Metadata-Version: 2.1
Name: lifescale-utils
Version: 0.0.7
Summary: Lifescale utility software.
Home-page: https://gitlab.com/hellerdev/lifescale_utils
Author: Andreas Hellerschmied
Author-email: heller182@gmx.at
License: GNU GPLv3
Keywords: Lifescale
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Programming Language :: Python :: 3
Requires-Python: <4,>=3.6
Description-Content-Type: text/markdown
License-File: LICENSE

# 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/). 
