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https://github.com/mikeroyal/photonics-guide

Photonics Guide
https://github.com/mikeroyal/photonics-guide

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Photonics Guide

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Photonics Guide

#### A guide covering the Photonics including the applications, libraries and tools that will make you a better and more efficient with developer with Photonic technologies.

**Note: You can easily convert this markdown file to a PDF in [VSCode](https://code.visualstudio.com/) using this handy extension [Markdown PDF](https://marketplace.visualstudio.com/items?itemName=yzane.markdown-pdf).**





# Table of Contents

1. [Photonics Learning Resources](https://github.com/mikeroyal/Photonics-Guide#photonics-learning-resources)

2. [Photonics Tools, Libraries, and Frameworks](https://github.com/mikeroyal/Photonics-Guide#photonics-tools-libraries-and-frameworks)

3. [Machine Learning](https://github.com/mikeroyal/Photonics-Guide#machine-learning)

4. [MATLAB Development](https://github.com/mikeroyal/Photonics-Guide#matlab-development)

5. [R Development](https://github.com/mikeroyal/Photonics-Guide#r-development)

6. [Python Development](https://github.com/mikeroyal/Photonics-Guide#python-development)

# Photonics Learning Resources
[Back to the Top](https://github.com/mikeroyal/Photonics-Guide#table-of-contents)

[Photonics](https://en.wikipedia.org/wiki/Photonics) is the application of light (photon) generation, detection, and manipulation through emission, transmission, modulation, signal processing, switching, amplification, and sensing.

[Photonic System Design and Simulation | Synopsys](https://www.synopsys.com/photonic-solutions/rsoft-system-design-tools.html)

[Synopsys Photonic Process Design Kits (PDKs)](https://www.synopsys.com/photonic-solutions/pic-design-suite/process-design-kits.html)

[RSoft Photonic Device Tools](https://www.synopsys.com/photonic-solutions/rsoft-photonic-device-tools.html)

[Intel® Silicon Photonics](https://www.intel.com/content/www/us/en/architecture-and-technology/silicon-photonics/silicon-photonics-overview.html)

[The future of packaging with silicon photonics I | IBM](https://www.ibm.com/downloads/cas/M0NL8N85)

[Silicon Nanophotonic Packaging | IBM](https://researcher.watson.ibm.com/researcher/view_group.php?id=5517)

[In-Memory Computing Using Photonic Memory Devices | IBM](https://www.ibm.com/blogs/research/2019/02/photonic-memory-devices/)

[Fundamentals of Photonics: Quantum Electronics | MIT](https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-974-fundamentals-of-photonics-quantum-electronics-spring-2006/)

[Mathematical Methods in Nanophotonics | MIT ](https://ocw.mit.edu/courses/mathematics/18-369-mathematical-methods-in-nanophotonics-spring-2008/)

[Nanophotonics | Stanford Online Course](https://online.stanford.edu/courses/ee336-nanophotonics)

[Stanford | Stanford Photonics Research Center](https://photonics.stanford.edu/)

[Photonic Integrated Circuits 1 Course | edX](https://www.edx.org/course/photonic-integrated-circuits-1)

[Nanophotonic Modeling Course | edX](https://www.edx.org/course/nanophotonic-modeling)

[Nanophotonics and Detectors Course | Coursera](https://www.coursera.org/learn/nanophotonics-detectors)

[Silicon Photonics Design, Fabrication and Data Analysis Course | edX](https://www.edx.org/course/silicon-photonics-design-fabrication-and-data-ana)

[Photonics Courses | AIM Academy](https://www.manufacturingworkforce.org)

[Metal–organic frameworks(MOFs) for electronics and photonics](https://www.cambridge.org/core/journals/mrs-bulletin/article/metalorganic-frameworks-for-electronics-and-photonics/38E2F4C127950AF8CFD84A586D76EA61#)

[Lightmatter](https://lightmatter.co) is a company that has created a photonic processor and interconnect that are faster, more efficient, and cooler than anything else on earth (or anything ever experienced before) to power the next giant leaps in human progress.

# Photonics Tools, Libraries, and Frameworks
[Back to the Top](https://github.com/mikeroyal/Photonics-Guide#table-of-contents)

[EM Photonics CULA Tools](https://developer.nvidia.com/em-photonics-cula-tools) is a GPU-accelerated linear algebra library that utilizes the NVIDIA CUDA parallel computing architecture to dramatically improve the computation speed of sophisticated mathematics.

[Photonic integrated circuits (PICs)](https://www.sbir.gov/node/1836075) is the integration of multiple lithographically defined photonic and electronic components and devices (lasers, detectors, waveguides/passive structures, modulators, electronic control, and optical interconnects) on a single platform with nanometer-scale feature sizes.

[OptSim™](https://www.synopsys.com/photonic-solutions/rsoft-system-design-tools/system-network-optsim.html) is an award-winning software tool for the design and simulation of optical communication systems at the signal propagation level. With state-of-the-art simulation techniques, an easy-to-use graphical user interface and lab-like measurement instruments, OptSim provides unmatched accuracy and usability.

