General HDF5 Reader #30
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…ta according to recipes (dictionaries see `masci_tools/io/parsers/hdf5/recipes.py`). Based on the reader from the `studentproject18ws` branch. Simplified and stripped down to always return a dict Transformations are implemented with a decorator (equivalent to conversion_function decorator for the fleur outxml_parser)
janssenhenning
changed the title
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+ Coverage 68.43% 69.09% +0.65%
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+ Hits 7095 7392 +297
- Misses 3272 3307 +35 |
…eaders output. This makes it easier to create recipes which can just be plugged into a pandas dataframe for example Also fixed one wrong import in `transforms`
…om weights are missing atm) For this a couple of extensions had to be made to the transformation system. Added explicit and recursive move_to_memory and conversion to string entries in datasets can now call transformation functions using a value from the attributes (not datasets) At the moment there is only a multiply function for example for multiplying kpoints with the reciprocal_cell matrix More matrix manipulation was added: -multiplication (both orders) and multiply each element in list with matrix -calculating norm of list of vectors or distances between neighbours in the list -calculate the cumulative sum of an array Some entries will be in the form of a dict after processing (if for example you use the get_all_child_dataset transformation). Now there is an additional option to unpack the keys into the root dictionary after all transformations
…n pattern. Could make a fixed version of this. At the moment it is used to create the total atom sums and so is formatted according to the atom types
…sier to understand
…do not need to be converted to eV
…d them up This file contains: -Something similar to h5dump for seeing the structure of a hdf file -A simple hdf reader that just builds up a nested dictionary with numpy arrays, which mirrors the exact filestructure of the hdf file Also removed the really old hdf reading routine for the `banddos.hdf` file
…tion made some names of transformations more consistent and added errors for currently not implemented cases for transformations
For this I copied the PERIODIC_TABLE_ELEMENTS from the move_aiida_fleur_methods branch
…litting spin-up/down) and flattening arrays
…eds on namedtuples are a python 3.7+ feature
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This PR implements a generic
HDF5Readerheavily inspired by the one on thestudenproject18wsbranch.It can be used with filepaths and file handles and reads and transformed the data according to a given recipe dictionary.
For an example see
masci_tools.io.parsers.hdf5.recipes.FleurDOS.The data is always returned in a python dict. The possible transformations are implemented using the
masci_tools.io.parsers.hdf5.transforms.hdf5_transformationdecorator, which works in the exact same way as theconversion_functiondecorator in theoutxml_parserBasic Usage with filepath:
Basic Usage with file handle: