063 ........ 0.0168 ...... 0.0039 ........ 0.0030
16-bit uint #1 ....... 0.0092 ........ 0.0222 ...... 0.0049 ........ 0.0030
16-bit uint #2 ....... 0.0096 ........ 0.0227 ...... 0.0042 ........ 0.0046
16-bit uint #3 ....... 0.0123 ........ 0.0274 ...... 0.0059 ........ 0.0051
32-bit uint #1 ....... 0.0136 ........ 0.0331 ...... 0.0060 ........ 0.0048
32-bit uint #2 ....... 0.0130 ........ 0.0336 ...... 0.0070 ........ 0.0048
32-bit uint #3 ....... 0.0127 ........ 0.0329 ...... 0.0051 ........ 0.0048
64-bit uint #1 ....... 0.0126 ........ 0.0268 ...... 0.0055 ........ 0.0049
64-bit uint #2 ....... 0.0135 ........ 0.0281 ...... 0.0052 ........ 0.0046
64-bit uint #3 ....... 0.0131 ........ 0.0274 ...... 0.0069 ........ 0.0044
8-bit int #1 ......... 0.0077 ........ 0.0236 ...... 0.0058 ........ 0.0044
8-bit int #2 ......... 0.0087 ........ 0.0244 ...... 0.0058 ........ 0.0048
8-bit int #3 ......... 0.0084 ........ 0.0241 ...... 0.0055 ........ 0.0049
16-bit int #1 ........ 0.0112 ........ 0.0271 ...... 0.0048 ........ 0.0045
16-bit int #2 ........ 0.0124 ........ 0.0292 ...... 0.0057 ........ 0.0049
16-bit int #3 ........ 0.0118 ........ 0.0270 ...... 0.0058 ........ 0.0050
32-bit int #1 ........ 0.0137 ........ 0.0366 ...... 0.0058 ........ 0.0051
32-bit int #2 ........ 0.0133 ........ 0.0366 ...... 0.0056 ........ 0.0049
32-bit int #3 ........ 0.0129 ........ 0.0350 ...... 0.0052 ........ 0.0048
64-bit int #1 ........ 0.0145 ........ 0.0254 ...... 0.0034 ........ 0.0025
64-bit int #2 ........ 0.0097 ........ 0.0214 ...... 0.0034 ........ 0.0025
64-bit int #3 ........ 0.0096 ........ 0.0287 ...... 0.0059 ........ 0.0050
64-bit int #4 ........ 0.0143 ........ 0.0277 ...... 0.0059 ........ 0.0046
64-bit float #1 ...... 0.0134 ........ 0.0281 ...... 0.0057 ........ 0.0052
64-bit float #2 ...... 0.0141 ........ 0.0281 ...... 0.0057 ........ 0.0050
64-bit float #3 ...... 0.0144 ........ 0.0282 ...... 0.0057 ........ 0.0050
fix string #1 ........ 0.0036 ........ 0.0143 ...... 0.0066 ........ 0.0053
fix string #2 ........ 0.0107 ........ 0.0222 ...... 0.0065 ........ 0.0068
fix string #3 ........ 0.0116 ........ 0.0245 ...... 0.0063 ........ 0.0069
fix string #4 ........ 0.0105 ........ 0.0253 ...... 0.0083 ........ 0.0077
8-bit string #1 ...... 0.0126 ........ 0.0318 ...... 0.0075 ........ 0.0088
8-bit string #2 ...... 0.0121 ........ 0.0295 ...... 0.0076 ........ 0.0086
8-bit string #3 ...... 0.0125 ........ 0.0293 ...... 0.0130 ........ 0.0093
16-bit string #1 ..... 0.0159 ........ 0.0368 ...... 0.0117 ........ 0.0086
16-bit string #2 ..... 0.1547 ........ 0.1686 ...... 0.1516 ........ 0.1373
32-bit string ........ 0.1558 ........ 0.1729 ...... 0.1511 ........ 0.1396
wide char string #1 .. 0.0098 ........ 0.0237 ...... 0.0066 ........ 0.0065
wide char string #2 .. 0.0128 ........ 0.0291 ...... 0.0061 ........ 0.0082
8-bit binary #1 ........... I ............. I ........... F ............. I
8-bit binary #2 ........... I ............. I ........... F ............. I
8-bit binary #3 ........... I ............. I ........... F ............. I
16-bit binary ............. I ............. I ........... F ............. I
32-bit binary ............. I ............. I ........... F ............. I
fix array #1 ......... 0.0040 ........ 0.0129 ...... 0.0120 ........ 0.0058
fix array #2 ......... 0.0279 ........ 0.0390 ...... 0.0143 ........ 0.0165
fix array #3 ......... 0.0415 ........ 0.0463 ...... 0.0162 ........ 0.0187
16-bit array #1 ...... 0.1349 ........ 0.1628 ...... 0.0334 ........ 0.0341
16-bit array #2 ........... S ............. S ........... S ............. S
32-bit array .............. S ............. S ........... S ............. S
complex array ............. I ............. I ........... F ............. F
fix map #1 ................ I ............. I ........... F ............. I
fix map #2 ........... 0.0345 ........ 0.0391 ...... 0.0143 ........ 0.0168
fix map #3 ................ I ............. I ........... F ............. I
fix map #4 ........... 0.0459 ........ 0.0473 ...... 0.0151 ........ 0.0163
16-bit map #1 ........ 0.2518 ........ 0.2962 ...... 0.0400 ........ 0.0490
16-bit map #2 ............. S ............. S ........... S ............. S
32-bit map ................ S ............. S ........... S ............. S
complex map .......... 0.2380 ........ 0.2682 ...... 0.0545 ........ 0.0579
fixext 1 .................. I ............. I ........... F ............. F
fixext 2 .................. I ............. I ........... F ............. F
fixext 4 .................. I ............. I ........... F ............. F
fixext 8 .................. I ............. I ........... F ............. F
fixext 16 ................. I ............. I ........... F ............. F
8-bit ext ................. I ............. I ........... F ............. F
16-bit ext ................ I ............. I ........... F ............. F
32-bit ext ................ I ............. I ........... F ............. F
32-bit timestamp #1 ....... I ............. I ........... F ............. F
32-bit timestamp #2 ....... I ............. I ........... F ............. F
64-bit timestamp #1 ....... I ............. I ........... F ............. F
64-bit timestamp #2 ....... I ............. I ........... F ............. F
64-bit timestamp #3 ....... I ............. I ........... F ............. F
96-bit timestamp #1 ....... I ............. I ........... F ............. F
96-bit timestamp #2 ....... I ............. I ........... F ............. F
96-bit timestamp #3 ....... I ............. I ........... F ............. F
===========================================================================
Total                  1.5625          2.3866        0.7735          0.7243
Skipped                     4               4             4               4
Failed                      0               0            24              17
Ignored                    24              24             0               7

With JIT:

MP_BENCH_TARGETS=pure_p,pure_u,pecl_p,pecl_u \
php -n -dextension=msgpack.so -dzend_extension=opcache.so \
-dpcre.jit=1 -dopcache.jit_buffer_size=64M -dopcache.jit=tracing -dopcache.enable=1 -dopcache.enable_cli=1 \
tests/bench.php

