# lifescale_utils
Data analysis utilities for lifescale.
# Programs:
## lsgui
*lsgui* starts the graphical user interface (gui) of lifescale-utils. It provides toe following main features:
* Read lifescale xlsm files
* Visualize the data from the xlsm file and calculate various statistics
* Assess the mass distribution of samples by histograms and flag invalid data
* Write the cleand data to csv files (see *ls2csv*)
### Usage:
```
usage: lsgui [-h]
Starts lifescale utils gui.
optional arguments:
-h, --help show this help message and exit
```
## ls2csv
*ls2csv* is a command line program that converts xlsm files written by lifescale units to csv files. The following files
are created:
* `Masses_<run-name>_<guid>.csv`: Data series from the sheet AcquisitionIntervals.
* `Metadata_<run-name>_<guid>.csv`: Data from the sheet PanelData.
* `SampleSummary_<run-name>_<guid>.csv`: Data from the sheet IntervalAnalysis plus sample related data from AcquisitionIntervals.
`<run-name>` and `<guid>` are the taken from the fields `Name` and `Guid` (if available) from the settings sheet of the xml file.
### Usage:
```
usage: ls2csv [-h] -i INPUT_XLSM -o OUT_DIR [-nv] [-s] [-t]
Conversion from lifescale xlsm output to csv files
options:
-h, --help show this help message and exit
-i INPUT_XLSM, --input-xlsm INPUT_XLSM
Path and name of the input xlsm file created by
lifescale. (default: None)
-o OUT_DIR, --out-dir OUT_DIR
Output directory for the CSV files. (default: None)
-nv, --not-verbose Disable command line status messages. (default: False)
-s, --sample-stats Calculate sample statistics of masses (median, std.
deviation, quartiles, interquartile range) and add
them to the SampleSummary output CSV file (columns:
Mass_median, Mass_std, Mass_q25, Mass_q75,Mass_iqr).
(default: False)
-t, --sort-masses-by-time
Sort data in the Masses CSV file by acquisition time.
(default: False)
```
# Python package and installation
Lifescale_utils is available at https://pypi.org/project/lifescale-utils/
Installation: ```pip install lifescale_utils```
# License and copyright
Copyright (C) 2023 Andreas Hellerschmied (<heller182@gmx.at>)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
# Funding
lifescale_utils was funded by the Centre for Microbiology and Environmental Systems Science (CMES) of the University of
Vienna (https://cmess.univie.ac.at/).
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