Elegant SciPy by Juan Nunez-Iglesias, Stéfan van der Walt, Harriet Dashnow -- Read -- Imperial Library of Trantor

Index

Preface

Who Is This Book For? Why SciPy?

What Is the SciPy Ecosystem?

The Great Cataclysm: Python 2 Versus Python 3 SciPy Ecosystem and Community

Free and Open Source Software (FOSS)

Open source, open science Open source licenses

GitHub: Taking Coding Social Make Your Mark on the SciPy Ecosystem A Touch of Whimsy with Your Py

Getting Help Installing Python

Accessing the Book Materials

Diving In Conventions Used in This Book Use of Color Using Code Examples O’Reilly Safari How to Contact Us Acknowledgments

1. Elegant NumPy: The Foundation of Scientific Python

Introduction to the Data: What Is Gene Expression? NumPy N-Dimensional Arrays

Why Use ndarrays Instead of Python Lists? Vectorization Broadcasting

Exploring a Gene Expression Dataset

Reading in the Data with pandas

Normalization

Between Samples

Normalizing library size between samples

Between Genes Normalizing Over Samples and Genes: RPKM

Broadcasting rules RPKM between gene normalization

Taking Stock

2. Quantile Normalization with NumPy and SciPy

Getting the Data Gene Expression Distribution Differences Between Individuals Biclustering the Counts Data Visualizing Clusters Predicting Survival

Further Work: Using the TCGA’s Patient Clusters Further Work: Reproducing the TCGA’s clusters

3. Networks of Image Regions with ndimage

Images Are Just NumPy Arrays

Exercise: Adding a Grid Overlay

Filters in Signal Processing Filtering Images (2D Filters) Generic Filters: Arbitrary Functions of Neighborhood Values

Exercise: Conway’s Game of Life Exercise: Sobel Gradient Magnitude

Graphs and the NetworkX library

Exercise: Curve Fitting with SciPy

Region Adjacency Graphs Elegant ndimage: How to Build Graphs from Image Regions Putting It All Together: Mean Color Segmentation

4. Frequency and the Fast Fourier Transform

Introducing Frequency Illustration: A Birdsong Spectrogram History Implementation Choosing the Length of the DFT More DFT Concepts

Frequencies and Their Ordering Windowing

Real-World Application: Analyzing Radar Data

Signal Properties in the Frequency Domain Windowing, Applied Radar Images

3D visualization

Further Applications of the FFT Further Reading Exercise: Image Convolution

5. Contingency Tables Using Sparse Coordinate Matrices

Contingency Tables

Exercise: Computational Complexity of Confusion Matrices Exercise: Alternative Algorithm to Compute the Confusion Matrix Exercise: Multiclass Confusion Matrix

scipy.sparse Data Formats

COO Format Exercise: COO Representation Compressed Sparse Row Format

Applications of Sparse Matrices: Image Transformations

Exercise: Image Rotation

Back to Contingency Tables

Exercise: Reducing the Memory Footprint

Contingency Tables in Segmentation Information Theory in Brief

Exercise: Computing Conditional Entropy

Information Theory in Segmentation: Variation of Information Converting NumPy Array Code to Use Sparse Matrices Using Variation of Information

Further Work: Segmentation in Practice

6. Linear Algebra in SciPy

Linear Algebra Basics Laplacian Matrix of a Graph

Exercise: Rotation Matrix

Laplacians with Brain Data

Exercise: Showing the Affinity View Exercise Challenge: Linear Algebra with Sparse Matrices

PageRank: Linear Algebra for Reputation and Importance

Exercise: Dealing with Dangling Nodes Exercise: Equivalence of Different Eigenvector Methods

Concluding Remarks

7. Function Optimization in SciPy

Optimization in SciPy: scipy.optimize

An Example: Computing Optimal Image Shift

Image Registration with Optimize Avoiding Local Minima with Basin Hopping

Exercise: Modify the align Function

“What Is Best?”: Choosing the Right Objective Function

8. Big Data in Little Laptop with Toolz

Streaming with yield Introducing the Toolz Streaming Library k-mer Counting and Error Correction Currying: The Spice of Streaming Back to Counting k-mers

Exercise: PCA of Streaming Data

Markov Model from a Full Genome

Exercise: Online Unzip

Epilogue

Where to Next?

Mailing Lists GitHub Conferences

Beyond SciPy Contributing to This Book Until Next Time...

A. Exercise Solutions

Solution: Adding a Grid Overlay Solution: Conway’s Game of Life Solution: Sobel Gradient Magnitude Solution: Curve Fitting with SciPy Solution: Image Convolution Solution: Computational Complexity of Confusion Matrices Solution: Alternative Confusion Matrix Computing Solution: Computing the Confusion Matrix Solution: COO Representation Solution: Image Rotation Solution: Reducing the Memory Footprint Solution: Computing Conditional Entropy Solution: Rotation Matrix Solution: Showing the Affinity View Challenge Accepted: Linear Algebra with Sparse Matrices Solution: Dealing with Dangling Nodes Solution: Verify Methods Solution: Modify the align Function Solution: scikit-learn Library Solution: Add a Step to the Start of the Pipe

Index

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