Andrew Collette

Python and HDF5 (eBook, PDF)

Unlocking Scientific Data

• Format: PDF

Produktbeschreibung

Gain hands-on experience with HDF5 for storing scientific data in Python. This practical guide quickly gets you up to speed on the details, best practices, and pitfalls of using HDF5 to archive and share numerical datasets ranging in size from gigabytes to terabytes.Through real-world examples and practical exercises, youll explore topics such as scientific datasets, hierarchically organized groups, user-defined metadata, and interoperable files. Examples are applicable for users of both Python 2 and Python 3. If youre familiar with the basics of Python data analysis, this is an ideal introduction to HDF5.Get set up with HDF5 tools and create your first HDF5 fileWork with datasets by learning the HDF5 Dataset objectUnderstand advanced features like dataset chunking and compressionLearn how to work with HDF5s hierarchical structure, using groupsCreate self-describing files by adding metadata with HDF5 attributesTake advantage of HDF5s type system to create interoperable filesExpress relationships among data with references, named types, and dimension scalesDiscover how Python mechanisms for writing parallel code interact with HDF5

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Produktdetails

• Verlag: O'Reilly Media
• Seitenzahl: 152
• Erscheinungstermin: 21. Oktober 2013
• Englisch
• ISBN-13: 9781491945018
• Artikelnr.: 39930662

Autorenporträt

Andrew Collette holds a Ph.D. in physics from UCLA, and works as a laboratory research scientist at the University of Colorado. He has worked with the Python-NumPy-HDF5 stack at two multimillion-dollar research facilities; the first being the Large Plasma Device at UCLA (entirely standardized on HDF5), and the second being the hypervelocity dust accelerator at the Colorado Center for Lunar Dust and Atmospheric Studies, University of Colorado at Boulder. Additionally, Dr. Collette is a leading developer of the HDF5 for Python (h5py) project.

Inhaltsangabe

Preface
Conventions Used in This Book
Using Code Examples
Safari® Books Online
How to Contact Us
Acknowledgments
Chapter 1: Introduction
1.1 Python and HDF5
1.2 What Exactly Is HDF5?
Chapter 2: Getting Started
2.1 HDF5 Basics
2.2 Setting Up
2.3 The HDF5 Tools
2.4 Your First HDF5 File
Chapter 3: Working with Datasets
3.1 Dataset Basics
3.2 Reading and Writing Data
3.3 Resizing Datasets
Chapter 4: How Chunking and Compression Can Help You
4.1 Contiguous Storage
4.2 Chunked Storage
4.3 Setting the Chunk Shape
4.4 Performance Example: Resizable Datasets
4.5 Filters and Compression
4.6 Other Filters
4.7 Third-Party Filters
Chapter 5: Groups, Links, and Iteration: The "H" in HDF5
5.1 The Root Group and Subgroups
5.2 Group Basics
5.3 Working with Links
5.4 Iteration and Containership
5.5 Multilevel Iteration with the Visitor Pattern
5.6 Copying Objects
5.7 Object Comparison and Hashing
Chapter 6: Storing Metadata with Attributes
6.1 Attribute Basics
6.2 Real-World Example: Accelerator Particle Database
Chapter 7: More About Types
7.1 The HDF5 Type System
7.2 Integers and Floats
7.3 Fixed-Length Strings
7.4 Variable-Length Strings
7.5 Compound Types
7.6 Complex Numbers
7.7 Enumerated Types
7.8 Booleans
7.9 The array Type
7.10 Opaque Types
7.11 Dates and Times
Chapter 8: Organizing Data with References, Types, and Dimension Scales
8.1 Object References
8.2 Region References
8.3 Named Types
8.4 Dimension Scales
Chapter 9: Concurrency: Parallel HDF5, Threading, and Multiprocessing
9.1 Python Parallel Basics
9.2 Threading
9.3 Multiprocessing
9.4 MPI and Parallel HDF5
Chapter 10: Next Steps
10.1 Asking for Help
10.2 Contributing
Index
Colophon