Example output

Filter: MessagePack\Tests\Perf\Filter\ListFilter
Rounds: 3
Iterations: 100000

===========================================================================
Test/Target            Packer  BufferUnpacker  msgpack_pack  msgpack_unpack
---------------------------------------------------------------------------
nil .................. 0.0001 ........ 0.0052 ...... 0.0053 ........ 0.0042
false ................ 0.0007 ........ 0.0060 ...... 0.0057 ........ 0.0043
true ................. 0.0008 ........ 0.0060 ...... 0.0056 ........ 0.0041
7-bit uint #1 ........ 0.0031 ........ 0.0046 ...... 0.0062 ........ 0.0041
7-bit uint #2 ........ 0.0021 ........ 0.0043 ...... 0.0062 ........ 0.0041
7-bit uint #3 ........ 0.0022 ........ 0.0044 ...... 0.0061 ........ 0.0040
5-bit sint #1 ........ 0.0030 ........ 0.0048 ...... 0.0062 ........ 0.0040
5-bit sint #2 ........ 0.0032 ........ 0.0046 ...... 0.0062 ........ 0.0040
5-bit sint #3 ........ 0.0031 ........ 0.0046 ...... 0.0062 ........ 0.0040
8-bit uint #1 ........ 0.0054 ........ 0.0079 ...... 0.0062 ........ 0.0050
8-bit uint #2 ........ 0.0051 ........ 0.0079 ...... 0.0064 ........ 0.0044
8-bit uint #3 ........ 0.0051 ........ 0.0082 ...... 0.0062 ........ 0.0044
16-bit uint #1 ....... 0.0077 ........ 0.0094 ...... 0.0065 ........ 0.0045
16-bit uint #2 ....... 0.0077 ........ 0.0094 ...... 0.0063 ........ 0.0045
16-bit uint #3 ....... 0.0077 ........ 0.0095 ...... 0.0064 ........ 0.0047
32-bit uint #1 ....... 0.0088 ........ 0.0119 ...... 0.0063 ........ 0.0043
32-bit uint #2 ....... 0.0089 ........ 0.0117 ...... 0.0062 ........ 0.0039
32-bit uint #3 ....... 0.0089 ........ 0.0118 ...... 0.0063 ........ 0.0044
64-bit uint #1 ....... 0.0097 ........ 0.0155 ...... 0.0063 ........ 0.0045
64-bit uint #2 ....... 0.0095 ........ 0.0153 ...... 0.0061 ........ 0.0045
64-bit uint #3 ....... 0.0096 ........ 0.0156 ...... 0.0063 ........ 0.0047
8-bit int #1 ......... 0.0053 ........ 0.0083 ...... 0.0062 ........ 0.0044
8-bit int #2 ......... 0.0052 ........ 0.0080 ...... 0.0062 ........ 0.0044
8-bit int #3 ......... 0.0052 ........ 0.0080 ...... 0.0062 ........ 0.0043
16-bit int #1 ........ 0.0089 ........ 0.0097 ...... 0.0069 ........ 0.0046
16-bit int #2 ........ 0.0075 ........ 0.0093 ...... 0.0063 ........ 0.0043
16-bit int #3 ........ 0.0075 ........ 0.0094 ...... 0.0062 ........ 0.0046
32-bit int #1 ........ 0.0086 ........ 0.0122 ...... 0.0063 ........ 0.0044
32-bit int #2 ........ 0.0087 ........ 0.0120 ...... 0.0066 ........ 0.0046
32-bit int #3 ........ 0.0086 ........ 0.0121 ...... 0.0060 ........ 0.0044
64-bit int #1 ........ 0.0096 ........ 0.0149 ...... 0.0060 ........ 0.0045
64-bit int #2 ........ 0.0096 ........ 0.0157 ...... 0.0062 ........ 0.0044
64-bit int #3 ........ 0.0096 ........ 0.0160 ...... 0.0063 ........ 0.0046
64-bit int #4 ........ 0.0097 ........ 0.0157 ...... 0.0061 ........ 0.0044
64-bit float #1 ...... 0.0079 ........ 0.0153 ...... 0.0056 ........ 0.0044
64-bit float #2 ...... 0.0079 ........ 0.0152 ...... 0.0057 ........ 0.0045
64-bit float #3 ...... 0.0079 ........ 0.0155 ...... 0.0057 ........ 0.0044
fix string #1 ........ 0.0010 ........ 0.0045 ...... 0.0071 ........ 0.0044
fix string #2 ........ 0.0048 ........ 0.0075 ...... 0.0070 ........ 0.0060
fix string #3 ........ 0.0048 ........ 0.0086 ...... 0.0068 ........ 0.0060
fix string #4 ........ 0.0050 ........ 0.0088 ...... 0.0070 ........ 0.0059
8-bit string #1 ...... 0.0081 ........ 0.0129 ...... 0.0069 ........ 0.0062
8-bit string #2 ...... 0.0086 ........ 0.0128 ...... 0.0069 ........ 0.0065
8-bit string #3 ...... 0.0086 ........ 0.0126 ...... 0.0115 ........ 0.0065
16-bit string #1 ..... 0.0105 ........ 0.0137 ...... 0.0128 ........ 0.0068
16-bit string #2 ..... 0.1510 ........ 0.1486 ...... 0.1526 ........ 0.1391
32-bit string ........ 0.1517 ........ 0.1475 ...... 0.1504 ........ 0.1370
wide char string #1 .. 0.0044 ........ 0.0085 ...... 0.0067 ........ 0.0057
wide char string #2 .. 0.0081 ........ 0.0125 ...... 0.0069 ........ 0.0063
8-bit binary #1 ........... I ............. I ........... F ............. I
8-bit binary #2 ........... I ............. I ........... F ............. I
8-bit binary #3 ........... I ............. I ........... F ............. I
16-bit binary ............. I ............. I ........... F ............. I
32-bit binary ............. I ............. I ........... F ............. I
fix array #1 ......... 0.0014 ........ 0.0059 ...... 0.0132 ........ 0.0055
fix array #2 ......... 0.0146 ........ 0.0156 ...... 0.0155 ........ 0.0148
fix array #3 ......... 0.0211 ........ 0.0229 ...... 0.0179 ........ 0.0180
16-bit array #1 ...... 0.0673 ........ 0.0498 ...... 0.0343 ........ 0.0388
16-bit array #2 ........... S ............. S ........... S ............. S
32-bit array .............. S ............. S ........... S ............. S
complex array ............. I ............. I ........... F ............. F
fix map #1 ................ I ............. I ........... F ............. I
fix map #2 ........... 0.0148 ........ 0.0180 ...... 0.0156 ........ 0.0179
fix map #3 ................ I ............. I ........... F ............. I
fix map #4 ........... 0.0252 ........ 0.0201 ...... 0.0214 ........ 0.0167
16-bit map #1 ........ 0.1027 ........ 0.0836 ...... 0.0388 ........ 0.0510
16-bit map #2 ............. S ............. S ........... S ............. S
32-bit map ................ S ............. S ........... S ............. S
complex map .......... 0.1104 ........ 0.1010 ...... 0.0556 ........ 0.0602
fixext 1 .................. I ............. I ........... F ............. F
fixext 2 .................. I ............. I ........... F ............. F
fixext 4 .................. I ............. I ........... F ............. F
fixext 8 .................. I ............. I ........... F ............. F
fixext 16 ................. I ............. I ........... F ............. F
8-bit ext ................. I ............. I ........... F ............. F
16-bit ext ................ I ............. I ........... F ............. F
32-bit ext ................ I ............. I ........... F ............. F
32-bit timestamp #1 ....... I ............. I ........... F ............. F
32-bit timestamp #2 ....... I ............. I ........... F ............. F
64-bit timestamp #1 ....... I ............. I ........... F ............. F
64-bit timestamp #2 ....... I ............. I ........... F ............. F
64-bit timestamp #3 ....... I ............. I ........... F ............. F
96-bit timestamp #1 ....... I ............. I ........... F ............. F
96-bit timestamp #2 ....... I ............. I ........... F ............. F
96-bit timestamp #3 ....... I ............. I ........... F ............. F
===========================================================================
Total                  0.9642          1.0909        0.8224          0.7213
Skipped                     4               4             4               4
Failed                      0               0            24              17
Ignored                    24              24             0               7

Note that the msgpack extension (v2.1.2) doesn't support ext, bin and UTF-8 str types.