[Bidirectional Module for OptSim](https://www.synopsys.com/photonic-solutions/rsoft-system-design-tools/system-network-optsim/bidirectional-module.html) is a tool that simulates the impact of bidirectional signal propagation in fiber-optic systems across multiple components and is an add-on product to Synopsys’ award-winning fiber-optic communication system simulation tool, OptSim. It is also useful for system applications that require bidirectional propagation of optical and electrical signals, including transmission, reflections, and resonances.

[ModeSYS™](https://www.synopsys.com/photonic-solutions/rsoft-system-design-tools/system-network-modesys.html) is a tool that supports the design and simulation of multimode optical communication systems. With a primary focus on data communication applications, ModeSYS allows users to evaluate both temporal and spatial attributes of optical signal propagation. It can be used as standalone tool or combined with OptSim to form a comprehensive single mode and multimode optical communication system design suite.

[CODE V](https://www.synopsys.com/optical-solutions/codev.html) is a very powerful optical design software providing intelligent tools that let you take on any optical design task, from the simple to the complex, and design better solutions.

[LightTools](https://www.synopsys.com/optical-solutions/lighttools.html) is a tool that enables you to quickly create illumination designs that work right on the first try, reducing prototype iterations.

[FullWAVE™](https://www.synopsys.com/photonic-solutions/rsoft-photonic-device-tools/passive-device-fullwave.html) is a simulation tool employs the [finite-difference time-domain (FDTD) method](https://www.synopsys.com/glossary/what-is-fdtd.html) to perform a full-vector simulation of photonic structures. It is a highly sophisticated tool for studying the propagation of light in a wide variety of photonic structures, including integrated and fiber-optic waveguide devices, as well as circuits and nanophotonic devices such as photonic crystals.

[BeamPROP™](https://www.synopsys.com/photonic-solutions/rsoft-photonic-device-tools/passive-device-beamprop.html) is the industry-leading design tool based on the Beam Propagation Method (BPM) for the design and simulation of integrated and fiber-optic waveguide devices and circuits.

[DiffractMOD™](https://www.synopsys.com/photonic-solutions/rsoft-photonic-device-tools/passive-device-diffractmod.html) is a design and simulation tool for diffractive optical structures such as diffractive optical elements, subwavelength periodic structures, and photonic bandgap crystals. It is based on the Rigorous Coupled Wave Analysis (RCWA) technique that has been implemented using advanced algorithms including fast Fourier factorization and generalized transmission line formulation.

[PrimeSim™ HSPICE®](https://www.synopsys.com/implementation-and-signoff/ams-simulation/primesim-hspice.html) is a circuit simulator for accurate circuit simulation and offers foundries-certified MOS device models with state-of-the-art simulation and analysis algorithms. It includes extensive usage in chip/package/board/backplane signal integrity simulation, cell and memory characterization, and analog mixed signal IC design, PrimeSim HSPICE is the industry’s most popular, trusted and comprehensive circuit simulator.

[Technology Computer-Aided Design (TCAD)](https://www.synopsys.com/silicon/tcad.html) is the use of computer simulations to develop and optimize semiconductor process technologies and devices. Synopsys TCAD offers a comprehensive suite of products that includes industry-leading process and device simulation tools, as well as a powerful graphical user interface (GUI) driven simulation environment for managing simulation tasks and analyzing simulation results. In addition, Synopsys TCAD provides tools for interconnect modeling and extraction, providing critical parasitic information for optimizing chip performance.

[APSUNY Silicon Photonics Process Design Kit (PDK)](https://www.aimphotonics.com/process-design-kit) is a toolkit that provides access to the most up-to-date silicon photonics PDK, but also access to a community driving and enabling future silicon photonics design methodologies.

[Passage](http://lightmatter.co/products/passage/) is a wafer-scale, programmable photonic interconnect that enables arrays of heterogeneous chips to communicate with unprecedented bandwidth and energy efficiency.

[Idiom](http://lightmatter.co/products/idiom/) is a software that interfaces with standard deep learning frameworks and model exchange formats, while providing the transformations and tools required by deep learning model authors and deployers. It also provides the required compiler, runtime, and tools support to achieve optimal inference speeds and accuracy on [Envise](http://lightmatter.co/products/envise/).

# Machine Learning
[Back to the Top](https://github.com/mikeroyal/Photonics-Guide#table-of-contents)

**Machine Learning/Deep Learning Frameworks.**

# Learning Resources for ML

[Machine Learning](https://www.ibm.com/cloud/learn/machine-learning) is a branch of artificial intelligence (AI) focused on building apps using algorithms that learn from data models and improve their accuracy over time without needing to be programmed.

