Rupert  Beatty

Rupert Beatty

1665909720

Jazzy: Soulful Docs for Swift & Objective-C

Jazzy

jazzy is a command-line utility that generates documentation for Swift or Objective-C

About

Both Swift and Objective-C projects are supported.

Instead of parsing your source files, jazzy hooks into Clang and SourceKit to use the AST representation of your code and its comments for more accurate results. The output matches the look and feel of Apple’s official reference documentation, post WWDC 2014.

Jazzy can also generate documentation from compiled Swift modules using their symbol graph instead of source code.

Screenshot

This project adheres to the Contributor Covenant Code of Conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to info@realm.io.

Requirements

You need development tools to build the project you wish to document. Jazzy supports both Xcode and Swift Package Manager projects.

Jazzy expects to be running on macOS. See below for tips to run Jazzy on Linux.

Installation

[sudo] gem install jazzy

See Installation Problems for solutions to some common problems.

Usage

Run jazzy from your command line. Run jazzy -h for a list of additional options.

If your Swift module is the first thing to build, and it builds fine when running xcodebuild or swift build without any arguments from the root of your project, then just running jazzy (without any arguments) from the root of your project should succeed too!

If Jazzy generates docs for the wrong module then use --module to tell it which one you'd prefer. If this doesn't help, and you're using Xcode, then try passing extra arguments to xcodebuild, for example jazzy --build-tool-arguments -scheme,MyScheme,-target,MyTarget.

You can set options for your project’s documentation in a configuration file, .jazzy.yaml by default. For a detailed explanation and an exhaustive list of all available options, run jazzy --help config.

Supported documentation keywords

Swift documentation is written in markdown and supports a number of special keywords. Here are some resources with tutorials and examples, starting with the most modern:

For Objective-C documentation the same keywords are supported, but note that the format is slightly different. In Swift you would write - returns:, but in Objective-C you write @return. See Apple's HeaderDoc User Guide for more details. Note: jazzy currently does not support all Objective-C keywords listed in this document, only @param, @return, @warning, @see, @note, @code, @endcode, and @c.

Jazzy can also generate cross-references within your documentation. A symbol name in backticks generates a link, for example:

  • `MyClass` - a link to documentation for MyClass.
  • `MyClass.method(param1:)` - a link to documentation for that method.
  • `MyClass.method(...)` - shortcut syntax for the same thing.
  • `method(...)` - shortcut syntax to link to method from the documentation of another method or property in the same class.
  • `[MyClass method1]` - a link to an Objective-C method.
  • `-[MyClass method2:param1]` - a link to another Objective-C method.

Jazzy understands Apple's DocC-style links too, for example:

  • ``MyClass/method(param1:)`` - a link to the documentation for that method that appears as just method(param1:) in the rendered page.
  • ``<doc:method(_:)-e873>`` - a link to a specific overload of method(_:). Jazzy can't tell which overload you intend and links to the first one.

Math

Jazzy can render math equations written in LaTeX embedded in your markdown:

  • `$equation$` renders the equation in an inline style.
  • `$$equation$$` renders the equation in a display style, centered on a line of its own.

For example, the markdown:

Inline: `$ax^2+bx+c=0$`

Block: `$$x={\frac {-b\pm {\sqrt {b^{2}-4ac}}}{2a}}$$`

..renders as:

math

Math support is provided by KaTeX.

Swift

Swift documentation is generated by default.

Example

This is how Realm Swift docs are generated:

jazzy \
  --clean \
  --author Realm \
  --author_url https://realm.io \
  --source-host github \
  --source-host-url https://github.com/realm/realm-cocoa \
  --source-host-files-url https://github.com/realm/realm-cocoa/tree/v0.96.2 \
  --module-version 0.96.2 \
  --build-tool-arguments -scheme,RealmSwift \
  --module RealmSwift \
  --root-url https://realm.io/docs/swift/0.96.2/api/ \
  --output docs/swift_output \
  --theme docs/themes

This is how docs are generated for a project that uses the Swift Package Manager:

jazzy \
  --module DeckOfPlayingCards \
  --swift-build-tool spm \
  --build-tool-arguments -Xswiftc,-swift-version,-Xswiftc,5

Objective-C

To generate documentation for a simple Objective-C project, you must pass the following parameters:

  • --objc
  • --umbrella-header ...
  • --framework-root ...

...and optionally:

  • --sdk [iphone|watch|appletv][os|simulator]|macosx (default value of macosx)
  • --hide-declarations [objc|swift] (hides the selected language declarations)

For example, this is how the AFNetworking docs are generated:

jazzy \
  --objc \
  --author AFNetworking \
  --author_url http://afnetworking.com \
  --source-host github \
  --source-host-url https://github.com/AFNetworking/AFNetworking \
  --source-host-files-url https://github.com/AFNetworking/AFNetworking/tree/2.6.2 \
  --module-version 2.6.2 \
  --umbrella-header AFNetworking/AFNetworking.h \
  --framework-root . \
  --module AFNetworking

For a more complicated Objective-C project, instead use --build-tool-arguments to pass arbitrary compiler flags. For example, this is how Realm Objective-C docs are generated:

jazzy \
  --objc \
  --clean \
  --author Realm \
  --author_url https://realm.io \
  --source-host github \
  --source-host-url https://github.com/realm/realm-cocoa \
  --source-host-files-url https://github.com/realm/realm-cocoa/tree/v2.2.0 \
  --module-version 2.2.0 \
  --build-tool-arguments --objc,Realm/Realm.h,--,-x,objective-c,-isysroot,$(xcrun --show-sdk-path),-I,$(pwd) \
  --module Realm \
  --root-url https://realm.io/docs/objc/2.2.0/api/ \
  --output docs/objc_output \
  --head "$(cat docs/custom_head.html)"

See the Objective-C docs for more information and some tips on troubleshooting.

Mixed Objective-C / Swift

This feature is new and has some rough edges.

To generate documentation for a mixed Swift and Objective-C project you must first generate two SourceKitten files: one for Swift and one for Objective-C.

Then pass these files to Jazzy together using --sourcekitten-sourcefile.

Example

This is how docs are generated from an Xcode project for a module containing both Swift and Objective-C files:

# Generate Swift SourceKitten output
sourcekitten doc -- -workspace MyProject.xcworkspace -scheme MyScheme > swiftDoc.json

# Generate Objective-C SourceKitten output
sourcekitten doc --objc $(pwd)/MyProject/MyProject.h \
      -- -x objective-c  -isysroot $(xcrun --show-sdk-path --sdk iphonesimulator) \
      -I $(pwd) -fmodules > objcDoc.json

# Feed both outputs to Jazzy as a comma-separated list
jazzy --sourcekitten-sourcefile swiftDoc.json,objcDoc.json

Docs from .swiftmodules or frameworks

This feature is new and relies on a new Swift feature: there may be crashes and mistakes: reports welcome.

Swift 5.3 adds support for symbol graph generation from .swiftmodule files. This looks to be part of Apple's toolchain for generating their online docs.

Jazzy can use this to generate API documentation. This is faster than using the source code directly but does have limitations: for example documentation comments are available only for public declarations, and the presentation of Swift extensions may not match the way they are written in code.