License

The library is released under the MIT License. See the bundled LICENSE file for details.

Author: rybakit
Source Code: https://github.com/rybakit/msgpack.php
License: MIT License

#php 

Matplotlib Cheat Sheet: Plotting in Python

This Matplotlib cheat sheet introduces you to the basics that you need to plot your data with Python and includes code samples.

Data visualization and storytelling with your data are essential skills that every data scientist needs to communicate insights gained from analyses effectively to any audience out there. 

For most beginners, the first package that they use to get in touch with data visualization and storytelling is, naturally, Matplotlib: it is a Python 2D plotting library that enables users to make publication-quality figures. But, what might be even more convincing is the fact that other packages, such as Pandas, intend to build more plotting integration with Matplotlib as time goes on.

However, what might slow down beginners is the fact that this package is pretty extensive. There is so much that you can do with it and it might be hard to still keep a structure when you're learning how to work with Matplotlib.   

DataCamp has created a Matplotlib cheat sheet for those who might already know how to use the package to their advantage to make beautiful plots in Python, but that still want to keep a one-page reference handy. Of course, for those who don't know how to work with Matplotlib, this might be the extra push be convinced and to finally get started with data visualization in Python. 

You'll see that this cheat sheet presents you with the six basic steps that you can go through to make beautiful plots. 

Check out the infographic by clicking on the button below:

With this handy reference, you'll familiarize yourself in no time with the basics of Matplotlib: you'll learn how you can prepare your data, create a new plot, use some basic plotting routines to your advantage, add customizations to your plots, and save, show and close the plots that you make.

What might have looked difficult before will definitely be more clear once you start using this cheat sheet! Use it in combination with the Matplotlib Gallery, the documentation.

Matplotlib 

Matplotlib is a Python 2D plotting library which produces publication-quality figures in a variety of hardcopy formats and interactive environments across platforms.

Prepare the Data 

1D Data 

>>> import numpy as np
>>> x = np.linspace(0, 10, 100)
>>> y = np.cos(x)
>>> z = np.sin(x)

2D Data or Images 

>>> data = 2 * np.random.random((10, 10))
>>> data2 = 3 * np.random.random((10, 10))
>>> Y, X = np.mgrid[-3:3:100j, -3:3:100j]
>>> U = 1 X** 2 + Y
>>> V = 1 + X Y**2
>>> from matplotlib.cbook import get_sample_data
>>> img = np.load(get_sample_data('axes_grid/bivariate_normal.npy'))

Create Plot

>>> import matplotlib.pyplot as plt

Figure 

>>> fig = plt.figure()
>>> fig2 = plt.figure(figsize=plt.figaspect(2.0))

Axes 

>>> fig.add_axes()
>>> ax1 = fig.add_subplot(221) #row-col-num
>>> ax3 = fig.add_subplot(212)
>>> fig3, axes = plt.subplots(nrows=2,ncols=2)
>>> fig4, axes2 = plt.subplots(ncols=3)

Save Plot 

>>> plt.savefig('foo.png') #Save figures
>>> plt.savefig('foo.png',  transparent=True) #Save transparent figures

Show Plot

>>> plt.show()

Plotting Routines 

1D Data 

>>> fig, ax = plt.subplots()
>>> lines = ax.plot(x,y) #Draw points with lines or markers connecting them
>>> ax.scatter(x,y) #Draw unconnected points, scaled or colored
>>> axes[0,0].bar([1,2,3],[3,4,5]) #Plot vertical rectangles (constant width)
>>> axes[1,0].barh([0.5,1,2.5],[0,1,2]) #Plot horiontal rectangles (constant height)
>>> axes[1,1].axhline(0.45) #Draw a horizontal line across axes
>>> axes[0,1].axvline(0.65) #Draw a vertical line across axes
>>> ax.fill(x,y,color='blue') #Draw filled polygons
>>> ax.fill_between(x,y,color='yellow') #Fill between y values and 0

2D Data 

>>> fig, ax = plt.subplots()
>>> im = ax.imshow(img, #Colormapped or RGB arrays
      cmap= 'gist_earth', 
      interpolation= 'nearest',
      vmin=-2,
      vmax=2)
>>> axes2[0].pcolor(data2) #Pseudocolor plot of 2D array
>>> axes2[0].pcolormesh(data) #Pseudocolor plot of 2D array
>>> CS = plt.contour(Y,X,U) #Plot contours
>>> axes2[2].contourf(data1) #Plot filled contours
>>> axes2[2]= ax.clabel(CS) #Label a contour plot

Vector Fields 

>>> axes[0,1].arrow(0,0,0.5,0.5) #Add an arrow to the axes
>>> axes[1,1].quiver(y,z) #Plot a 2D field of arrows
>>> axes[0,1].streamplot(X,Y,U,V) #Plot a 2D field of arrows

Data Distributions 

>>> ax1.hist(y) #Plot a histogram
>>> ax3.boxplot(y) #Make a box and whisker plot
>>> ax3.violinplot(z)  #Make a violin plot

Plot Anatomy & Workflow 

Plot Anatomy 

 y-axis      

                           x-axis 

Workflow 

The basic steps to creating plots with matplotlib are:

1 Prepare Data
2 Create Plot
3 Plot
4 Customized Plot
5 Save Plot
6 Show Plot

>>> import matplotlib.pyplot as plt
>>> x = [1,2,3,4]  #Step 1
>>> y = [10,20,25,30] 
>>> fig = plt.figure() #Step 2
>>> ax = fig.add_subplot(111) #Step 3
>>> ax.plot(x, y, color= 'lightblue', linewidth=3)  #Step 3, 4
>>> ax.scatter([2,4,6],
          [5,15,25],
          color= 'darkgreen',
          marker= '^' )
>>> ax.set_xlim(1, 6.5)
>>> plt.savefig('foo.png' ) #Step 5
>>> plt.show() #Step 6

Close and Clear 

>>> plt.cla()  #Clear an axis
>>> plt.clf(). #Clear the entire figure
>>> plt.close(). #Close a window

Plotting Customize Plot 

Colors, Color Bars & Color Maps 

>>> plt.plot(x, x, x, x**2, x, x** 3)
>>> ax.plot(x, y, alpha = 0.4)
>>> ax.plot(x, y, c= 'k')
>>> fig.colorbar(im, orientation= 'horizontal')
>>> im = ax.imshow(img,
            cmap= 'seismic' )

Markers 

>>> fig, ax = plt.subplots()
>>> ax.scatter(x,y,marker= ".")
>>> ax.plot(x,y,marker= "o")

Linestyles 

>>> plt.plot(x,y,linewidth=4.0)
>>> plt.plot(x,y,ls= 'solid') 
>>> plt.plot(x,y,ls= '--') 
>>> plt.plot(x,y,'--' ,x**2,y**2,'-.' ) 
>>> plt.setp(lines,color= 'r',linewidth=4.0)

