bvareader 0.2.0

Package to read and process BVA data from LF Motol

BVA reader

Python package which reads and parses xml data from LF in Motol.

Installation

The project is currently hosted on test PyPi and can be downloaded from such https://test.pypi.org/project/bvareader/

Use examples

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")

Timestamp

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-settings-to-csv commands

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"

FAQ

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