Some examples:

Generate docs for the Apple Combine framework for macOS:

jazzy --module Combine --swift-build-tool symbolgraph

The SDK's library directories are included in the search path by default.

Same but for iOS:

jazzy --module Combine --swift-build-tool symbolgraph
      --sdk iphoneos
      --build-tool-arguments -target,arm64-apple-ios14.1

The target is the LLVM target triple and needs to match the SDK. The default here is the target of the host system that Jazzy is running on, something like x86_64-apple-darwin19.6.0.

Generate docs for a personal .swiftmodule:

jazzy --module MyMod --swift-build-tool symbolgraph
      --build-tool-arguments -I,/Build/Products

This implies that /Build/Products/MyMod.swiftmodule exists. Jazzy's --source-directory (default current directory) is searched by default, so you only need the -I override if that's not enough.

For a personal framework:

jazzy --module MyMod --swift-build-tool symbolgraph
      --build-tool-arguments -F,/Build/Products

This implies that /Build/Products/MyMod.framework exists and contains a .swiftmodule. Again the --source-directory is searched by default if -F is not passed in.

With pre-generated symbolgraph files:

jazzy --module MyMod --swift-build-tool symbolgraph
      --symbolgraph-directory Build/symbolgraphs

If you've separately generated symbolgraph files by the use of -emit-symbol-graph, you can pass the location of these files using --symbolgraph-directory from where they can be parsed directly.

See swift symbolgraph-extract -help for all the things you can pass via --build-tool-arguments: if your module has dependencies then you may need to add various search path options to let Swift load it.

Themes

Three themes are provided with jazzy: apple (default), fullwidth and jony.

You can specify which theme to use by passing in the --theme option. You can also provide your own custom theme by passing in the path to your theme directory.

Guides

DescriptionCommand
Command line option--documentation={file pattern}
Example--documentation=Docs/*.md
jazzy.yaml exampledocumentation: Docs/*.md

By default, jazzy looks for one of README.md, README.markdown, README.mdown or README (in that order) in the directory from where it runs to render the index page at the root of the docs output directory. Using the --documentation option, extra markdown files can be integrated into the generated docs and sidebar navigation.

Any files found matching the file pattern will be parsed and included as a document with the type 'Guide' when generated. If the files are not included using the custom_categories config option, they will be grouped under 'Other Guides' in the sidebar navigation.

There are a few limitations:

  • File names must be unique from source files.
  • Readme should be specified separately using the readme option.

Section description abstracts

DescriptionCommand
Command line option--abstract={file pattern}
Example--abstract=Docs/Sections/*.md
jazzy.yaml exampleabstract: Docs/Sections/*.md

Using the --abstract options, extra markdown can be included after the heading of section overview pages. Think of it as a template include.

The list of files matching the pattern is compared against the list of sections generated and if a match is found, it's contents will be included in that section before listing source output.

Unlike the --documentation option, these files are not included in navigation and if a file does not match a section title, it is not included at all.

This is very helpful when using custom_categories for grouping types and including relevant documentation in those sections.

For an example of a project using both --documentation and --abstract see: https://reswift.github.io/ReSwift/

Controlling what is documented

In Swift mode, Jazzy by default documents only public and open declarations. To include declarations with a lower access level, set the --min-acl flag to internal, fileprivate, or private.

By default, Jazzy does not document declarations marked @_spi when --min-acl is set to public or open. Set the --include-spi-declarations flag to include them.

In Objective-C mode, Jazzy documents all declarations found in the --umbrella-header header file and any other header files included by it.

You can control exactly which declarations should be documented using --exclude, --include, or :nodoc:.

The --include and --exclude flags list source files that should be included/excluded respectively in the documentation. Entries in the list can be absolute pathnames beginning with / or relative pathnames. Relative pathnames are interpreted relative to the directory from where you run jazzy or, if the flags are set in the config file, relative to the directory containing the config file. Entries in the list can match multiple files using * to match any number of characters including /. For example:

  • jazzy --include=/Users/fred/project/Sources/Secret.swift -- include a specific file
  • jazzy --exclude=/*/Internal* -- exclude all files with names that begin with Internal and any files under any directory with a name beginning Internal.
  • jazzy --exclude=Impl1/*,Impl2/* -- exclude all files under the directories Impl1 and Impl2 found in the current directory.

Note that the --include option is applied before the --exclude option. For example:

  • jazzy --include=/*/Internal* --exclude=Impl1/*,Impl2/* -- include all files with names that begin with Internal and any files under any directory with a name beginning Internal, except for those under the directories Impl1 and Impl2 found in the current directory

Declarations with a documentation comment containing :nodoc: are excluded from the documentation.

Documentation structure

By default Jazzy does not create separate web pages for declarations that do not have any members: instead they are nested into some parent page. Use the --separate-global-declarations flag to change this and always create pages for declarations that can be directly accessed from client code.

Choosing the Swift language version

Jazzy normally uses the Swift compiler from the Xcode currently configured by xcode-select. Use the --swift-version flag to compile with a different Xcode.

The value you pass to --swift-version must be the Swift language version given by swift --version in the Xcode you want to use.

For example to use Xcode 9.4:

jazzy --swift-version 4.1.2

Linux

Jazzy uses SourceKitten to communicate with the Swift build environment and compiler. The sourcekitten binary included in the Jazzy gem is built for macOS and so does not run on other operating systems.

To use Jazzy on Linux you first need to install and build sourcekitten following instructions from SourceKitten's GitHub repository.

Then to generate documentation for a SwiftPM project, instead of running just jazzy do:

sourcekitten doc --spm > doc.json
jazzy --sourcekitten-sourcefile doc.json

We hope to improve this process in the future.

Troubleshooting

Swift

Only extensions are listed in the documentation?

Check the --min-acl setting -- see above.

Unable to find an Xcode with swift version X

  1. The value passed with --swift-version must exactly match the version number from swiftc --version. For example Xcode 10.1 needs --swift-version 4.2.1. See the flag documentation.
  2. The Xcode you want to use must be in the Spotlight index. You can check this using mdfind 'kMDItemCFBundleIdentifier == com.apple.dt.Xcode'. Some users have reported this issue being fixed by a reboot; mdutil -E may also help. If none of these work then you can set the DEVELOPER_DIR environment variable to point to the Xcode you want before running Jazzy without the --swift-version flag.

Objective-C

See this document.

Installation Problems

Can't find header files / clang

Some of the Ruby gems that Jazzy depends on have native C extensions. This means you need the Xcode command-line developer tools installed to build them: run xcode-select --install to install the tools.

/Applications/Xcode: No such file or directory

The path of your active Xcode installation must not contain spaces. So /Applications/Xcode.app/ is fine, /Applications/Xcode-10.2.app/ is fine, but /Applications/Xcode 10.2.app/ is not. This restriction applies only when installing Jazzy, not running it.

MacOS Before 10.14.4

Starting with Jazzy 0.10.0, if you see an error similar to dyld: Symbol not found: _$s11SubSequenceSlTl then you need to install the Swift 5 Runtime Support for Command Line Tools.

Alternatively, you can:

  • Update to macOS 10.14.4 or later; or
  • Install Xcode 10.2 or later at /Applications/Xcode.app.