Text & Annotations 

>>> ax.text(1,
           -2.1, 
           'Example Graph', 
            style= 'italic' )
>>> ax.annotate("Sine", 
xy=(8, 0),
xycoords= 'data', 
xytext=(10.5, 0),
textcoords= 'data', 
arrowprops=dict(arrowstyle= "->", 
connectionstyle="arc3"),)

Mathtext 

>>> plt.title(r '$sigma_i=15$', fontsize=20)

Limits, Legends and Layouts 

Limits & Autoscaling 

>>> ax.margins(x=0.0,y=0.1) #Add padding to a plot
>>> ax.axis('equal')  #Set the aspect ratio of the plot to 1
>>> ax.set(xlim=[0,10.5],ylim=[-1.5,1.5])  #Set limits for x-and y-axis
>>> ax.set_xlim(0,10.5) #Set limits for x-axis

Legends 

>>> ax.set(title= 'An Example Axes',  #Set a title and x-and y-axis labels
            ylabel= 'Y-Axis', 
            xlabel= 'X-Axis')
>>> ax.legend(loc= 'best')  #No overlapping plot elements

Ticks 

>>> ax.xaxis.set(ticks=range(1,5),  #Manually set x-ticks
             ticklabels=[3,100, 12,"foo" ])
>>> ax.tick_params(axis= 'y', #Make y-ticks longer and go in and out
             direction= 'inout', 
              length=10)

Subplot Spacing 

>>> fig3.subplots_adjust(wspace=0.5,   #Adjust the spacing between subplots
             hspace=0.3,
             left=0.125,
             right=0.9,
             top=0.9,
             bottom=0.1)
>>> fig.tight_layout() #Fit subplot(s) in to the figure area

Axis Spines 

>>> ax1.spines[ 'top'].set_visible(False) #Make the top axis line for a plot invisible
>>> ax1.spines['bottom' ].set_position(( 'outward',10))  #Move the bottom axis line outward

Have this Cheat Sheet at your fingertips

Original article source at https://www.datacamp.com

#matplotlib #cheatsheet #python

Exploratory Data Analysis(EDA) with Python

Exploratory Data Analysis Tutorial | Basics of EDA with Python

Exploratory data analysis is used by data scientists to analyze and investigate data sets and summarize their main characteristics, often employing data visualization methods. It helps determine how best to manipulate data sources to get the answers you need, making it easier for data scientists to discover patterns, spot anomalies, test a hypothesis, or check assumptions. EDA is primarily used to see what data can reveal beyond the formal modeling or hypothesis testing task and provides a better understanding of data set variables and the relationships between them. It can also help determine if the statistical techniques you are considering for data analysis are appropriate or not.

🔹 Topics Covered:
00:00:00 Basics of EDA with Python
01:40:10 Multiple Variate Analysis
02:30:26 Outlier Detection
03:44:48 Cricket World Cup Analysis using Exploratory Data Analysis

---

Learning the basics of Exploratory Data Analysis using Python with Numpy, Matplotlib, and Pandas.

What is Exploratory Data Analysis(EDA)?

If we want to explain EDA in simple terms, it means trying to understand the given data much better, so that we can make some sense out of it.

We can find a more formal definition in Wikipedia.

In statistics, exploratory data analysis is an approach to analyzing data sets to summarize their main characteristics, often with visual methods. A statistical model can be used or not, but primarily EDA is for seeing what the data can tell us beyond the formal modeling or hypothesis testing task.

EDA in Python uses data visualization to draw meaningful patterns and insights. It also involves the preparation of data sets for analysis by removing irregularities in the data.

Based on the results of EDA, companies also make business decisions, which can have repercussions later.

• If EDA is not done properly then it can hamper the further steps in the machine learning model building process.
• If done well, it may improve the efficacy of everything we do next.

In this article we’ll see about the following topics:

1. Data Sourcing
2. Data Cleaning
3. Univariate analysis
4. Bivariate analysis
5. Multivariate analysis

1. Data Sourcing

Data Sourcing is the process of finding and loading the data into our system. Broadly there are two ways in which we can find data.

1. Private Data
2. Public Data

Private Data

As the name suggests, private data is given by private organizations. There are some security and privacy concerns attached to it. This type of data is used for mainly organizations internal analysis.

Public Data

This type of Data is available to everyone. We can find this in government websites and public organizations etc. Anyone can access this data, we do not need any special permissions or approval.

We can get public data on the following sites.

• https://data.gov
• https://data.gov.uk
• https://data.gov.in
• https://www.kaggle.com/
• https://archive.ics.uci.edu/ml/index.php
• https://github.com/awesomedata/awesome-public-datasets

The very first step of EDA is Data Sourcing, we have seen how we can access data and load into our system. Now, the next step is how to clean the data.

2. Data Cleaning

After completing the Data Sourcing, the next step in the process of EDA is Data Cleaning. It is very important to get rid of the irregularities and clean the data after sourcing it into our system.

Irregularities are of different types of data.

• Missing Values
• Incorrect Format
• Incorrect Headers
• Anomalies/Outliers

To perform the data cleaning we are using a sample data set, which can be found here.

We are using Jupyter Notebook for analysis.

First, let’s import the necessary libraries and store the data in our system for analysis.

#import the useful libraries.
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
%matplotlib inline

# Read the data set of "Marketing Analysis" in data.
data= pd.read_csv("marketing_analysis.csv")

# Printing the data
data

Now, the data set looks like this,

If we observe the above dataset, there are some discrepancies in the Column header for the first 2 rows. The correct data is from the index number 1. So, we have to fix the first two rows.

This is called Fixing the Rows and Columns. Let’s ignore the first two rows and load the data again.

#import the useful libraries.
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
%matplotlib inline

# Read the file in data without first two rows as it is of no use.
data = pd.read_csv("marketing_analysis.csv",skiprows = 2)

#print the head of the data frame.
data.head()

Now, the dataset looks like this, and it makes more sense.

Dataset after fixing the rows and columns

Following are the steps to be taken while Fixing Rows and Columns:

1. Delete Summary Rows and Columns in the Dataset.
2. Delete Header and Footer Rows on every page.
3. Delete Extra Rows like blank rows, page numbers, etc.
4. We can merge different columns if it makes for better understanding of the data
5. Similarly, we can also split one column into multiple columns based on our requirements or understanding.
6. Add Column names, it is very important to have column names to the dataset.

Now if we observe the above dataset, the customerid column has of no importance to our analysis, and also the jobedu column has both the information of job and education in it.

So, what we’ll do is, we’ll drop the customerid column and we’ll split the jobedu column into two other columns job and education and after that, we’ll drop the jobedu column as well.

# Drop the customer id as it is of no use.
data.drop('customerid', axis = 1, inplace = True)

#Extract job  & Education in newly from "jobedu" column.
data['job']= data["jobedu"].apply(lambda x: x.split(",")[0])
data['education']= data["jobedu"].apply(lambda x: x.split(",")[1])

# Drop the "jobedu" column from the dataframe.
data.drop('jobedu', axis = 1, inplace = True)

# Printing the Dataset
data

Now, the dataset looks like this,

Dropping Customerid and jobedu columns and adding job and education columns

Missing Values

If there are missing values in the Dataset before doing any statistical analysis, we need to handle those missing values.

There are mainly three types of missing values.

1. MCAR(Missing completely at random): These values do not depend on any other features.
2. MAR(Missing at random): These values may be dependent on some other features.
3. MNAR(Missing not at random): These missing values have some reason for why they are missing.

