The wt5 File Format

WrightTools stores data in binary wt5 files.

wt5 is a sub-format of HDF5.

wt5

wt5 files are hdf5 files with particular structure and attributes defined. wt5 objects may appear embedded within a larger hdf5 file or vise-versa, however this is untested. At the root of a wt5 file, a Collection or Data object is found. Collection and Data are hdf5 groups. A Collection may have children consisting of Collection and/or Data. A Data may have children consisting of Variable and/or Channel. Variable and Channel are hdf5 datasets.

Metadata

The following metadata is handled within WrightTools and define the necessary attributes to be a wt5 file. It is recommended not to write over these attributes manually except at import time (e.g. from_<x> function).

name	Collection	Data	Variable	Channel	description/notes
`name`	yes	yes	yes	yes	Usually matches the last component of the path, except for root, `/`, which does not have a path with it’s name
`class`	yes	yes	yes	yes	Identifies which kind of WrightTools object it is.
`created`	yes	yes			Timestamp of when the object was made, can be overwritten with source file creation time by `from_<x>` functions.
`__version__`	yes	yes			`wt5` version identifier
`item_names`	yes	yes			Ordered list of the children
`variable_names`		yes			Ordered list of all Variables
`channel_names`		yes			Ordered list of all Channels
`axes`		yes			Ordered list of axes expressions which define how a Data object is represented
`constants`		yes			Ordered list of expressions for values which are constant
`kind`		yes			Short description of what type of file it originated from, usually the instrument
`source`		yes			File path/url to the original file as read in
`label`			yes	yes	Identifier used to create more complex labels in Axes or Constants, which are used to plot
`units`			yes	yes	Units assigned to the dataset
`min`			yes	yes	Cached minimum value
`max`			yes	yes	Cached maximum value
`argmin`			yes	yes	Cached index of minimum value
`argmax`			yes	yes	Cached index of maximum value
`signed`				yes	Boolean for treating channel as signed/unsigned

HDF5

The HDF5 data model contains two primary objects: the group and the dataset. Groups are used to hierarchically organize content within the file. Each group is a container for datasets and other groups. Think of groups like folders in your computers file system. Every HDF5 file contains a top-level root group, signified by /.

Datasets are specialty containers for raw data values. Think of datasets like multidimensional arrays, similar to the numpy ndarray. Each dataset has a specific data type, such as integer, float, or character.

Groups and datasets can contain additional metadata. This metadata is stored in a key: value pair system called attrs, similar to a python dictionary.

Much more information can be found on the HDF5 tutorial.

WrightTools relies upon the h5py package, a Pythonic interface to HDF5.

Access

wt5 is a binary format, so it cannot be interpreted with traditional text editors. Since wt5 is a sub-format of HDF5, WrightTools benefits from the ecosystem of HDF5 tools that already exists. This means that it is possible to import and interact with wt5 files without WrightTools, or even without python.

ASCII

Export an HDF5 file to a human-readable ASCII file using h5dump.

Fortran

Use the official HDF5 Fortran Library.

Graphical

HDF COMPASS, a simple tool for navigating and viewing data within HDF5 files (no editing functionality).

HDF VIEW, a visual tool for browsing and editing HDF5 files.

MATLAB

MATLAB offers built-in high-level HDF5 functions including h5disp, h5read, and h5readatt.

Python (without WrightTools)

We reccomend the amazing h5py package.

Shell

h5cli: bash-like interface to interacting with HDF5 files.

h5diff: compare two HDF5 files, reporting the differences.

h5ls: print information about one or more HDF5 files.

Complete list of official HDF5 tools

Changes

Version 1.0.0

Initial release of the format.

Version 1.0.1

Changes internal handling of strings. Bare strings are no longer required to call encode() before storing.

Version 1.0.2

Adds “constants” as a stored attribute in the attrs dictionary, a list of strings just like axes.

Version 1.0.3

Changed identity as stored in attrs dictionary (axis and constant) to use the expression including operators. Previous versions exhibited a bug where decimal points would be ignored when the expression was generated from the attrs (thus “2.0” would be stored as “2_0” and read in as “20”).