Development

Please review jazzy's contributing guidelines when submitting pull requests.

jazzy is composed of two parts:

  1. The parser, SourceKitten (written in Swift)
  2. The site generator (written in ruby)

To build and run jazzy from source:

  1. Install bundler.
  2. Run bundle install from the root of this repo.
  3. Run jazzy from source by running bin/jazzy.

Instructions to build SourceKitten from source can be found at SourceKitten's GitHub repository.

Design Goals

  • Generate source code docs matching Apple's official reference documentation
  • Support for standard Objective-C and Swift documentation comment syntax
  • Leverage modern HTML templating (Mustache)
  • Leverage the power and accuracy of the Clang AST and SourceKit
  • Support for Dash docsets
  • Support Swift and Objective-C

Download Details:

Author: Realm
Source Code: https://github.com/realm/jazzy 
License: MIT license

#swift #ruby #objective-c 

What is GEEK

Buddha Community

Jazzy: Soulful Docs for Swift & Objective-C
Sasha  Lee

Sasha Lee

1650636000

Dl4clj: Clojure Wrapper for Deeplearning4j.

dl4clj

Port of deeplearning4j to clojure

Contact info

If you have any questions,

  • my email is will@yetanalytics.com
  • I'm will_hoyt in the clojurians slack
  • twitter is @FeLungz (don't check very often)

TODO

  • update examples dir
  • finish README
    • add in examples using Transfer Learning
  • finish tests
    • eval is missing regression tests, roc tests
    • nn-test is missing regression tests
    • spark tests need to be redone
    • need dl4clj.core tests
  • revist spark for updates
  • write specs for user facing functions
    • this is very important, match isnt strict for maps
    • provides 100% certianty of the input -> output flow
    • check the args as they come in, dispatch once I know its safe, test the pure output
  • collapse overlapping api namespaces
  • add to core use case flows

Features

Stable Features with tests

  • Neural Networks DSL
  • Early Stopping Training
  • Transfer Learning
  • Evaluation
  • Data import

Features being worked on for 0.1.0

  • Clustering (testing in progress)
  • Spark (currently being refactored)
  • Front End (maybe current release, maybe future release. Not sure yet)
  • Version of dl4j is 0.0.8 in this project. Current dl4j version is 0.0.9
  • Parallelism
  • Kafka support
  • Other items mentioned in TODO

Features being worked on for future releases

  • NLP
  • Computational Graphs
  • Reinforement Learning
  • Arbiter

Artifacts

NOT YET RELEASED TO CLOJARS

  • fork or clone to try it out

If using Maven add the following repository definition to your pom.xml:

<repository>
  <id>clojars.org</id>
  <url>http://clojars.org/repo</url>
</repository>

Latest release

With Leiningen:

n/a

With Maven:

n/a

<dependency>
  <groupId>_</groupId>
  <artifactId>_</artifactId>
  <version>_</version>
</dependency>

Usage

Things you need to know

All functions for creating dl4j objects return code by default

  • All of these functions have an option to return the dl4j object
    • :as-code? = false
  • This because all builders require the code representation of dl4j objects
    • this requirement is not going to change
  • INDarray creation fns default to objects, this is for convenience
    • :as-code? is still respected

API functions return code when all args are provided as code

API functions return the value of calling the wrapped method when args are provided as a mixture of objects and code or just objects

The tests are there to help clarify behavior, if you are unsure of how to use a fn, search the tests

  • for questions about spark, refer to the spark section bellow

Example of obj/code duality

(ns my.ns
  (:require [dl4clj.nn.conf.builders.layers :as l]))

;; as code (the default)

(l/dense-layer-builder
 :activation-fn :relu
 :learning-rate 0.006
 :weight-init :xavier
 :layer-name "example layer"
 :n-in 10
 :n-out 1)

;; =>

(doto
 (org.deeplearning4j.nn.conf.layers.DenseLayer$Builder.)
 (.nOut 1)
 (.activation (dl4clj.constants/value-of {:activation-fn :relu}))
 (.weightInit (dl4clj.constants/value-of {:weight-init :xavier}))
 (.nIn 10)
 (.name "example layer")
 (.learningRate 0.006))

;; as an object

(l/dense-layer-builder
 :activation-fn :relu
 :learning-rate 0.006
 :weight-init :xavier
 :layer-name "example layer"
 :n-in 10
 :n-out 1
 :as-code? false)

;; =>

#object[org.deeplearning4j.nn.conf.layers.DenseLayer 0x69d7d160 "DenseLayer(super=FeedForwardLayer(super=Layer(layerName=example layer, activationFn=relu, weightInit=XAVIER, biasInit=NaN, dist=null, learningRate=0.006, biasLearningRate=NaN, learningRateSchedule=null, momentum=NaN, momentumSchedule=null, l1=NaN, l2=NaN, l1Bias=NaN, l2Bias=NaN, dropOut=NaN, updater=null, rho=NaN, epsilon=NaN, rmsDecay=NaN, adamMeanDecay=NaN, adamVarDecay=NaN, gradientNormalization=null, gradientNormalizationThreshold=NaN), nIn=10, nOut=1))"]

General usage examples

Importing data

Loading data from a file (here its a csv)


(ns my.ns
 (:require [dl4clj.datasets.input-splits :as s]
           [dl4clj.datasets.record-readers :as rr]
           [dl4clj.datasets.api.record-readers :refer :all]
           [dl4clj.datasets.iterators :as ds-iter]
           [dl4clj.datasets.api.iterators :refer :all]
           [dl4clj.helpers :refer [data-from-iter]]))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; file splits (convert the data to records)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def poker-path "resources/poker-hand-training.csv")
;; this is not a complete dataset, it is just here to sever as an example

(def file-split (s/new-filesplit :path poker-path))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; record readers, (read the records created by the file split)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def csv-rr (initialize-rr! :rr (rr/new-csv-record-reader :skip-n-lines 0 :delimiter ",")
                                 :input-split file-split))

;; lets look at some data
(println (next-record! :rr csv-rr :as-code? false))
;; => #object[java.util.ArrayList 0x2473e02d [1, 10, 1, 11, 1, 13, 1, 12, 1, 1, 9]]
;; this is our first line from the csv


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; record readers dataset iterators (turn our writables into a dataset)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def rr-ds-iter (ds-iter/new-record-reader-dataset-iterator
                 :record-reader csv-rr
                 :batch-size 1
                 :label-idx 10
                 :n-possible-labels 10))

;; we use our record reader created above
;; we want to see one example per dataset obj returned (:batch-size = 1)
;; we know our label is at the last index, so :label-idx = 10
;; there are 10 possible types of poker hands so :n-possible-labels = 10
;; you can also set :label-idx to -1 to use the last index no matter the size of the seq

(def other-rr-ds-iter (ds-iter/new-record-reader-dataset-iterator
                       :record-reader csv-rr
                       :batch-size 1
                       :label-idx -1
                       :n-possible-labels 10))

(str (next-example! :iter rr-ds-iter :as-code? false))
;; =>
;;===========INPUT===================
;;[1.00, 10.00, 1.00, 11.00, 1.00, 13.00, 1.00, 12.00, 1.00, 1.00]
;;=================OUTPUT==================
;;[0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 1.00]


;; and to show that :label-idx = -1 gives us the same output

(= (next-example! :iter rr-ds-iter :as-code? false)
   (next-example! :iter other-rr-ds-iter :as-code? false)) ;; => true