Let’s see which columns have missing values in the dataset.

# Checking the missing values
data.isnull().sum()

The output will be,

As we can see three columns contain missing values. Let’s see how to handle the missing values. We can handle missing values by dropping the missing records or by imputing the values.

Drop the missing Values

Let’s handle missing values in the age column.

# Dropping the records with age missing in data dataframe.
data = data[~data.age.isnull()].copy()

# Checking the missing values in the dataset.
data.isnull().sum()

Let’s check the missing values in the dataset now.

Let’s impute values to the missing values for the month column.

Since the month column is of an object type, let’s calculate the mode of that column and impute those values to the missing values.

# Find the mode of month in data
month_mode = data.month.mode()[0]

# Fill the missing values with mode value of month in data.
data.month.fillna(month_mode, inplace = True)

# Let's see the null values in the month column.
data.month.isnull().sum()

Now output is,

# Mode of month is
'may, 2017'
# Null values in month column after imputing with mode
0

Handling the missing values in the Response column. Since, our target column is Response Column, if we impute the values to this column it’ll affect our analysis. So, it is better to drop the missing values from Response Column.

#drop the records with response missing in data.
data = data[~data.response.isnull()].copy()
# Calculate the missing values in each column of data frame
data.isnull().sum()

Let’s check whether the missing values in the dataset have been handled or not,

All the missing values have been handled

We can also, fill the missing values as ‘NaN’ so that while doing any statistical analysis, it won’t affect the outcome.

Handling Outliers

We have seen how to fix missing values, now let’s see how to handle outliers in the dataset.

Outliers are the values that are far beyond the next nearest data points.

There are two types of outliers:

1. Univariate outliers: Univariate outliers are the data points whose values lie beyond the range of expected values based on one variable.
2. Multivariate outliers: While plotting data, some values of one variable may not lie beyond the expected range, but when you plot the data with some other variable, these values may lie far from the expected value.

So, after understanding the causes of these outliers, we can handle them by dropping those records or imputing with the values or leaving them as is, if it makes more sense.

Standardizing Values

To perform data analysis on a set of values, we have to make sure the values in the same column should be on the same scale. For example, if the data contains the values of the top speed of different companies’ cars, then the whole column should be either in meters/sec scale or miles/sec scale.

Now, that we are clear on how to source and clean the data, let’s see how we can analyze the data.

3. Univariate Analysis

If we analyze data over a single variable/column from a dataset, it is known as Univariate Analysis.

Categorical Unordered Univariate Analysis:

An unordered variable is a categorical variable that has no defined order. If we take our data as an example, the job column in the dataset is divided into many sub-categories like technician, blue-collar, services, management, etc. There is no weight or measure given to any value in the ‘job’ column.

Now, let’s analyze the job category by using plots. Since Job is a category, we will plot the bar plot.

# Let's calculate the percentage of each job status category.
data.job.value_counts(normalize=True)

#plot the bar graph of percentage job categories
data.job.value_counts(normalize=True).plot.barh()
plt.show()

The output looks like this,

By the above bar plot, we can infer that the data set contains more number of blue-collar workers compared to other categories.

Categorical Ordered Univariate Analysis:

Ordered variables are those variables that have a natural rank of order. Some examples of categorical ordered variables from our dataset are:

• Month: Jan, Feb, March……
• Education: Primary, Secondary,……

Now, let’s analyze the Education Variable from the dataset. Since we’ve already seen a bar plot, let’s see how a Pie Chart looks like.

#calculate the percentage of each education category.
data.education.value_counts(normalize=True)

#plot the pie chart of education categories
data.education.value_counts(normalize=True).plot.pie()
plt.show()

The output will be,

By the above analysis, we can infer that the data set has a large number of them belongs to secondary education after that tertiary and next primary. Also, a very small percentage of them have been unknown.

This is how we analyze univariate categorical analysis. If the column or variable is of numerical then we’ll analyze by calculating its mean, median, std, etc. We can get those values by using the describe function.

data.salary.describe()

The output will be,

4. Bivariate Analysis

If we analyze data by taking two variables/columns into consideration from a dataset, it is known as Bivariate Analysis.

a) Numeric-Numeric Analysis:

Analyzing the two numeric variables from a dataset is known as numeric-numeric analysis. We can analyze it in three different ways.

• Scatter Plot
• Pair Plot
• Correlation Matrix

Scatter Plot

Let’s take three columns ‘Balance’, ‘Age’ and ‘Salary’ from our dataset and see what we can infer by plotting to scatter plot between salary balance and age balance

#plot the scatter plot of balance and salary variable in data
plt.scatter(data.salary,data.balance)
plt.show()

#plot the scatter plot of balance and age variable in data
data.plot.scatter(x="age",y="balance")
plt.show()

Now, the scatter plots looks like,

Pair Plot

Now, let’s plot Pair Plots for the three columns we used in plotting Scatter plots. We’ll use the seaborn library for plotting Pair Plots.

#plot the pair plot of salary, balance and age in data dataframe.
sns.pairplot(data = data, vars=['salary','balance','age'])
plt.show()

The Pair Plot looks like this,

Correlation Matrix

Since we cannot use more than two variables as x-axis and y-axis in Scatter and Pair Plots, it is difficult to see the relation between three numerical variables in a single graph. In those cases, we’ll use the correlation matrix.

# Creating a matrix using age, salry, balance as rows and columns
data[['age','salary','balance']].corr()

#plot the correlation matrix of salary, balance and age in data dataframe.
sns.heatmap(data[['age','salary','balance']].corr(), annot=True, cmap = 'Reds')
plt.show()

First, we created a matrix using age, salary, and balance. After that, we are plotting the heatmap using the seaborn library of the matrix.

b) Numeric - Categorical Analysis

Analyzing the one numeric variable and one categorical variable from a dataset is known as numeric-categorical analysis. We analyze them mainly using mean, median, and box plots.

Let’s take salary and response columns from our dataset.

First check for mean value using groupby

#groupby the response to find the mean of the salary with response no & yes separately.
data.groupby('response')['salary'].mean()

The output will be,

There is not much of a difference between the yes and no response based on the salary.

Let’s calculate the median,

#groupby the response to find the median of the salary with response no & yes separately.
data.groupby('response')['salary'].median()

The output will be,

By both mean and median we can say that the response of yes and no remains the same irrespective of the person’s salary. But, is it truly behaving like that, let’s plot the box plot for them and check the behavior.

#plot the box plot of salary for yes & no responses.
sns.boxplot(data.response, data.salary)
plt.show()

The box plot looks like this,

As we can see, when we plot the Box Plot, it paints a very different picture compared to mean and median. The IQR for customers who gave a positive response is on the higher salary side.

This is how we analyze Numeric-Categorical variables, we use mean, median, and Box Plots to draw some sort of conclusions.

c) Categorical — Categorical Analysis

Since our target variable/column is the Response rate, we’ll see how the different categories like Education, Marital Status, etc., are associated with the Response column. So instead of ‘Yes’ and ‘No’ we will convert them into ‘1’ and ‘0’, by doing that we’ll get the “Response Rate”.

#create response_rate of numerical data type where response "yes"= 1, "no"= 0
data['response_rate'] = np.where(data.response=='yes',1,0)
data.response_rate.value_counts()

The output looks like this,

Let’s see how the response rate varies for different categories in marital status.