[Machine Learning by Stanford University from Coursera](https://www.coursera.org/learn/machine-learning)

[AWS Training and Certification for Machine Learning (ML) Courses](https://aws.amazon.com/training/learning-paths/machine-learning/)

[Machine Learning Scholarship Program for Microsoft Azure from Udacity](https://www.udacity.com/scholarships/machine-learning-scholarship-microsoft-azure)

[Microsoft Certified: Azure Data Scientist Associate](https://docs.microsoft.com/en-us/learn/certifications/azure-data-scientist)

[Microsoft Certified: Azure AI Engineer Associate](https://docs.microsoft.com/en-us/learn/certifications/azure-ai-engineer)

[Azure Machine Learning training and deployment](https://docs.microsoft.com/en-us/azure/devops/pipelines/targets/azure-machine-learning)

[Learning Machine learning and artificial intelligence from Google Cloud Training](https://cloud.google.com/training/machinelearning-ai)

[Machine Learning Crash Course for Google Cloud](https://developers.google.com/machine-learning/crash-course/)

[JupyterLab](https://jupyterlab.readthedocs.io/)

[Scheduling Jupyter notebooks on Amazon SageMaker ephemeral instances](https://aws.amazon.com/blogs/machine-learning/scheduling-jupyter-notebooks-on-sagemaker-ephemeral-instances/)

[How to run Jupyter Notebooks in your Azure Machine Learning workspace](https://docs.microsoft.com/en-us/azure/machine-learning/how-to-run-jupyter-notebooks)

[Machine Learning Courses Online from Udemy](https://www.udemy.com/topic/machine-learning/)

[Machine Learning Courses Online from Coursera](https://www.coursera.org/courses?query=machine%20learning&)

[Learn Machine Learning with Online Courses and Classes from edX](https://www.edx.org/learn/machine-learning)

# ML Frameworks, Libraries, and Tools

[TensorFlow](https://www.tensorflow.org) is an end-to-end open source platform for machine learning. It has a comprehensive, flexible ecosystem of tools, libraries and community resources that lets researchers push the state-of-the-art in ML and developers easily build and deploy ML powered applications.

[Keras](https://keras.io) is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.It was developed with a focus on enabling fast experimentation. It is capable of running on top of TensorFlow, Microsoft Cognitive Toolkit, R, Theano, or PlaidML.

[PyTorch](https://pytorch.org) is a library for deep learning on irregular input data such as graphs, point clouds, and manifolds. Primarily developed by Facebook's AI Research lab.

[Amazon SageMaker](https://aws.amazon.com/sagemaker/) is a fully managed service that provides every developer and data scientist with the ability to build, train, and deploy machine learning (ML) models quickly. SageMaker removes the heavy lifting from each step of the machine learning process to make it easier to develop high quality models.

[Azure Databricks](https://azure.microsoft.com/en-us/services/databricks/) is a fast and collaborative Apache Spark-based big data analytics service designed for data science and data engineering. Azure Databricks, sets up your Apache Spark environment in minutes, autoscale, and collaborate on shared projects in an interactive workspace. Azure Databricks supports Python, Scala, R, Java, and SQL, as well as data science frameworks and libraries including TensorFlow, PyTorch, and scikit-learn.

[Microsoft Cognitive Toolkit (CNTK)](https://docs.microsoft.com/en-us/cognitive-toolkit/) is an open-source toolkit for commercial-grade distributed deep learning. It describes neural networks as a series of computational steps via a directed graph. CNTK allows the user to easily realize and combine popular model types such as feed-forward DNNs, convolutional neural networks (CNNs) and recurrent neural networks (RNNs/LSTMs). CNTK implements stochastic gradient descent (SGD, error backpropagation) learning with automatic differentiation and parallelization across multiple GPUs and servers.

[Apple CoreML](https://developer.apple.com/documentation/coreml) is a framework that helps integrate machine learning models into your app. Core ML provides a unified representation for all models. Your app uses Core ML APIs and user data to make predictions, and to train or fine-tune models, all on the user's device. A model is the result of applying a machine learning algorithm to a set of training data. You use a model to make predictions based on new input data.

[Tensorflow_macOS](https://github.com/apple/tensorflow_macos) is a Mac-optimized version of TensorFlow and TensorFlow Addons for macOS 11.0+ accelerated using Apple's ML Compute framework.

[Apache OpenNLP](https://opennlp.apache.org/) is an open-source library for a machine learning based toolkit used in the processing of natural language text. It features an API for use cases like [Named Entity Recognition](https://en.wikipedia.org/wiki/Named-entity_recognition), [Sentence Detection](), [POS(Part-Of-Speech) tagging](https://en.wikipedia.org/wiki/Part-of-speech_tagging), [Tokenization](https://en.wikipedia.org/wiki/Tokenization_(data_security)) [Feature extraction](https://en.wikipedia.org/wiki/Feature_extraction), [Chunking](https://en.wikipedia.org/wiki/Chunking_(psychology)), [Parsing](https://en.wikipedia.org/wiki/Parsing), and [Coreference resolution](https://en.wikipedia.org/wiki/Coreference).