INDArrays and Datasets from clojure data structures


(ns my.ns
  (:require [nd4clj.linalg.factory.nd4j :refer [vec->indarray matrix->indarray
                                                indarray-of-zeros indarray-of-ones
                                                indarray-of-rand vec-or-matrix->indarray]]
            [dl4clj.datasets.new-datasets :refer [new-ds]]
            [dl4clj.datasets.api.datasets :refer [as-list]]
            [dl4clj.datasets.iterators :refer [new-existing-dataset-iterator]]
            [dl4clj.datasets.api.iterators :refer :all]
            [dl4clj.datasets.pre-processors :as ds-pp]
            [dl4clj.datasets.api.pre-processors :refer :all]
            [dl4clj.core :as c]))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; INDArray creation
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;;TODO: consider defaulting to code

;; can create from a vector

(vec->indarray [1 2 3 4])
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x269df212 [1.00, 2.00, 3.00, 4.00]]

;; or from a matrix

(matrix->indarray [[1 2 3 4] [2 4 6 8]])
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x20aa7fe1
;; [[1.00, 2.00, 3.00, 4.00], [2.00, 4.00, 6.00, 8.00]]]


;; will fill in spareness with zeros

(matrix->indarray [[1 2 3 4] [2 4 6 8] [10 12]])
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x8b7796c
;;[[1.00, 2.00, 3.00, 4.00],
;; [2.00, 4.00, 6.00, 8.00],
;; [10.00, 12.00, 0.00, 0.00]]]

;; can create an indarray of all zeros with specified shape
;; defaults to :rows = 1 :columns = 1

(indarray-of-zeros :rows 3 :columns 2)
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x6f586a7e
;;[[0.00, 0.00],
;; [0.00, 0.00],
;; [0.00, 0.00]]]

(indarray-of-zeros) ;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0xe59ffec 0.00]

;; and if only one is supplied, will get a vector of specified length

(indarray-of-zeros :rows 2)
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x2899d974 [0.00, 0.00]]

(indarray-of-zeros :columns 2)
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0xa5b9782 [0.00, 0.00]]

;; same considerations/defaults for indarray-of-ones and indarray-of-rand

(indarray-of-ones :rows 2 :columns 3)
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x54f08662 [[1.00, 1.00, 1.00], [1.00, 1.00, 1.00]]]

(indarray-of-rand :rows 2 :columns 3)
;; all values are greater than 0 but less than 1
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x2f20293b [[0.85, 0.86, 0.13], [0.94, 0.04, 0.36]]]



;; vec-or-matrix->indarray is built into all functions which require INDArrays
;; so that you can use clojure data structures
;; but you still have the option of passing existing INDArrays

(def example-array (vec-or-matrix->indarray [1 2 3 4]))
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x5c44c71f [1.00, 2.00, 3.00, 4.00]]

(vec-or-matrix->indarray example-array)
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x607b03b0 [1.00, 2.00, 3.00, 4.00]]

(vec-or-matrix->indarray (indarray-of-rand :rows 2))
;; => #object[org.nd4j.linalg.cpu.nativecpu.NDArray 0x49143b08 [0.76, 0.92]]

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; data-set creation
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def ds-with-single-example (new-ds :input [1 2 3 4]
                                    :output [0.0 1.0 0.0]))

(as-list :ds ds-with-single-example :as-code? false)
;; =>
;; #object[java.util.ArrayList 0x5d703d12
;;[===========INPUT===================
;;[1.00, 2.00, 3.00, 4.00]
;;=================OUTPUT==================
;;[0.00, 1.00, 0.00]]]

(def ds-with-multiple-examples (new-ds
                                :input [[1 2 3 4] [2 4 6 8]]
                                :output [[0.0 1.0 0.0] [0.0 0.0 1.0]]))

(as-list :ds ds-with-multiple-examples :as-code? false)
;; =>
;;#object[java.util.ArrayList 0x29c7a9e2
;;[===========INPUT===================
;;[1.00, 2.00, 3.00, 4.00]
;;=================OUTPUT==================
;;[0.00, 1.00, 0.00],
;;===========INPUT===================
;;[2.00, 4.00, 6.00, 8.00]
;;=================OUTPUT==================
;;[0.00, 0.00, 1.00]]]

;; we can create a dataset iterator from the code which creates datasets
;; and set the labels for our outputs (optional)

(def ds-with-multiple-examples
  (new-ds
   :input [[1 2 3 4] [2 4 6 8]]
   :output [[0.0 1.0 0.0] [0.0 0.0 1.0]]))

;; iterator
(def training-rr-ds-iter
  (new-existing-dataset-iterator
   :dataset ds-with-multiple-examples
   :labels ["foo" "baz" "foobaz"]))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; data-set normalization
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; this gathers statistics on the dataset and normalizes the data
;; and applies the transformation to all dataset objects in the iterator
(def train-iter-normalized
  (c/normalize-iter! :iter training-rr-ds-iter
                     :normalizer (ds-pp/new-standardize-normalization-ds-preprocessor)
                     :as-code? false))

;; above returns the normalized iterator
;; to get fit normalizer

(def the-normalizer
  (get-pre-processor train-iter-normalized))

Model configuration

Creating a neural network configuration with singe and multiple layers

(ns my.ns
  (:require [dl4clj.nn.conf.builders.layers :as l]
            [dl4clj.nn.conf.builders.nn :as nn]
            [dl4clj.nn.conf.distributions :as dist]
            [dl4clj.nn.conf.input-pre-processor :as pp]
            [dl4clj.nn.conf.step-fns :as s-fn]))

;; nn/builder has 3 types of args
;; 1) args which set network configuration params
;; 2) args which set default values for layers
;; 3) args which set multi layer network configuration params

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; single layer nn configuration
;; here we are setting network configuration
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(nn/builder :optimization-algo :stochastic-gradient-descent
            :seed 123
            :iterations 1
            :minimize? true
            :use-drop-connect? false
            :lr-score-based-decay-rate 0.002
            :regularization? false
            :step-fn :default-step-fn
            :layers {:dense-layer {:activation-fn :relu
                                   :updater :adam
                                   :adam-mean-decay 0.2
                                   :adam-var-decay 0.1
                                   :learning-rate 0.006
                                   :weight-init :xavier
                                   :layer-name "single layer model example"
                                   :n-in 10
                                   :n-out 20}})

;; there are several options within a nn-conf map which can be configuration maps
;; or calls to fns
;; It doesn't matter which option you choose and you don't have to stay consistent
;; the list of params which can be passed as config maps or fn calls will
;; be enumerated at a later date

(nn/builder :optimization-algo :stochastic-gradient-descent
            :seed 123
            :iterations 1
            :minimize? true
            :use-drop-connect? false
            :lr-score-based-decay-rate 0.002
            :regularization? false
            :step-fn (s-fn/new-default-step-fn)
            :build? true
            ;; dont need to specify layer order, theres only one
            :layers (l/dense-layer-builder
                    :activation-fn :relu
                    :updater :adam
                    :adam-mean-decay 0.2
                    :adam-var-decay 0.1
                    :dist (dist/new-normal-distribution :mean 0 :std 1)
                    :learning-rate 0.006
                    :weight-init :xavier
                    :layer-name "single layer model example"
                    :n-in 10
                    :n-out 20))

