Package to read and process BVA data from LF Motol
Python package which reads and parses xml data from LF in Motol.
The project is currently hosted on test PyPi and can be downloaded from such https://test.pypi.org/project/bvareader/
Main use can be through the command line prompts, which doesn't require you to run your own preprocessing scripts. But if you prefer, you can preprocess and save the data in your own way.
from bvareader.reader import read_xml_bva from bvareader.reader import read_xml_sync from bvareader.reader import read_sync_file from bvareader.reader import save_csv from bvareader.preprocessing import preprocess_bva_data from bvareader.preprocessing import add_rotation pd_bva = read_xml_bva("example_data/example.xml") pd_bva_clean = preprocess_bva_data(pd_bva) pd_bva = add_rotation(pd_bva) save_csv(pd_bva_clean, "bva.csv") save_csv(pd_bva, "bva_full.csv") bva_sync = read_xml_sync("example_data/example.xml") save_csv(pd_sync, "bva_sync.csv") pd_sync = read_sync_file("example_data/example.csv") save_csv(pd_sync, "sync.csv")
Bva outputs real timestamp (date and time of each recording). This package converts this datetime number as the POSIX timestamp (number of seconds since 1.1.1970) as per
datetime.timestamp() function described in here
Command line prompt
By installing the package from PyPI, you will get the python entry point which you can use in the command line. You can investigate each command with the
--help tag. e.g.
bva-preprocess-xmx --help. Mostly you will need only the
bva-preprocess-xml and potentially
BVA xml output preprocessing
bva-preprocess-xml "path_to_xml" -o/--output "output-prefix" bva-settings-to-csv "path_to_xml"-o/--output "output-prefix" bva-phases-table "path_to_xml" -o/--output "output-prefix" bva-measures-start-stop-table "path_to_xml" -o/--output "output-prefix"
Q: The command line commands are not found.
A: If you are using conda or virtual envs, make sure you are in a correct environment
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