[Apache Airflow](https://airflow.apache.org) is an open-source workflow management platform created by the community to programmatically author, schedule and monitor workflows. Install. Principles. Scalable. Airflow has a modular architecture and uses a message queue to orchestrate an arbitrary number of workers. Airflow is ready to scale to infinity.

[Open Neural Network Exchange(ONNX)](https://github.com/onnx) is an open ecosystem that empowers AI developers to choose the right tools as their project evolves. ONNX provides an open source format for AI models, both deep learning and traditional ML. It defines an extensible computation graph model, as well as definitions of built-in operators and standard data types.

[Apache MXNet](https://mxnet.apache.org/) is a deep learning framework designed for both efficiency and flexibility. It allows you to mix symbolic and imperative programming to maximize efficiency and productivity. At its core, MXNet contains a dynamic dependency scheduler that automatically parallelizes both symbolic and imperative operations on the fly. A graph optimization layer on top of that makes symbolic execution fast and memory efficient. MXNet is portable and lightweight, scaling effectively to multiple GPUs and multiple machines. Support for Python, R, Julia, Scala, Go, Javascript and more.

[AutoGluon](https://autogluon.mxnet.io/index.html) is toolkit for Deep learning that automates machine learning tasks enabling you to easily achieve strong predictive performance in your applications. With just a few lines of code, you can train and deploy high-accuracy deep learning models on tabular, image, and text data.

[Anaconda](https://www.anaconda.com/) is a very popular Data Science platform for machine learning and deep learning that enables users to develop models, train them, and deploy them.

[PlaidML](https://github.com/plaidml/plaidml) is an advanced and portable tensor compiler for enabling deep learning on laptops, embedded devices, or other devices where the available computing hardware is not well supported or the available software stack contains unpalatable license restrictions.

[OpenCV](https://opencv.org) is a highly optimized library with focus on real-time computer vision applications. The C++, Python, and Java interfaces support Linux, MacOS, Windows, iOS, and Android.

[Scikit-Learn](https://scikit-learn.org/stable/index.html) is a Python module for machine learning built on top of SciPy, NumPy, and matplotlib, making it easier to apply robust and simple implementations of many popular machine learning algorithms.

[Weka](https://www.cs.waikato.ac.nz/ml/weka/) is an open source machine learning software that can be accessed through a graphical user interface, standard terminal applications, or a Java API. It is widely used for teaching, research, and industrial applications, contains a plethora of built-in tools for standard machine learning tasks, and additionally gives transparent access to well-known toolboxes such as scikit-learn, R, and Deeplearning4j.

[Caffe](https://github.com/BVLC/caffe) is a deep learning framework made with expression, speed, and modularity in mind. It is developed by Berkeley AI Research (BAIR)/The Berkeley Vision and Learning Center (BVLC) and community contributors.

[Theano](https://github.com/Theano/Theano) is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently including tight integration with NumPy.

[nGraph](https://github.com/NervanaSystems/ngraph) is an open source C++ library, compiler and runtime for Deep Learning. The nGraph Compiler aims to accelerate developing AI workloads using any deep learning framework and deploying to a variety of hardware targets.It provides the freedom, performance, and ease-of-use to AI developers.

[NVIDIA cuDNN](https://developer.nvidia.com/cudnn) is a GPU-accelerated library of primitives for [deep neural networks](https://developer.nvidia.com/deep-learning). cuDNN provides highly tuned implementations for standard routines such as forward and backward convolution, pooling, normalization, and activation layers. cuDNN accelerates widely used deep learning frameworks, including [Caffe2](https://caffe2.ai/), [Chainer](https://chainer.org/), [Keras](https://keras.io/), [MATLAB](https://www.mathworks.com/solutions/deep-learning.html), [MxNet](https://mxnet.incubator.apache.org/), [PyTorch](https://pytorch.org/), and [TensorFlow](https://www.tensorflow.org/).

[Jupyter Notebook](https://jupyter.org/) is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Jupyter is used widely in industries that do data cleaning and transformation, numerical simulation, statistical modeling, data visualization, data science, and machine learning.

[Apache Spark](https://spark.apache.org/) is a unified analytics engine for large-scale data processing. It provides high-level APIs in Scala, Java, Python, and R, and an optimized engine that supports general computation graphs for data analysis. It also supports a rich set of higher-level tools including Spark SQL for SQL and DataFrames, MLlib for machine learning, GraphX for graph processing, and Structured Streaming for stream processing.

[Apache Spark Connector for SQL Server and Azure SQL](https://github.com/microsoft/sql-spark-connector) is a high-performance connector that enables you to use transactional data in big data analytics and persists results for ad-hoc queries or reporting. The connector allows you to use any SQL database, on-premises or in the cloud, as an input data source or output data sink for Spark jobs.

[Apache PredictionIO](https://predictionio.apache.org/) is an open source machine learning framework for developers, data scientists, and end users. It supports event collection, deployment of algorithms, evaluation, querying predictive results via REST APIs. It is based on scalable open source services like Hadoop, HBase (and other DBs), Elasticsearch, Spark and implements what is called a Lambda Architecture.