#plot the bar graph of marital status with average value of response_rate
data.groupby('marital')['response_rate'].mean().plot.bar()
plt.show()

The graph looks like this,

By the above graph, we can infer that the positive response is more for Single status members in the data set. Similarly, we can plot the graphs for Loan vs Response rate, Housing Loans vs Response rate, etc.

5. Multivariate Analysis

If we analyze data by taking more than two variables/columns into consideration from a dataset, it is known as Multivariate Analysis.

Let’s see how ‘Education’, ‘Marital’, and ‘Response_rate’ vary with each other.

First, we’ll create a pivot table with the three columns and after that, we’ll create a heatmap.

result = pd.pivot_table(data=data, index='education', columns='marital',values='response_rate')
print(result)

#create heat map of education vs marital vs response_rate
sns.heatmap(result, annot=True, cmap = 'RdYlGn', center=0.117)
plt.show()

The Pivot table and heatmap looks like this,

Based on the Heatmap we can infer that the married people with primary education are less likely to respond positively for the survey and single people with tertiary education are most likely to respond positively to the survey.

Similarly, we can plot the graphs for Job vs marital vs response, Education vs poutcome vs response, etc.

Conclusion

This is how we’ll do Exploratory Data Analysis. Exploratory Data Analysis (EDA) helps us to look beyond the data. The more we explore the data, the more the insights we draw from it. As a data analyst, almost 80% of our time will be spent understanding data and solving various business problems through EDA.

Thank you for reading and Happy Coding!!!

#dataanalysis #python

Zoofs: A Feature Selection Library Based on Evolutionary Algorithms

🐾 zoofs ( Zoo Feature Selection )

zoofs is a Python library for performing feature selection using a variety of nature inspired wrapper algorithms. The algorithms range from swarm-intelligence to physics based to Evolutionary. It's an easy to use, flexible and powerful tool to reduce your feature size.

🔗 Whats new in V0.1.24

• pass kwargs through objective function
• improved logger for results
• added harris hawk algorithm
• now you can pass timeout as a parameter to stop operation after the given number of second(s). An amazing alternative to passing number of iterations
• Feature score hashing of visited feature sets to increase the overall performance

🛠 Installation

Using pip

Use the package manager to install zoofs.

pip install zoofs

📜 Available Algorithms

Algorithm Name	Class Name	Description	References doi
Particle Swarm Algorithm	ParticleSwarmOptimization	Utilizes swarm behaviour	https://doi.org/10.1007/978-3-319-13563-2_51
Grey Wolf Algorithm	GreyWolfOptimization	Utilizes wolf hunting behaviour	https://doi.org/10.1016/j.neucom.2015.06.083
Dragon Fly Algorithm	DragonFlyOptimization	Utilizes dragonfly swarm behaviour	https://doi.org/10.1016/j.knosys.2020.106131
Harris Hawk Algorithm	HarrisHawkOptimization	Utilizes hawk hunting behaviour	https://link.springer.com/chapter/10.1007/978-981-32-9990-0_12
Genetic Algorithm Algorithm	GeneticOptimization	Utilizes genetic mutation behaviour	https://doi.org/10.1109/ICDAR.2001.953980
Gravitational Algorithm	GravitationalOptimization	Utilizes newtons gravitational behaviour	https://doi.org/10.1109/ICASSP.2011.5946916

More algos soon, stay tuned !

• [Try It Now?]

⚡️ Usage

Define your own objective function for optimization !

Classification Example

from sklearn.metrics import log_loss
# define your own objective function, make sure the function receives four parameters,
#  fit your model and return the objective value !
def objective_function_topass(model,X_train, y_train, X_valid, y_valid):      
    model.fit(X_train,y_train)  
    P=log_loss(y_valid,model.predict_proba(X_valid))
    return P

# import an algorithm !  
from zoofs import ParticleSwarmOptimization
# create object of algorithm
algo_object=ParticleSwarmOptimization(objective_function_topass,n_iteration=20,
                                       population_size=20,minimize=True)
import lightgbm as lgb
lgb_model = lgb.LGBMClassifier()                                       
# fit the algorithm
algo_object.fit(lgb_model,X_train, y_train, X_valid, y_valid,verbose=True)
#plot your results
algo_object.plot_history()

Regression Example

from sklearn.metrics import mean_squared_error
# define your own objective function, make sure the function receives four parameters,
#  fit your model and return the objective value !
def objective_function_topass(model,X_train, y_train, X_valid, y_valid):      
    model.fit(X_train,y_train)  
    P=mean_squared_error(y_valid,model.predict(X_valid))
    return P

# import an algorithm !  
from zoofs import ParticleSwarmOptimization
# create object of algorithm
algo_object=ParticleSwarmOptimization(objective_function_topass,n_iteration=20,
                                       population_size=20,minimize=True)
import lightgbm as lgb
lgb_model = lgb.LGBMRegressor()                                       
# fit the algorithm
algo_object.fit(lgb_model,X_train, y_train, X_valid, y_valid,verbose=True)
#plot your results
algo_object.plot_history()

Suggestions for Usage

• As available algorithms are wrapper algos, it is better to use ml models that build quicker, e.g lightgbm, catboost.
• Take sufficient amount for 'population_size' , as this will determine the extent of exploration and exploitation of the algo.
• Ensure that your ml model has its hyperparamters optimized before passing it to zoofs algos.

objective score plot

Algorithms

Particle Swarm Algorithm

In computational science, particle swarm optimization (PSO) is a computational method that optimizes a problem by iteratively trying to improve a candidate solution with regard to a given measure of quality. It solves a problem by having a population of candidate solutions, here dubbed particles, and moving these particles around in the search-space according to simple mathematical formula over the particle's position and velocity. Each particle's movement is influenced by its local best known position, but is also guided toward the best known positions in the search-space, which are updated as better positions are found by other particles. This is expected to move the swarm toward the best solutions.

---

class zoofs.ParticleSwarmOptimization(objective_function,n_iteration=50,population_size=50,minimize=True,c1=2,c2=2,w=0.9)

---

Parameters	objective_function : user made function of the signature 'func(model,X_train,y_train,X_test,y_test)'.    The function must return a value, that needs to be minimized/maximized. n_iteration : int, default=1000    Number of time the algorithm will run timeout: int = None    Stop operation after the given number of second(s). If this argument is set to None, the operation is executed without time limitation and n_iteration is followed population_size : int, default=50    Total size of the population minimize : bool, default=True    Defines if the objective value is to be maximized or minimized c1 : float, default=2.0    first acceleration coefficient of particle swarm c2 : float, default=2.0    second acceleration coefficient of particle swarm w : float, default=0.9    weight parameter
Attributes	best_feature_list : array-like    Final best set of features

Methods

Methods	Class Name
fit	Run the algorithm
plot_history	Plot results achieved across iteration

fit(model,X_train, y_train, X_test, y_test,verbose=True)

Parameters	model :    machine learning model's object X_train : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Training input samples to be used for machine learning model y_train : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The target values (class labels in classification, real numbers in regression). X_valid : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Validation input samples y_valid : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The Validation target values . verbose : bool,default=True    Print results for iterations
Returns	best_feature_list : array-like    Final best set of features

plot_history()

Plot results across iterations

Example

from sklearn.metrics import log_loss
# define your own objective function, make sure the function receives four parameters,
#  fit your model and return the objective value !
def objective_function_topass(model,X_train, y_train, X_valid, y_valid):      
    model.fit(X_train,y_train)  
    P=log_loss(y_valid,model.predict_proba(X_valid))
    return P

# import an algorithm !  
from zoofs import ParticleSwarmOptimization
# create object of algorithm
algo_object=ParticleSwarmOptimization(objective_function_topass,n_iteration=20,
                                       population_size=20,minimize=True,c1=2,c2=2,w=0.9)
import lightgbm as lgb
lgb_model = lgb.LGBMClassifier()                      
# fit the algorithm
algo_object.fit(lgb_model,X_train, y_train, X_valid, y_valid,verbose=True)
#plot your results
algo_object.plot_history()

Grey Wolf Algorithm

The Grey Wolf Optimizer (GWO) mimics the leadership hierarchy and hunting mechanism of grey wolves in nature. Four types of grey wolves such as alpha, beta, delta, and omega are employed for simulating the leadership hierarchy. In addition, three main steps of hunting, searching for prey, encircling prey, and attacking prey, are implemented to perform optimization.