;; these configurations are the same

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; multi-layer configuration
;; here we are also setting layer defaults
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; defaults will apply to layers which do not specify those value in their config

(nn/builder
 :optimization-algo :stochastic-gradient-descent
 :seed 123
 :iterations 1
 :minimize? true
 :use-drop-connect? false
 :lr-score-based-decay-rate 0.002
 :regularization? false
 :default-activation-fn :sigmoid
 :default-weight-init :uniform

 ;; we need to specify the layer order
 :layers {0 (l/activation-layer-builder
             :activation-fn :relu
             :updater :adam
             :adam-mean-decay 0.2
             :adam-var-decay 0.1
             :learning-rate 0.006
             :weight-init :xavier
             :layer-name "example first layer"
             :n-in 10
             :n-out 20)
          1 {:output-layer {:n-in 20
                            :n-out 2
                            :loss-fn :mse
                            :layer-name "example output layer"}}})

;; specifying multi-layer config params

(nn/builder
 ;; network args
 :optimization-algo :stochastic-gradient-descent
 :seed 123
 :iterations 1
 :minimize? true
 :use-drop-connect? false
 :lr-score-based-decay-rate 0.002
 :regularization? false

 ;; layer defaults
 :default-activation-fn :sigmoid
 :default-weight-init :uniform

 ;; the layers
 :layers {0 (l/activation-layer-builder
             :activation-fn :relu
             :updater :adam
             :adam-mean-decay 0.2
             :adam-var-decay 0.1
             :learning-rate 0.006
             :weight-init :xavier
             :layer-name "example first layer"
             :n-in 10
             :n-out 20)
          1 {:output-layer {:n-in 20
                            :n-out 2
                            :loss-fn :mse
                            :layer-name "example output layer"}}}
 ;; multi layer network args
 :backprop? true
 :backprop-type :standard
 :pretrain? false
 :input-pre-processors {0 (pp/new-zero-mean-pre-pre-processor)
                        1 {:unit-variance-processor {}}})

Configuration to Trained models

Multi Layer models

(ns my.ns
  (:require [dl4clj.datasets.iterators :as iter]
            [dl4clj.datasets.input-splits :as split]
            [dl4clj.datasets.record-readers :as rr]
            [dl4clj.optimize.listeners :as listener]
            [dl4clj.nn.conf.builders.nn :as nn]
            [dl4clj.nn.multilayer.multi-layer-network :as mln]
            [dl4clj.nn.api.model :refer [init! set-listeners!]]
            [dl4clj.nn.api.multi-layer-network :refer [evaluate-classification]]
            [dl4clj.datasets.api.record-readers :refer [initialize-rr!]]
            [dl4clj.eval.api.eval :refer [get-stats get-accuracy]]
            [dl4clj.core :as c]))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; nn-conf -> multi-layer-network
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def nn-conf
  (nn/builder
   ;; network args
   :optimization-algo :stochastic-gradient-descent
   :seed 123 :iterations 1 :regularization? true

   ;; setting layer defaults
   :default-activation-fn :relu :default-l2 7.5e-6
   :default-weight-init :xavier :default-learning-rate 0.0015
   :default-updater :nesterovs :default-momentum 0.98

   ;; setting layer configuration
   :layers {0 {:dense-layer
               {:layer-name "example first layer"
                :n-in 784 :n-out 500}}
            1 {:dense-layer
               {:layer-name "example second layer"
                :n-in 500 :n-out 100}}
            2 {:output-layer
               {:n-in 100 :n-out 10
                ;; layer specific params
                :loss-fn :negativeloglikelihood
                :activation-fn :softmax
                :layer-name "example output layer"}}}

   ;; multi layer args
   :backprop? true
   :pretrain? false))

(def multi-layer-network (c/model-from-conf nn-conf))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; local cpu training with dl4j pre-built iterators
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; lets use the pre-built Mnist data set iterator

(def train-mnist-iter
  (iter/new-mnist-data-set-iterator
   :batch-size 64
   :train? true
   :seed 123))

(def test-mnist-iter
  (iter/new-mnist-data-set-iterator
   :batch-size 64
   :train? false
   :seed 123))

;; and lets set a listener so we can know how training is going

(def score-listener (listener/new-score-iteration-listener :print-every-n 5))

;; and attach it to our model

;; TODO: listeners are broken, look into log4j warnning
(def mln-with-listener (set-listeners! :model multi-layer-network
                                       :listeners [score-listener]))

(def trained-mln (mln/train-mln-with-ds-iter! :mln mln-with-listener
                                              :iter train-mnist-iter
                                              :n-epochs 15
                                              :as-code? false))

;; training happens because :as-code? = false
;; if it was true, we would still just have a data structure
;; we now have a trained model that has seen the training dataset 15 times
;; time to evaluate our model

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;Create an evaluation object
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def eval-obj (evaluate-classification :mln trained-mln
                                       :iter test-mnist-iter))

;; always remember that these objects are stateful, dont use the same eval-obj
;; to eval two different networks
;; we trained the model on a training dataset.  We evaluate on a test set

(println (get-stats :evaler eval-obj))
;; this will print the stats to standard out for each feature/label pair