[Cluster Manager for Apache Kafka(CMAK)](https://github.com/yahoo/CMAK) is a tool for managing [Apache Kafka](https://kafka.apache.org/) clusters.

[BigDL](https://bigdl-project.github.io/) is a distributed deep learning library for Apache Spark. With BigDL, users can write their deep learning applications as standard Spark programs, which can directly run on top of existing Spark or Hadoop clusters.

[Eclipse Deeplearning4J (DL4J)](https://deeplearning4j.konduit.ai/) is a set of projects intended to support all the needs of a JVM-based(Scala, Kotlin, Clojure, and Groovy) deep learning application. This means starting with the raw data, loading and preprocessing it from wherever and whatever format it is in to building and tuning a wide variety of simple and complex deep learning networks.

[Tensorman](https://github.com/pop-os/tensorman) is a utility for easy management of Tensorflow containers by developed by [System76]( https://system76.com).Tensorman allows Tensorflow to operate in an isolated environment that is contained from the rest of the system. This virtual environment can operate independent of the base system, allowing you to use any version of Tensorflow on any version of a Linux distribution that supports the Docker runtime.

[Numba](https://github.com/numba/numba) is an open source, NumPy-aware optimizing compiler for Python sponsored by Anaconda, Inc. It uses the LLVM compiler project to generate machine code from Python syntax. Numba can compile a large subset of numerically-focused Python, including many NumPy functions. Additionally, Numba has support for automatic parallelization of loops, generation of GPU-accelerated code, and creation of ufuncs and C callbacks.

[Chainer](https://chainer.org/) is a Python-based deep learning framework aiming at flexibility. It provides automatic differentiation APIs based on the define-by-run approach (dynamic computational graphs) as well as object-oriented high-level APIs to build and train neural networks. It also supports CUDA/cuDNN using [CuPy](https://github.com/cupy/cupy) for high performance training and inference.

[XGBoost](https://xgboost.readthedocs.io/) is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. It implements machine learning algorithms under the Gradient Boosting framework. XGBoost provides a parallel tree boosting (also known as GBDT, GBM) that solve many data science problems in a fast and accurate way. It supports distributed training on multiple machines, including AWS, GCE, Azure, and Yarn clusters. Also, it can be integrated with Flink, Spark and other cloud dataflow systems.

[cuML](https://github.com/rapidsai/cuml) is a suite of libraries that implement machine learning algorithms and mathematical primitives functions that share compatible APIs with other RAPIDS projects. cuML enables data scientists, researchers, and software engineers to run traditional tabular ML tasks on GPUs without going into the details of CUDA programming. In most cases, cuML's Python API matches the API from scikit-learn.

# MATLAB Development
[Back to the Top](https://github.com/mikeroyal/Photonics-Guide#table-of-contents)





## MATLAB Learning Resources

[MATLAB](https://www.mathworks.com/products/matlab.html) is a programming language that does numerical computing such as expressing matrix and array mathematics directly.

[MATLAB Documentation](https://www.mathworks.com/help/matlab/)

[Getting Started with MATLAB ](https://www.mathworks.com/help/matlab/getting-started-with-matlab.html)

[MATLAB and Simulink Training from MATLAB Academy](https://matlabacademy.mathworks.com)

[MathWorks Certification Program](https://www.mathworks.com/services/training/certification.html)

[MATLAB Online Courses from Udemy](https://www.udemy.com/topic/matlab/)

[MATLAB Online Courses from Coursera](https://www.coursera.org/courses?query=matlab)

[MATLAB Online Courses from edX](https://www.edx.org/learn/matlab)

[Building a MATLAB GUI](https://www.mathworks.com/discovery/matlab-gui.html)

[MATLAB Style Guidelines 2.0](https://www.mathworks.com/matlabcentral/fileexchange/46056-matlab-style-guidelines-2-0)

[Setting Up Git Source Control with MATLAB & Simulink](https://www.mathworks.com/help/matlab/matlab_prog/set-up-git-source-control.html)

[Pull, Push and Fetch Files with Git with MATLAB & Simulink](https://www.mathworks.com/help/matlab/matlab_prog/push-and-fetch-with-git.html)

[Create New Repository with MATLAB & Simulink](https://www.mathworks.com/help/matlab/matlab_prog/add-folder-to-source-control.html)

[PRMLT](http://prml.github.io/) is Matlab code for machine learning algorithms in the PRML book.

## MATLAB Tools

[MATLAB Online](https://matlab.mathworks.com) allows to users to uilitize MATLAB and Simulink through a web browser such as Google Chrome.

[Simulink](https://www.mathworks.com/products/simulink.html) is a block diagram environment for Model-Based Design. It supports simulation, automatic code generation, and continuous testing of embedded systems.

[MATLAB Schemer](https://github.com/scottclowe/matlab-schemer) is a MATLAB package makes it easy to change the color scheme (theme) of the MATLAB display and GUI.

