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The HDF Group Introduction to HDF5 Session ? HDF5 Mathematical Concepts 1 Copyright © 2010 The HDF Group. All Rights Reserved.

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Presentation on theme: "The HDF Group Introduction to HDF5 Session ? HDF5 Mathematical Concepts 1 Copyright © 2010 The HDF Group. All Rights Reserved."— Presentation transcript:

1 www.hdfgroup.org The HDF Group Introduction to HDF5 Session ? HDF5 Mathematical Concepts 1 Copyright © 2010 The HDF Group. All Rights Reserved

2 www.hdfgroup.org Fundamental HDF5 Objects Groups Containers of links Allow creating arbitrary directed graphs, including non- treelike and cyclic structures Datasets Multi-dimensional arrays (currently) Based on mathematical concept of “fiber bundle” – representing the values of a field over a space Copyright © 2010 The HDF Group. All Rights Reserved2

3 www.hdfgroup.org Groups - Overview Groups are container objects in a file that follow a “set” data structure semantic: Groups contain links No two links in a group can have the same name Links have two components: Name Destination Three types of links currently: Hard – Destination is object in same file Soft – Destination is path to object in same file External – Destination is path to object in another file Copyright © 2010 The HDF Group. All Rights Reserved3

4 www.hdfgroup.org Groups Tree, with hard links Copyright © 2010 The HDF Group. All Rights Reserved4

5 www.hdfgroup.org Groups Non-Tree, with hard links Copyright © 2010 The HDF Group. All Rights Reserved5

6 www.hdfgroup.org Groups Cyclic, with hard links Copyright © 2010 The HDF Group. All Rights Reserved6

7 www.hdfgroup.org Groups Tree, with soft links Copyright © 2010 The HDF Group. All Rights Reserved7

8 www.hdfgroup.org Groups Tree, with external links Copyright © 2010 The HDF Group. All Rights Reserved8

9 www.hdfgroup.org Groups - Discussion What would happen if links didn’t have names, but objects had names? What other types of links are useful? Copyright © 2010 The HDF Group. All Rights Reserved9

10 www.hdfgroup.org Datasets - Overview Datasets are objects in an HDF5 that represent “real” application data Array-like currently Datasets have three components: Dataspace describes current and maximum dimensions of array Datatype describes type of elements in array Elements are the values stored in the array Copyright © 2010 The HDF Group. All Rights Reserved10

11 www.hdfgroup.org Datasets – Measurement Example Think of algebraic concept of independent and dependent variables X-Y Plot: Copyright © 2010 The HDF Group. All Rights Reserved11

12 www.hdfgroup.org Dataset – Measurement Example, 2 X-Y Plot data in Database: Copyright © 2010 The HDF Group. All Rights Reserved12

13 www.hdfgroup.org Dataset – Measurement Example, 3 X-Y Plot data in HDF5 Dataset: Copyright © 2010 The HDF Group. All Rights Reserved13

14 www.hdfgroup.org Dataset – Measurement Example, 4 In HDF5, independent variables are implicit and not stored (they are the coordinates of elements in array) In Database, independent variables are explicitly stored in each record A “packed” HDF5 dataset of N dimensions is up to N times smaller than database table storing the same data. Copyright © 2010 The HDF Group. All Rights Reserved14

15 www.hdfgroup.org Datasets - Discussion When would storing data in a database table be better than storing the same data in an HDF5 dataset? If you were measuring two dependent values at each coordinate, what are the trade-offs between storing them as a pair for each element in a single dataset and storing each one in a separate dataset? Copyright © 2010 The HDF Group. All Rights Reserved15

16 www.hdfgroup.org Review Fundamental HDF5 Objects are: Groups Containers of links to objects Create arbitrary directed graph structures Datasets Multi-dimensional arrays of elements Based on mathematical concept of fiber bundles, but can be thought of in terms of independent and dependent variables Copyright © 2010 The HDF Group. All Rights Reserved16

17 www.hdfgroup.org Stretch Break Copyright © 2010 The HDF Group. All Rights Reserved17

18 www.hdfgroup.org Dataset – Fiber Bundles HDF5 Datasets actually based on mathematical concept of “fiber bundles” Copyright © 2010 The HDF Group. All Rights Reserved18 A fiber bundle consists of the data (E, B, π, F), where E, B, and F are topological spaces and π : E → B is a continuous surjection satisfying a local triviality condition outlined below. The space B is called the base space of the bundle, E the total space, and F the fiber.

19 www.hdfgroup.org Dataset – Fiber Bundles, 2 Copyright © 2010 The HDF Group. All Rights Reserved19 MathematicHDF5 Fiber BundleDataset Base SpaceDataspace Fiber SpaceDatatype SectionElements

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