;;Examples labeled as 0 classified by model as 0: 968 times
;;Examples labeled as 0 classified by model as 1: 1 times
;;Examples labeled as 0 classified by model as 2: 1 times
;;Examples labeled as 0 classified by model as 3: 1 times
;;Examples labeled as 0 classified by model as 5: 1 times
;;Examples labeled as 0 classified by model as 6: 3 times
;;Examples labeled as 0 classified by model as 7: 1 times
;;Examples labeled as 0 classified by model as 8: 2 times
;;Examples labeled as 0 classified by model as 9: 2 times
;;Examples labeled as 1 classified by model as 1: 1126 times
;;Examples labeled as 1 classified by model as 2: 2 times
;;Examples labeled as 1 classified by model as 3: 1 times
;;Examples labeled as 1 classified by model as 5: 1 times
;;Examples labeled as 1 classified by model as 6: 2 times
;;Examples labeled as 1 classified by model as 7: 1 times
;;Examples labeled as 1 classified by model as 8: 2 times
;;Examples labeled as 2 classified by model as 0: 3 times
;;Examples labeled as 2 classified by model as 1: 2 times
;;Examples labeled as 2 classified by model as 2: 1006 times
;;Examples labeled as 2 classified by model as 3: 2 times
;;Examples labeled as 2 classified by model as 4: 3 times
;;Examples labeled as 2 classified by model as 6: 3 times
;;Examples labeled as 2 classified by model as 7: 7 times
;;Examples labeled as 2 classified by model as 8: 6 times
;;Examples labeled as 3 classified by model as 2: 4 times
;;Examples labeled as 3 classified by model as 3: 990 times
;;Examples labeled as 3 classified by model as 5: 3 times
;;Examples labeled as 3 classified by model as 7: 3 times
;;Examples labeled as 3 classified by model as 8: 3 times
;;Examples labeled as 3 classified by model as 9: 7 times
;;Examples labeled as 4 classified by model as 2: 2 times
;;Examples labeled as 4 classified by model as 3: 1 times
;;Examples labeled as 4 classified by model as 4: 967 times
;;Examples labeled as 4 classified by model as 6: 4 times
;;Examples labeled as 4 classified by model as 7: 1 times
;;Examples labeled as 4 classified by model as 9: 7 times
;;Examples labeled as 5 classified by model as 0: 2 times
;;Examples labeled as 5 classified by model as 3: 6 times
;;Examples labeled as 5 classified by model as 4: 1 times
;;Examples labeled as 5 classified by model as 5: 874 times
;;Examples labeled as 5 classified by model as 6: 3 times
;;Examples labeled as 5 classified by model as 7: 1 times
;;Examples labeled as 5 classified by model as 8: 3 times
;;Examples labeled as 5 classified by model as 9: 2 times
;;Examples labeled as 6 classified by model as 0: 4 times
;;Examples labeled as 6 classified by model as 1: 3 times
;;Examples labeled as 6 classified by model as 3: 2 times
;;Examples labeled as 6 classified by model as 4: 4 times
;;Examples labeled as 6 classified by model as 5: 4 times
;;Examples labeled as 6 classified by model as 6: 939 times
;;Examples labeled as 6 classified by model as 7: 1 times
;;Examples labeled as 6 classified by model as 8: 1 times
;;Examples labeled as 7 classified by model as 1: 7 times
;;Examples labeled as 7 classified by model as 2: 4 times
;;Examples labeled as 7 classified by model as 3: 3 times
;;Examples labeled as 7 classified by model as 7: 1005 times
;;Examples labeled as 7 classified by model as 8: 2 times
;;Examples labeled as 7 classified by model as 9: 7 times
;;Examples labeled as 8 classified by model as 0: 3 times
;;Examples labeled as 8 classified by model as 2: 3 times
;;Examples labeled as 8 classified by model as 3: 2 times
;;Examples labeled as 8 classified by model as 4: 4 times
;;Examples labeled as 8 classified by model as 5: 3 times
;;Examples labeled as 8 classified by model as 6: 2 times
;;Examples labeled as 8 classified by model as 7: 4 times
;;Examples labeled as 8 classified by model as 8: 947 times
;;Examples labeled as 8 classified by model as 9: 6 times
;;Examples labeled as 9 classified by model as 0: 2 times
;;Examples labeled as 9 classified by model as 1: 2 times
;;Examples labeled as 9 classified by model as 3: 4 times
;;Examples labeled as 9 classified by model as 4: 8 times
;;Examples labeled as 9 classified by model as 6: 1 times
;;Examples labeled as 9 classified by model as 7: 4 times
;;Examples labeled as 9 classified by model as 8: 2 times
;;Examples labeled as 9 classified by model as 9: 986 times

;;==========================Scores========================================
;; Accuracy:        0.9808
;; Precision:       0.9808
;; Recall:          0.9807
;; F1 Score:        0.9807
;;========================================================================

;; can get the stats that are printed via fns in the evaluation namespace
;; after running eval-model-whole-ds

(get-accuracy :evaler evaler-with-stats) ;; => 0.9808

Model Tuning

Early Stopping (controlling training)

it is recommened you start here when designing models

using dl4clj.core


(ns my.ns
  (:require [dl4clj.earlystopping.termination-conditions :refer :all]
            [dl4clj.earlystopping.model-saver :refer [new-in-memory-saver]]
            [dl4clj.nn.api.multi-layer-network :refer [evaluate-classification]]
            [dl4clj.eval.api.eval :refer [get-stats]]
            [dl4clj.nn.conf.builders.nn :as nn]
            [dl4clj.datasets.iterators :as iter]
            [dl4clj.core :as c]))

(def nn-conf
  (nn/builder
   ;; network args
   :optimization-algo :stochastic-gradient-descent
   :seed 123
   :iterations 1
   :regularization? true

   ;; setting layer defaults
   :default-activation-fn :relu
   :default-l2 7.5e-6
   :default-weight-init :xavier
   :default-learning-rate 0.0015
   :default-updater :nesterovs
   :default-momentum 0.98

   ;; setting layer configuration
   :layers {0 {:dense-layer
               {:layer-name "example first layer"
                :n-in 784 :n-out 500}}
            1 {:dense-layer
               {:layer-name "example second layer"
                :n-in 500 :n-out 100}}
            2 {:output-layer
               {:n-in 100 :n-out 10
                ;; layer specific params
                :loss-fn :negativeloglikelihood
                :activation-fn :softmax
                :layer-name "example output layer"}}}

   ;; multi layer args
   :backprop? true
   :pretrain? false))

(def train-iter
  (iter/new-mnist-data-set-iterator
   :batch-size 64
   :train? true
   :seed 123))

(def test-iter
  (iter/new-mnist-data-set-iterator
   :batch-size 64
   :train? false
   :seed 123))

(def invalid-score-condition (new-invalid-score-iteration-termination-condition))

(def max-score-condition (new-max-score-iteration-termination-condition
                          :max-score 20.0))

(def max-time-condition (new-max-time-iteration-termination-condition
                         :max-time-val 10
                         :max-time-unit :minutes))

(def score-doesnt-improve-condition (new-score-improvement-epoch-termination-condition
                                     :max-n-epoch-no-improve 5))

(def target-score-condition (new-best-score-epoch-termination-condition
                             :best-expected-score 0.009))

(def max-number-epochs-condition (new-max-epochs-termination-condition :max-n 20))

(def in-mem-saver (new-in-memory-saver))

(def trained-mln
;; defaults to returning the model
  (c/train-with-early-stopping
   :nn-conf nn-conf
   :training-iter train-mnist-iter
   :testing-iter test-mnist-iter
   :eval-every-n-epochs 1
   :iteration-termination-conditions [invalid-score-condition
                                      max-score-condition
                                      max-time-condition]
   :epoch-termination-conditions [score-doesnt-improve-condition
                                  target-score-condition
                                  max-number-epochs-condition]
   :save-last-model? true
   :model-saver in-mem-saver
   :as-code? false))

(def model-evaler
  (evaluate-classification :mln trained-mln :iter test-mnist-iter))

(println (get-stats :evaler model-evaler))
  • explicit, step by step way of doing this
(ns my.ns
  (:require [dl4clj.earlystopping.early-stopping-config :refer [new-early-stopping-config]]
            [dl4clj.earlystopping.termination-conditions :refer :all]
            [dl4clj.earlystopping.model-saver :refer [new-in-memory-saver new-local-file-model-saver]]
            [dl4clj.earlystopping.score-calc :refer [new-ds-loss-calculator]]
            [dl4clj.earlystopping.early-stopping-trainer :refer [new-early-stopping-trainer]]
            [dl4clj.earlystopping.api.early-stopping-trainer :refer [fit-trainer!]]
            [dl4clj.nn.conf.builders.nn :as nn]
            [dl4clj.nn.multilayer.multi-layer-network :as mln]
            [dl4clj.utils :refer [load-model!]]
            [dl4clj.datasets.iterators :as iter]
            [dl4clj.core :as c]))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; start with our network config
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def nn-conf
  (nn/builder
   ;; network args
   :optimization-algo :stochastic-gradient-descent
   :seed 123 :iterations 1 :regularization? true
   ;; setting layer defaults
   :default-activation-fn :relu :default-l2 7.5e-6
   :default-weight-init :xavier :default-learning-rate 0.0015
   :default-updater :nesterovs :default-momentum 0.98
   ;; setting layer configuration
   :layers {0 {:dense-layer
               {:layer-name "example first layer"
                :n-in 784 :n-out 500}}
            1 {:dense-layer
               {:layer-name "example second layer"
                :n-in 500 :n-out 100}}
            2 {:output-layer
               {:n-in 100 :n-out 10
                ;; layer specific params
                :loss-fn :negativeloglikelihood
                :activation-fn :softmax
                :layer-name "example output layer"}}}
   ;; multi layer args
   :backprop? true
   :pretrain? false))