---

class zoofs.GreyWolfOptimization(objective_function,n_iteration=50,population_size=50,minimize=True)

---

Parameters	objective_function : user made function of the signature 'func(model,X_train,y_train,X_test,y_test)'.    The function must return a value, that needs to be minimized/maximized. n_iteration : int, default=50    Number of time the algorithm will run timeout: int = None    Stop operation after the given number of second(s). If this argument is set to None, the operation is executed without time limitation and n_iteration is followed population_size : int, default=50    Total size of the population method : {1, 2}, default=1    Choose the between the two methods of grey wolf optimization minimize : bool, default=True    Defines if the objective value is to be maximized or minimized
Attributes	best_feature_list : array-like    Final best set of features

Methods

Methods	Class Name
fit	Run the algorithm
plot_history	Plot results achieved across iteration

fit(model,X_train,y_train,X_valid,y_valid,method=1,verbose=True)

Parameters	model :    machine learning model's object X_train : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Training input samples to be used for machine learning model y_train : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The target values (class labels in classification, real numbers in regression). X_valid : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Validation input samples y_valid : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The Validation target values . verbose : bool,default=True    Print results for iterations
Returns	best_feature_list : array-like    Final best set of features

plot_history()

Plot results across iterations

Example

from sklearn.metrics import log_loss
# define your own objective function, make sure the function receives four parameters,
#  fit your model and return the objective value !
def objective_function_topass(model,X_train, y_train, X_valid, y_valid):      
    model.fit(X_train,y_train)  
    P=log_loss(y_valid,model.predict_proba(X_valid))
    return P

# import an algorithm !  
from zoofs import GreyWolfOptimization
# create object of algorithm
algo_object=GreyWolfOptimization(objective_function_topass,n_iteration=20,method=1,
                                    population_size=20,minimize=True)
import lightgbm as lgb
lgb_model = lgb.LGBMClassifier()                                       
# fit the algorithm
algo_object.fit(lgb_model,X_train, y_train, X_valid, y_valid,verbose=True)
#plot your results
algo_object.plot_history()

Dragon Fly Algorithm

The main inspiration of the Dragonfly Algorithm (DA) algorithm originates from static and dynamic swarming behaviours. These two swarming behaviours are very similar to the two main phases of optimization using meta-heuristics: exploration and exploitation. Dragonflies create sub swarms and fly over different areas in a static swarm, which is the main objective of the exploration phase. In the static swarm, however, dragonflies fly in bigger swarms and along one direction, which is favourable in the exploitation phase.

---

class zoofs.DragonFlyOptimization(objective_function,n_iteration=50,population_size=50,minimize=True)

---

Parameters	objective_function : user made function of the signature 'func(model,X_train,y_train,X_test,y_test)'.    The function must return a value, that needs to be minimized/maximized. n_iteration : int, default=50    Number of time the algorithm will run timeout: int = None    Stop operation after the given number of second(s). If this argument is set to None, the operation is executed without time limitation and n_iteration is followed population_size : int, default=50    Total size of the population method : {'linear','random','quadraic','sinusoidal'}, default='sinusoidal'    Choose the between the three methods of Dragon Fly optimization minimize : bool, default=True    Defines if the objective value is to be maximized or minimized
Attributes	best_feature_list : array-like    Final best set of features

Methods

Methods	Class Name
fit	Run the algorithm
plot_history	Plot results achieved across iteration

fit(model,X_train,y_train,X_valid,y_valid,method='sinusoidal',verbose=True)

Parameters	model :    machine learning model's object X_train : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Training input samples to be used for machine learning model y_train : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The target values (class labels in classification, real numbers in regression). X_valid : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Validation input samples y_valid : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The Validation target values . verbose : bool,default=True    Print results for iterations
Returns	best_feature_list : array-like    Final best set of features

plot_history()

Plot results across iterations

Example

from sklearn.metrics import log_loss
# define your own objective function, make sure the function receives four parameters,
#  fit your model and return the objective value !
def objective_function_topass(model,X_train, y_train, X_valid, y_valid):      
    model.fit(X_train,y_train)  
    P=log_loss(y_valid,model.predict_proba(X_valid))
    return P

# import an algorithm !  
from zoofs import DragonFlyOptimization
# create object of algorithm
algo_object=DragonFlyOptimization(objective_function_topass,n_iteration=20,method='sinusoidal',
                                    population_size=20,minimize=True)
import lightgbm as lgb
lgb_model = lgb.LGBMClassifier()                                     
# fit the algorithm
algo_object.fit(lgb_model,X_train, y_train, X_valid, y_valid,  verbose=True)
#plot your results
algo_object.plot_history()

Harris Hawk Optimization

HHO is a popular swarm-based, gradient-free optimization algorithm with several active and time-varying phases of exploration and exploitation. This algorithm initially published by the prestigious Journal of Future Generation Computer Systems (FGCS) in 2019, and from the first day, it has gained increasing attention among researchers due to its flexible structure, high performance, and high-quality results. The main logic of the HHO method is designed based on the cooperative behaviour and chasing styles of Harris' hawks in nature called "surprise pounce". Currently, there are many suggestions about how to enhance the functionality of HHO, and there are also several enhanced variants of the HHO in the leading Elsevier and IEEE transaction journals.

---

class zoofs.HarrisHawkOptimization(objective_function,n_iteration=50,population_size=50,minimize=True,beta=0.5)

---

Parameters	objective_function : user made function of the signature 'func(model,X_train,y_train,X_test,y_test)'.    The function must return a value, that needs to be minimized/maximized. n_iteration : int, default=1000    Number of time the algorithm will run timeout: int = None    Stop operation after the given number of second(s). If this argument is set to None, the operation is executed without time limitation and n_iteration is followed population_size : int, default=50    Total size of the population minimize : bool, default=True    Defines if the objective value is to be maximized or minimized beta : float, default=0.5    value for levy random walk
Attributes	best_feature_list : array-like    Final best set of features

Methods

Methods	Class Name
fit	Run the algorithm
plot_history	Plot results achieved across iteration

fit(model,X_train, y_train, X_test, y_test,verbose=True)

Parameters	model :    machine learning model's object X_train : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Training input samples to be used for machine learning model y_train : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The target values (class labels in classification, real numbers in regression). X_valid : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Validation input samples y_valid : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The Validation target values . verbose : bool,default=True    Print results for iterations
Returns	best_feature_list : array-like    Final best set of features

plot_history()

Plot results across iterations

Example

from sklearn.metrics import log_loss
# define your own objective function, make sure the function receives four parameters,
#  fit your model and return the objective value !
def objective_function_topass(model,X_train, y_train, X_valid, y_valid):      
    model.fit(X_train,y_train)  
    P=log_loss(y_valid,model.predict_proba(X_valid))
    return P

# import an algorithm !  
from zoofs import HarrisHawkOptimization
# create object of algorithm
algo_object=HarrisHawkOptimization(objective_function_topass,n_iteration=20,
                                       population_size=20,minimize=True)
import lightgbm as lgb
lgb_model = lgb.LGBMClassifier()                      
# fit the algorithm
algo_object.fit(lgb_model,X_train, y_train, X_valid, y_valid,verbose=True)
#plot your results
algo_object.plot_history()

Genetic Algorithm

In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA). Genetic algorithms are commonly used to generate high-quality solutions to optimization and search problems by relying on biologically inspired operators such as mutation, crossover and selection. Some examples of GA applications include optimizing decision trees for better performance, automatically solve sudoku puzzles, hyperparameter optimization, etc.