[LRSLibrary](https://github.com/andrewssobral/lrslibrary) is a Low-Rank and Sparse Tools for Background Modeling and Subtraction in Videos. The library was designed for moving object detection in videos, but it can be also used for other computer vision and machine learning problems.

[Robotics Toolbox for MATLAB](https://www.mathworks.com/products/robotics.html) provides a toolbox that brings robotics specific functionality(designing, simulating, and testing manipulators, mobile robots, and humanoid robots) to MATLAB, exploiting the native capabilities of MATLAB (linear algebra, portability, graphics). The toolbox also supports mobile robots with functions for robot motion models (bicycle), path planning algorithms (bug, distance transform, D*, PRM), kinodynamic planning (lattice, RRT), localization (EKF, particle filter), map building (EKF) and simultaneous localization and mapping (EKF), and a Simulink model a of non-holonomic vehicle. The Toolbox also including a detailed Simulink model for a quadrotor flying robot.

[SEA-MAT](https://sea-mat.github.io/sea-mat/) is a collaborative effort to organize and distribute Matlab tools for the Oceanographic Community.

[Gramm](https://github.com/piermorel/gramm) is a complete data visualization toolbox for Matlab. It provides an easy to use and high-level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.

[hctsa](https://hctsa-users.gitbook.io/hctsa-manual) is a software package for running highly comparative time-series analysis using Matlab.

[Plotly](https://plot.ly/matlab/) is a Graphing Library for MATLAB.

[YALMIP](https://yalmip.github.io/) is a MATLAB toolbox for optimization modeling.

[GNU Octave](https://www.gnu.org/software/octave/) is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation.

# R Development
[Back to the Top](https://github.com/mikeroyal/Photonics-Guide#table-of-contents)





# R Learning Resources

[R](https://www.r-project.org/) is an open source software environment for statistical computing and graphics. It compiles and runs on a wide variety of platforms such as Windows and MacOS.

[An Introduction to R](https://cran.r-project.org/doc/manuals/r-release/R-intro.pdf)

[Google's R Style Guide](https://google.github.io/styleguide/Rguide.html)

[R developer's guide to Azure](https://docs.microsoft.com/en-us/azure/architecture/data-guide/technology-choices/r-developers-guide)

[Running R at Scale on Google Compute Engine](https://cloud.google.com/solutions/running-r-at-scale)

[Running R on AWS](https://aws.amazon.com/blogs/big-data/running-r-on-aws/)

[RStudio Server Pro for AWS](https://aws.amazon.com/marketplace/pp/RStudio-RStudio-Server-Pro-for-AWS/B06W2G9PRY)

[Learn R by Codecademy](https://www.codecademy.com/learn/learn-r)

[Learn R Programming with Online Courses and Lessons by edX](https://www.edx.org/learn/r-programming)

[R Language Courses by Coursera](https://www.coursera.org/courses?query=r%20language)

[Learn R For Data Science by Udacity](https://www.udacity.com/course/programming-for-data-science-nanodegree-with-R--nd118)

# R Tools

[RStudio](https://rstudio.com/) is an integrated development environment for R and Python, with a console, syntax-highlighting editor that supports direct code execution, and tools for plotting, history, debugging and workspace management.

[Shiny](https://shiny.rstudio.com/) is a newer package from RStudio that makes it incredibly easy to build interactive web applications with R.

[Rmarkdown ](https://rmarkdown.rstudio.com/) is a package helps you create dynamic analysis documents that combine code, rendered output (such as figures), and prose.

[Rplugin](https://github.com/JetBrains/Rplugin) is R Language supported plugin for the IntelliJ IDE.

[Plotly](https://plotly-r.com/) is an R package for creating interactive web graphics via the open source JavaScript graphing library [plotly.js](https://github.com/plotly/plotly.js).

[Metaflow](https://metaflow.org/) is a Python/R library that helps scientists and engineers build and manage real-life data science projects. Metaflow was originally developed at Netflix to boost productivity of data scientists who work on a wide variety of projects from classical statistics to state-of-the-art deep learning.

[Prophet](https://facebook.github.io/prophet) is a procedure for forecasting time series data based on an additive model where non-linear trends are fit with yearly, weekly, and daily seasonality, plus holiday effects. It works best with time series that have strong seasonal effects and several seasons of historical data.

[LightGBM](https://lightgbm.readthedocs.io/) is a gradient boosting framework that uses tree based learning algorithms, used for ranking, classification and many other machine learning tasks.

[Dash](https://plotly.com/dash) is a Python framework for building analytical web applications in Python, R, Julia, and Jupyter.

[MLR](https://mlr.mlr-org.com/) is Machine Learning in R.

[ML workspace](https://github.com/ml-tooling/ml-workspace) is an all-in-one web-based IDE specialized for machine learning and data science. It is simple to deploy and gets you started within minutes to productively built ML solutions on your own machines. ML workspace is the ultimate tool for developers preloaded with a variety of popular data science libraries (Tensorflow, PyTorch, Keras, and MXnet) and dev tools (Jupyter, VS Code, and Tensorboard) perfectly configured, optimized, and integrated.