(def mln (c/model-from-conf nn-conf))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; the training/testing data
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def train-iter
  (iter/new-mnist-data-set-iterator
   :batch-size 64
   :train? true
   :seed 123))

(def test-iter
  (iter/new-mnist-data-set-iterator
   :batch-size 64
   :train? false
   :seed 123))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; we are going to need termination conditions
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; these allow us to control when we exit training

;; this can be based off of iterations or epochs

;; iteration termination conditions

(def invalid-score-condition (new-invalid-score-iteration-termination-condition))

(def max-score-condition (new-max-score-iteration-termination-condition
                          :max-score 20.0))

(def max-time-condition (new-max-time-iteration-termination-condition
                         :max-time-val 10
                         :max-time-unit :minutes))

;; epoch termination conditions

(def score-doesnt-improve-condition (new-score-improvement-epoch-termination-condition
                                     :max-n-epoch-no-improve 5))

(def target-score-condition (new-best-score-epoch-termination-condition :best-expected-score 0.009))

(def max-number-epochs-condition (new-max-epochs-termination-condition :max-n 20))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; we also need a way to save our model
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; can be in memory or to a local directory

(def in-mem-saver (new-in-memory-saver))

(def local-file-saver (new-local-file-model-saver :directory "resources/tmp/readme/"))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; set up your score calculator
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def score-calcer (new-ds-loss-calculator :iter test-iter
                                          :average? true))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; create an early stopping configuration
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; termination conditions
;; a way to save our model
;; a way to calculate the score of our model on the dataset

(def early-stopping-conf
  (new-early-stopping-config
   :epoch-termination-conditions [score-doesnt-improve-condition
                                  target-score-condition
                                  max-number-epochs-condition]
   :iteration-termination-conditions [invalid-score-condition
                                      max-score-condition
                                      max-time-condition]
   :eval-every-n-epochs 5
   :model-saver local-file-saver
   :save-last-model? true
   :score-calculator score-calcer))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; create an early stopping trainer from our data, model and early stopping conf
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def es-trainer (new-early-stopping-trainer :early-stopping-conf early-stopping-conf
                                            :mln mln
                                            :iter train-iter))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; fit and use our early stopping trainer
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def es-trainer-fitted (fit-trainer! es-trainer :as-code? false))

;; when the trainer terminates, you will see something like this
;;[nREPL-worker-24] BaseEarlyStoppingTrainer INFO  Completed training epoch 14
;;[nREPL-worker-24] BaseEarlyStoppingTrainer INFO  New best model: score = 0.005225599372851298,
;;                                                   epoch = 14 (previous: score = 0.018243224899038346, epoch = 7)
;;[nREPL-worker-24] BaseEarlyStoppingTrainer INFO Hit epoch termination condition at epoch 14.
;;                                           Details: BestScoreEpochTerminationCondition(0.009)

;; and if we look at the es-trainer-fitted object we see

;;#object[org.deeplearning4j.earlystopping.EarlyStoppingResult 0x5ab74f27 EarlyStoppingResult
;;(terminationReason=EpochTerminationCondition,details=BestScoreEpochTerminationCondition(0.009),
;; bestModelEpoch=14,bestModelScore=0.005225599372851298,totalEpochs=15)]

;; and our model has been saved to /resources/tmp/readme/bestModel.bin
;; there we have our model config, model params and our updater state

;; we can then load this model to use it or continue refining it

(def loaded-model (load-model! :path "resources/tmp/readme/bestModel.bin"
                               :load-updater? true))

Transfer Learning (freezing layers)


;; TODO: need to write up examples

Spark Training

dl4j Spark usage

How it is done in dl4clj

  • Uses dl4clj.core
    • This example uses a fn which takes care of most steps for you
      • allows you to pass args as code bc the fn accounts for the multiple spark contexts issue encountered when everything is just a data structure

(ns my.ns
  (:require [dl4clj.nn.conf.builders.layers :as l]
            [dl4clj.nn.conf.builders.nn :as nn]
            [dl4clj.datasets.iterators :refer [new-iris-data-set-iterator]]
            [dl4clj.eval.api.eval :refer [get-stats]]
            [dl4clj.spark.masters.param-avg :as master]
            [dl4clj.spark.data.java-rdd :refer [new-java-spark-context
                                                java-rdd-from-iter]]
            [dl4clj.spark.api.dl4j-multi-layer :refer [eval-classification-spark-mln
                                                       get-spark-context]]
            [dl4clj.core :as c]))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 1, create your model config
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def mln-conf
  (nn/builder
   :optimization-algo :stochastic-gradient-descent
   :default-learning-rate 0.006
   :layers {0 (l/dense-layer-builder :n-in 4 :n-out 2 :activation-fn :relu)
            1 {:output-layer
               {:loss-fn :negativeloglikelihood
                :n-in 2 :n-out 3
                :activation-fn :soft-max
                :weight-init :xavier}}}
   :backprop? true
   :backprop-type :standard))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 2, training master
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def training-master
  (master/new-parameter-averaging-training-master
   :build? true
   :rdd-n-examples 10
   :n-workers 4
   :averaging-freq 10
   :batch-size-per-worker 2
   :export-dir "resources/spark/master/"
   :rdd-training-approach :direct
   :repartition-data :always
   :repartition-strategy :balanced
   :seed 1234
   :save-updater? true
   :storage-level :none))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 3, spark context
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def your-spark-context
  (new-java-spark-context :app-name "example app"))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 4, training data
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def iris-iter
  (new-iris-data-set-iterator
   :batch-size 1
   :n-examples 5))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 5, spark mln
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def fitted-spark-mln
  (c/train-with-spark :spark-context your-spark-context
                      :mln-conf mln-conf
                      :training-master training-master
                      :iter iris-iter
                      :n-epochs 1
                      :as-code? false))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 5, use spark context from spark-mln to create rdd
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; TODO: eliminate this step

(def our-rdd
  (let [sc (get-spark-context fitted-spark-mln :as-code? false)]
    (java-rdd-from-iter :spark-context sc
                        :iter iris-iter)))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 6, evaluation model and print stats (poor performance of model expected)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def eval-obj
  (eval-classification-spark-mln
   :spark-mln fitted-spark-mln
   :rdd our-rdd))

(println (get-stats :evaler eval-obj))