---

class zoofs.GeneticOptimization(objective_function,n_iteration=20,population_size=20,selective_pressure=2,elitism=2,mutation_rate=0.05,minimize=True)

---

Parameters	objective_function : user made function of the signature 'func(model,X_train,y_train,X_test,y_test)'.    The function must return a value, that needs to be minimized/maximized. n_iteration: int, default=50    Number of time the algorithm will run timeout: int = None    Stop operation after the given number of second(s). If this argument is set to None, the operation is executed without time limitation and n_iteration is followed population_size : int, default=50    Total size of the population selective_pressure: int, default=2    measure of reproductive opportunities for each organism in the population elitism: int, default=2    number of top individuals to be considered as elites mutation_rate: float, default=0.05    rate of mutation in the population's gene minimize: bool, default=True    Defines if the objective value is to be maximized or minimized
Attributes	best_feature_list : array-like    Final best set of features

Methods

Methods	Class Name
fit	Run the algorithm
plot_history	Plot results achieved across iteration

fit(model,X_train,y_train,X_valid,y_valid,verbose=True)

Parameters	model :    machine learning model's object X_train : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Training input samples to be used for machine learning model y_train : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The target values (class labels in classification, real numbers in regression). X_valid : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Validation input samples y_valid : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The Validation target values . verbose : bool,default=True    Print results for iterations
Returns	best_feature_list : array-like    Final best set of features

plot_history()

Plot results across iterations

Example

from sklearn.metrics import log_loss
# define your own objective function, make sure the function receives four parameters,
#  fit your model and return the objective value !
def objective_function_topass(model,X_train, y_train, X_valid, y_valid):      
    model.fit(X_train,y_train)  
    P=log_loss(y_valid,model.predict_proba(X_valid))
    return P

# import an algorithm !  
from zoofs import GeneticOptimization
# create object of algorithm
algo_object=GeneticOptimization(objective_function_topass,n_iteration=20,
                            population_size=20,selective_pressure=2,elitism=2,
                            mutation_rate=0.05,minimize=True)
import lightgbm as lgb
lgb_model = lgb.LGBMClassifier()                            
# fit the algorithm
algo_object.fit(lgb_model,X_train, y_train,X_valid, y_valid, verbose=True)
#plot your results
algo_object.plot_history()

Gravitational Algorithm

Gravitational Algorithm is based on the law of gravity and mass interactions is introduced. In the algorithm, the searcher agents are a collection of masses which interact with each other based on the Newtonian gravity and the laws of motion.

---

class zoofs.GravitationalOptimization(self,objective_function,n_iteration=50,population_size=50,g0=100,eps=0.5,minimize=True)

---

Parameters	objective_function : user made function of the signature 'func(model,X_train,y_train,X_test,y_test)'.    The function must return a value, that needs to be minimized/maximized. n_iteration: int, default=50    Number of time the algorithm will run timeout: int = None    Stop operation after the given number of second(s). If this argument is set to None, the operation is executed without time limitation and n_iteration is followed population_size : int, default=50    Total size of the population g0: float, default=100    gravitational strength constant eps: float, default=0.5    distance constant minimize: bool, default=True    Defines if the objective value is to be maximized or minimized
Attributes	best_feature_list : array-like    Final best set of features

Methods

Methods	Class Name
fit	Run the algorithm
plot_history	Plot results achieved across iteration

fit(model,X_train,y_train,X_valid,y_valid,verbose=True)

Parameters	model :    machine learning model's object X_train : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Training input samples to be used for machine learning model y_train : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The target values (class labels in classification, real numbers in regression). X_valid : pandas.core.frame.DataFrame of shape (n_samples, n_features)    Validation input samples y_valid : pandas.core.frame.DataFrame or pandas.core.series.Series of shape (n_samples)    The Validation target values . verbose : bool,default=True    Print results for iterations
Returns	best_feature_list : array-like    Final best set of features

plot_history()

Plot results across iterations

Example

from sklearn.metrics import log_loss
# define your own objective function, make sure the function receives four parameters,
#  fit your model and return the objective value !
def objective_function_topass(model,X_train, y_train, X_valid, y_valid):      
    model.fit(X_train,y_train)  
    P=log_loss(y_valid,model.predict_proba(X_valid))
    return P

# import an algorithm !  
from zoofs import GravitationalOptimization
# create object of algorithm
algo_object=GravitationalOptimization(objective_function_topass,n_iteration=50,
                                population_size=50,g0=100,eps=0.5,minimize=True)
import lightgbm as lgb
lgb_model = lgb.LGBMClassifier()                                
# fit the algorithm
algo_object.fit(lgb_model,X_train, y_train, X_valid, y_valid, verbose=True)
#plot your results
algo_object.plot_history()

Support zoofs

The development of zoofs relies completely on contributions.

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

First roll out

18,08,2021

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🌟 Like this Project? Give us a star !

📘 Documentation

https://jaswinder9051998.github.io/zoofs/

---

Download Details:

Author: jaswinder9051998
Source Code: https://github.com/jaswinder9051998/zoofs 
License: Apache-2.0 license

#machinelearning #python #optimization #algorithm 

Scatter Plots - Python Matplotlib Tutorial #3

In this Python tutorial, you will learn everything you need to know about scatter plots using Matplotlib library. Scatter plots are great in showing the relationship between variables in our dataset, eventually revealing a correlation.

This is a complete tutorial on scatter plots including Bubble plots and an additional variable mapped to the marker’s color (you will also learn how to add colorbar and choose the best colormap to your case). We will discuss how to change the marker of your scatter plot using two different methods: 1. Symbols from Matplotlib and 2. Symbols from Latex. As usual, I will share several tips and tricks to save your time when customizing your graph.

We will cover from the very basic to more advanced aspects in 15 minutes. I hope you enjoy this tutorial.

Playlist: Matplotlib Course | Video #3
Access the code here: https://github.com/rscorrea1/youtube.git

Learn how to use Jupyter Notebooks: https://www.youtube.com/watch?v=gGYaFfAvYtg

Additional Courses:
Beginner Python Tutorials: https://www.youtube.com/watch?v=HG_E6EaKY90&list=PLJgwF35R54crXsGuSKR_MtUG2ABU_BFAq
Intermediate Python Tutorials: https://www.youtube.com/watch?v=oNwaOFZDAWo&list=PLJgwF35R54coNbQXGNJyawp-_3CC6I1B4
NumPy Tutorials: https://www.youtube.com/watch?v=YRes9M71_Ts&list=PLJgwF35R54cqqbFFHdArwQuBUUUoLKJ4V

#matplotlib #python #python matplotlib tutorial #scatter plots