[CatBoost](https://catboost.ai/) is a fast, scalable, high performance Gradient Boosting on Decision Trees library, used for ranking, classification, regression and other machine learning tasks for Python, R, Java, C++. Supports computation on CPU and GPU.

[Plumber](https://www.rplumber.io/) is a tool that allows you to create a web API by merely decorating your existing R source code with special comments.

[Drake](https://docs.ropensci.org/drake) is an R-focused pipeline toolkit for reproducibility and high-performance computing.

[DiagrammeR](https://visualizers.co/diagrammer/) is a package you can create, modify, analyze, and visualize network graph diagrams. The output can be incorporated into R Markdown documents, integrated with Shiny web apps, converted to other graph formats, or exported as image files.

[Knitr](https://yihui.org/knitr/) is a general-purpose literate programming engine in R, with lightweight API's designed to give users full control of the output without heavy coding work.

[Broom](https://broom.tidymodels.org/) is a tool that converts statistical analysis objects from R into tidy format.

# Python Development
[Back to the Top](https://github.com/mikeroyal/Photonics-Guide#table-of-contents)




## Python Learning Resources

[Python](https://www.python.org) is an interpreted, high-level programming language. Python is used heavily in the fields of Data Science and Machine Learning.

[Python Developer’s Guide](https://devguide.python.org) is a comprehensive resource for contributing to Python – for both new and experienced contributors. It is maintained by the same community that maintains Python.

[Azure Functions Python developer guide](https://docs.microsoft.com/en-us/azure/azure-functions/functions-reference-python) is an introduction to developing Azure Functions using Python. The content below assumes that you've already read the [Azure Functions developers guide](https://docs.microsoft.com/en-us/azure/azure-functions/functions-reference).

[CheckiO](https://checkio.org/) is a programming learning platform and a gamified website that teaches Python through solving code challenges and competing for the most elegant and creative solutions.

[Python Institute](https://pythoninstitute.org)

[PCEP – Certified Entry-Level Python Programmer certification](https://pythoninstitute.org/pcep-certification-entry-level/)

[PCAP – Certified Associate in Python Programming certification](https://pythoninstitute.org/pcap-certification-associate/)

[PCPP – Certified Professional in Python Programming 1 certification](https://pythoninstitute.org/pcpp-certification-professional/)

[PCPP – Certified Professional in Python Programming 2](https://pythoninstitute.org/pcpp-certification-professional/)

[MTA: Introduction to Programming Using Python Certification](https://docs.microsoft.com/en-us/learn/certifications/mta-introduction-to-programming-using-python)

[Getting Started with Python in Visual Studio Code](https://code.visualstudio.com/docs/python/python-tutorial)

[Google's Python Style Guide](https://google.github.io/styleguide/pyguide.html)

[Google's Python Education Class](https://developers.google.com/edu/python/)

[Real Python](https://realpython.com)

[The Python Open Source Computer Science Degree by Forrest Knight](https://github.com/ForrestKnight/open-source-cs-python)

[Intro to Python for Data Science](https://www.datacamp.com/courses/intro-to-python-for-data-science)

[Intro to Python by W3schools](https://www.w3schools.com/python/python_intro.asp)

[Codecademy's Python 3 course](https://www.codecademy.com/learn/learn-python-3)

[Learn Python with Online Courses and Classes from edX](https://www.edx.org/learn/python)

[Python Courses Online from Coursera](https://www.coursera.org/courses?query=python)

## Python Frameworks and Tools

[Python Package Index (PyPI)](https://pypi.org/) is a repository of software for the Python programming language. PyPI helps you find and install software developed and shared by the Python community.

[PyCharm](https://www.jetbrains.com/pycharm/) is the best IDE I've ever used. With PyCharm, you can access the command line, connect to a database, create a virtual environment, and manage your version control system all in one place, saving time by avoiding constantly switching between windows.

[Python Tools for Visual Studio(PTVS)](https://microsoft.github.io/PTVS/) is a free, open source plugin that turns Visual Studio into a Python IDE. It supports editing, browsing, IntelliSense, mixed Python/C++ debugging, remote Linux/MacOS debugging, profiling, IPython, and web development with Django and other frameworks.

[Pylance](https://github.com/microsoft/pylance-release) is an extension that works alongside Python in Visual Studio Code to provide performant language support. Under the hood, Pylance is powered by Pyright, Microsoft's static type checking tool.

[Pyright](https://github.com/Microsoft/pyright) is a fast type checker meant for large Python source bases. It can run in a “watch” mode and performs fast incremental updates when files are modified.

[Django](https://www.djangoproject.com/) is a high-level Python Web framework that encourages rapid development and clean, pragmatic design.

[Flask](https://flask.palletsprojects.com/) is a micro web framework written in Python. It is classified as a microframework because it does not require particular tools or libraries.