  • this example demonstrates the dl4j workflow
    • NOTE: unlike the previous example, this one requires dl4j objects to be used
      • this is becaues spark only wants you to have one spark context at a time
(ns my.ns
  (:require [dl4clj.nn.conf.builders.layers :as l]
            [dl4clj.nn.conf.builders.nn :as nn]
            [dl4clj.datasets.iterators :refer [new-iris-data-set-iterator]]
            [dl4clj.eval.api.eval :refer [get-stats]]
            [dl4clj.spark.masters.param-avg :as master]
            [dl4clj.spark.data.java-rdd :refer [new-java-spark-context java-rdd-from-iter]]
            [dl4clj.spark.dl4j-multi-layer :as spark-mln]
            [dl4clj.spark.api.dl4j-multi-layer :refer [fit-spark-mln!
                                                       eval-classification-spark-mln]]))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 1, create your model
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def mln-conf
  (nn/builder
   :optimization-algo :stochastic-gradient-descent
   :default-learning-rate 0.006
   :layers {0 (l/dense-layer-builder :n-in 4 :n-out 2 :activation-fn :relu)
            1 {:output-layer
               {:loss-fn :negativeloglikelihood
                :n-in 2 :n-out 3
                :activation-fn :soft-max
                :weight-init :xavier}}}
   :backprop? true
   :as-code? false
   :backprop-type :standard))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 2, create a training master
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; not all options specified, but most are

(def training-master
  (master/new-parameter-averaging-training-master
   :build? true
   :rdd-n-examples 10
   :n-workers 4
   :averaging-freq 10
   :batch-size-per-worker 2
   :export-dir "resources/spark/master/"
   :rdd-training-approach :direct
   :repartition-data :always
   :repartition-strategy :balanced
   :seed 1234
   :as-code? false
   :save-updater? true
   :storage-level :none))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 3, create a Spark Multi Layer Network
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def your-spark-context
  (new-java-spark-context :app-name "example app" :as-code? false))

;; new-java-spark-context will turn an existing spark-configuration into a java spark context
;; or create a new java spark context with master set to "local[*]" and the app name
;; set to :app-name


(def spark-mln
  (spark-mln/new-spark-multi-layer-network
   :spark-context your-spark-context
   :mln mln-conf
   :training-master training-master
   :as-code? false))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 4, load your data
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; one way is via a dataset-iterator
;; can make one directly from a dataset (iterator data-set)
;; see: nd4clj.linalg.dataset.api.data-set and nd4clj.linalg.dataset.data-set
;; we are going to use a pre-built one

(def iris-iter
  (new-iris-data-set-iterator
   :batch-size 1
   :n-examples 5
   :as-code? false))

;; now lets convert the data into a javaRDD

(def our-rdd
  (java-rdd-from-iter :spark-context your-spark-context
                      :iter iris-iter))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Step 5, fit and evaluate the model
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

(def fitted-spark-mln
  (fit-spark-mln!
   :spark-mln spark-mln
   :rdd our-rdd
   :n-epochs 1))
;; this fn also has the option to supply :path-to-data instead of :rdd
;; that path should point to a directory containing a number of dataset objects

(def eval-obj
  (eval-classification-spark-mln
   :spark-mln fitted-spark-mln
   :rdd our-rdd))
;; we would want to have different testing and training rdd's but here we are using
;; the data we trained on

;; lets get the stats for how our model performed

(println (get-stats :evaler eval-obj))

Terminology

Coming soon

Packages to come back to:

Implement ComputationGraphs and the classes which use them

NLP

Parallelism

TSNE

UI


Author: yetanalytics
Source Code: https://github.com/yetanalytics/dl4clj
License: BSD-2-Clause License

#machine-learning #deep-learning 

Arvel  Parker

Arvel Parker

1591611780

How to Find Ulimit For user on Linux

How can I find the correct ulimit values for a user account or process on Linux systems?

For proper operation, we must ensure that the correct ulimit values set after installing various software. The Linux system provides means of restricting the number of resources that can be used. Limits set for each Linux user account. However, system limits are applied separately to each process that is running for that user too. For example, if certain thresholds are too low, the system might not be able to server web pages using Nginx/Apache or PHP/Python app. System resource limits viewed or set with the NA command. Let us see how to use the ulimit that provides control over the resources available to the shell and processes.

#[object object] #[object object] #[object object] #[object object] #[object object] #[object object] #[object object] #[object object] #[object object] #[object object]

MEAN Stack Tutorial MongoDB ExpressJS AngularJS NodeJS

We are going to build a full stack Todo App using the MEAN (MongoDB, ExpressJS, AngularJS and NodeJS). This is the last part of three-post series tutorial.

MEAN Stack tutorial series:

AngularJS tutorial for beginners (Part I)
Creating RESTful APIs with NodeJS and MongoDB Tutorial (Part II)
MEAN Stack Tutorial: MongoDB, ExpressJS, AngularJS and NodeJS (Part III) 👈 you are here
Before completing the app, let’s cover some background about the this stack. If you rather jump to the hands-on part click here to get started.

#[object object] #[object object] #[object object] #[object object] #[object object] #[object object] #[object object] #[object object]

Creating RESTful APIs with NodeJS and MongoDB Tutorial

Welcome to this tutorial about RESTful API using Node.js (Express.js) and MongoDB (mongoose)! We are going to learn how to install and use each component individually and then proceed to create a RESTful API.

MEAN Stack tutorial series:

AngularJS tutorial for beginners (Part I)
Creating RESTful APIs with NodeJS and MongoDB Tutorial (Part II) 👈 you are here
MEAN Stack Tutorial: MongoDB, ExpressJS, AngularJS and NodeJS (Part III)

#[object object] #[object object] #[object object] #[object object] #[object object] #[object object] #[object object]

Yoshiko  Jones

Yoshiko Jones

1598195340

How to configure AWS SES with Postfix MTA

How do I configure Amazon SES With Postfix mail server to send email under a CentOS/RHEL/Fedora/Ubuntu/Debian Linux server?

Amazon Simple Email Service (SES) is a hosted email service for you to send and receive email using your email addresses and domains. Typically SES used for sending bulk email or routing emails without hosting MTA. We can use Perl/Python/PHP APIs to send an email via SES. Another option is to configure Linux or Unix box running Postfix to route all outgoing emails via SES.

  • » Remove sendmail
  • » Install postfix
  • » Configuring postfix for SES
  • » Test postfix

Procedure to configure AWS SES with Postfix

Before getting started with Amazon SES and Postfix, you need to sign up for AWS, including SES. You need to verify your email address and other settings. Make sure you create a user for SES access and download credentials too.

Step 1 – Uninstall Sendmail if installed

If sendmail installed remove it. Debian/Ubuntu Linux user type the following apt command/apt-get command:

$`` sudo apt --purge remove sendmail

CentOS/RHEL user type the following yum command or dnf command on Fedora/CentOS/RHEL 8.x:

$`` sudo yum remove sendmail

$`` sudo dnf remove sendmail

Sample outputs from CentOS 8 server:

Dependencies resolved.
===============================================================================
 Package           Architecture  Version               Repository         Size
===============================================================================
Removing:
 sendmail          x86_64        8.15.2-32.el8         @AppStream        2.4 M
Removing unused dependencies:
 cyrus-sasl        x86_64        2.1.27-1.el8          @BaseOS           160 k
 procmail          x86_64        3.22-47.el8           @AppStream        369 k

Transaction Summary
===============================================================================
Remove  3 Packages

Freed space: 2.9 M
Is this ok [y/N]: y

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