shipspy 1.1.0
processing of ship campaign data

# shipspy: ship campaign data processing and standardisation

With shipspy, data from ship campaigns can be processed and standardised. A number of instruments are included.

## Setup

Install shipspy:

```
pip install shipspy
```
## Using shipspy

The following processing options are available.

### DShip

With the dship subcommand, data from the ship integrated system can be processed. For an exemplary order to download underway data, see [1]. The following steps are done:
* Fixing time stamps 
* Averaging to minutely time stamps
* Removing unphysical values
* Renaming variables, changing units, and adding attributes
* Converting to netCDF

To process dship data run
```
shipspy dship -i <input file> -o <output file> -a <attribute dictionary> -s <ship>
```
with
* `input file`: downloaded data from BSH or GEOMAR (or directly from the ship) as txt or dat file with unix time stamp (seconds since 1970-01-01)
* `output file`: file name of netCDF output file
* `attribute dictionary`: yaml dictionary with variable names and attribute. For example dictionaries for the different research vessels see `rv_information` 
* `ship`: name of the ship. Options are `Merian`, `Sonne`, `Polarstern`, `Meteor`, and `Test`.

### Renaming

The rename command can be used to 
* fix the time stamps
* rename variables and add attributes
* convert units to SI
* remove unphysical values
* Convert and save the file as netCDF

To rename a data file run
```
shipspy rename -i <input file> -o <output file> -a <attribute dictionary> -d <instrument>
```
with 
* `input file`: input file, file format depends on the instrument
* `output file`: file name of netCDF output file
* `attribute dictionary`: yaml dictionary with variable names and attribute. For examples see [[1]](https://github.com/LauraKoehler/arc_processing)
* `instrument`: instrument name. Options are `calitoo`, `ceilometer`, `ctd`, `hatpro`, `microtops`, `radiosondes`, `test`, `uav`

### Sections

The section command adds a new coordinate and specifies the time period of the campaign. To use it run
```
shipspy sections -i <input file> -o <output file> -s <section file> -t <time dimension name> -a <global attribute dictionary>
```
with
* `input file`: input netCDF file
* `output file`: file name of netCDF output file
* `section file`: txt file specifying the campaign dates (start, end, break) and the sections in which it should be divided. For an example, see [[1]](https://github.com/LauraKoehler/arc_processing).
* `time dimension name`: name of the time dimension. Default is `time` but sometimes it can be something like `start_time`.
* `global attribute dictionary`: yaml file with global attributes if wanted. For example files see [[1]](https://github.com/LauraKoehler/arc_processing).

The [repository [1]](https://github.com/LauraKoehler/arc_processing) with the settings for the ARC and additional scripts can serve as a template.

### PAMOS

The pamos command can be used to process data from the instrument PAMOS (Portable Atmospheric Measurement box On Sea) which is particularly developed for (commercial) vessels. To you it run
```
shipspy pamos -i <input directory> -o <output file> -a <attribute dictionary> -c <header file> -f <quality flag dictionary> -e <additional attribute dictionary>
```
with
* `input directory`: input directory, where the raw data files are stored
* `output file`: file name of netCDF output file
* `attribute dictionary`: yaml dictionary with variable names and attribute.
* `header file`: text file which defines the columns of the raw data files. For an example, see [2].
* `quality flag dictionary`: optional yaml dictionary to be used to assess the quality flags. For an example see [2].
* `additional attribute dictionary`: optional yaml dictionary with extra variables like quality and pump flags.

The [repository [2]](https://github.com/LauraKoehler/pamos_processing) with the settings for PAMOS on the MS Fridtjof Nansen can serve as a template.

# References
[1] Köhler, L. (2023). ARC: Processing of atmospheric and oceanographic measurements (Version v1.0.0) [Computer software]. https://github.com/LauraKoehler/arc_processing

[2] Köhler, L. (2025). PAMOS processing (Version 1.0.0) [Computer software]. https://github.com/LauraKoehler/pamos_processing