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Read Thatec h5 formatting and convert it to netcdf files and xarray objects.

Project description


Project Description

This is a community package which helps reading .h5 files created by ThatecOS and converting them to xarray objects and netcdf files. This software is not maintained by and has no affiliations to THATec Innovation GmbH.


$ pip install PyThat

If not happened automatically, install following dependencies: netcdf4, scipy, h5netcdf, h5py, xarray

If you are using Conda/Anaconda, you can also install via pip. However, this may result in some dependency issues, rendering PyThat inoperable.


The package reconstructs the measurement tree and lets the user choose the row containing an indicator. It then uses the metadata from the measurement tree to construct an xarray object with n+m dimensions, where n is the dimension of the indicator in the specified row and m the number of indents/loops.

Since xarray is built around labeled arrays, it also reconstructs the coord and dims attributes of the xarray objects. For use of xarray see the documentation.

After starting at version 0.27 all data is read for all valid indicators and combined to a dataset. The old version with indexing should still work, however.

from PyThat import MeasurementTree
import xarray as xr
import matplotlib.pyplot as plt

# define path to h5 file, can be relative or absolute path
path = r'D:\Pycharm\PyThat\examples\M486 Dispersion 40 mT.h5'

# Get dataset from file
data = MeasurementTree(path, override=True).dataset

# Get variable name from printout
interesting_data_name = "2,1: Acquire spectrum"
interesting_data = data[interesting_data_name] 

# Select and plot data
interesting_data.sel(dict(Frequency=slice(5, 15, None))).plot(col='Set Field')

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