[Web2py](http://web2py.com/) is an open-source web application framework written in Python allowing allows web developers to program dynamic web content. One web2py instance can run multiple web sites using different databases.

[AWS Chalice](https://github.com/aws/chalice) is a framework for writing serverless apps in python. It allows you to quickly create and deploy applications that use AWS Lambda.

[Tornado](https://www.tornadoweb.org/) is a Python web framework and asynchronous networking library. Tornado uses a non-blocking network I/O, which can scale to tens of thousands of open connections.

[HTTPie](https://github.com/httpie/httpie) is a command line HTTP client that makes CLI interaction with web services as easy as possible. HTTPie is designed for testing, debugging, and generally interacting with APIs & HTTP servers.

[Scrapy](https://scrapy.org/) is a fast high-level web crawling and web scraping framework, used to crawl websites and extract structured data from their pages. It can be used for a wide range of purposes, from data mining to monitoring and automated testing.

[Sentry](https://sentry.io/) is a service that helps you monitor and fix crashes in realtime. The server is in Python, but it contains a full API for sending events from any language, in any application.

[Pipenv](https://github.com/pypa/pipenv) is a tool that aims to bring the best of all packaging worlds (bundler, composer, npm, cargo, yarn, etc.) to the Python world.

[Python Fire](https://github.com/google/python-fire) is a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.

[Bottle](https://github.com/bottlepy/bottle) is a fast, simple and lightweight [WSGI](https://www.wsgi.org/) micro web-framework for Python. It is distributed as a single file module and has no dependencies other than the [Python Standard Library](https://docs.python.org/library/).

[CherryPy](https://cherrypy.org) is a minimalist Python object-oriented HTTP web framework.

[Sanic](https://github.com/huge-success/sanic) is a Python 3.6+ web server and web framework that's written to go fast.

[Pyramid](https://trypyramid.com) is a small and fast open source Python web framework. It makes real-world web application development and deployment more fun and more productive.

[TurboGears](https://turbogears.org) is a hybrid web framework able to act both as a Full Stack framework or as a Microframework.

[Falcon](https://falconframework.org/) is a reliable, high-performance Python web framework for building large-scale app backends and microservices with support for MongoDB, Pluggable Applications and autogenerated Admin.

[Neural Network Intelligence(NNI)](https://github.com/microsoft/nni) is an open source AutoML toolkit for automate machine learning lifecycle, including [Feature Engineering](https://github.com/microsoft/nni/blob/master/docs/en_US/FeatureEngineering/Overview.md), [Neural Architecture Search](https://github.com/microsoft/nni/blob/master/docs/en_US/NAS/Overview.md), [Model Compression](https://github.com/microsoft/nni/blob/master/docs/en_US/Compressor/Overview.md) and [Hyperparameter Tuning](https://github.com/microsoft/nni/blob/master/docs/en_US/Tuner/BuiltinTuner.md).

[Dash](https://plotly.com/dash) is a popular Python framework for building ML & data science web apps for Python, R, Julia, and Jupyter.

[Luigi](https://github.com/spotify/luigi) is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built-in.

[Locust](https://github.com/locustio/locust) is an easy to use, scriptable and scalable performance testing tool.

[spaCy](https://github.com/explosion/spaCy) is a library for advanced Natural Language Processing in Python and Cython.

[NumPy](https://www.numpy.org/) is the fundamental package needed for scientific computing with Python.

[Pillow](https://python-pillow.org/) is a friendly PIL(Python Imaging Library) fork.

[IPython](https://ipython.org/) is a command shell for interactive computing in multiple programming languages, originally developed for the Python programming language, that offers enhanced introspection, rich media, additional shell syntax, tab completion, and rich history.

[GraphLab Create](https://turi.com/) is a Python library, backed by a C++ engine, for quickly building large-scale, high-performance machine learning models.

[Pandas](https://pandas.pydata.org/) is a fast, powerful, and easy to use open source data structrures, data analysis and manipulation tool, built on top of the Python programming language.

[PuLP](https://coin-or.github.io/pulp/) is an Linear Programming modeler written in python. PuLP can generate LP files and call on use highly optimized solvers, GLPK, COIN CLP/CBC, CPLEX, and GUROBI, to solve these linear problems.

[Matplotlib](https://matplotlib.org/) is a 2D plotting library for creating static, animated, and interactive visualizations in Python. Matplotlib produces publication-quality figures in a variety of hardcopy formats and interactive environments across platforms.

[Scikit-Learn](https://scikit-learn.org/stable/index.html) is a simple and efficient tool for data mining and data analysis. It is built on NumPy,SciPy, and mathplotlib.

## Contribute

- [x] If would you like to contribute to this guide simply make a [Pull Request](https://github.com/mikeroyal/Photonics-Guide/pulls).

## License
[Back to the Top](https://github.com/mikeroyal/Photonics-Guide#table-of-contents)

Distributed under the [Creative Commons Attribution 4.0 International (CC BY 4.0) Public License](https://creativecommons.org/licenses/by/4.0/).