UVP6_time_merge

Merge different acquisition sequences on a constant time step.

How to use it

Download this repo with git clone.

git clone [email protected]:ecotaxa/UVP_toolboxpy.git

Launch time_merge/format_time_series_project.py

/usr/bin/python UVP6_time_merge/time_merge/format_time_series_project.py

Look at your terminal to give the input needed (input folder, start date time, time step, output folder)

What does it do ?

While the time_merge/functions.py can help you formatting your project "by hand" the time_merge/format_time_series_project.py is a workflow easy to use that will do it for you. Here is the few step it goes through.

Invite the user to specify the project, date range and time step of the split/merge to execute

When you will execute format_time_series_project.py a message will prompt you to provide the path of a UVP project with a time series acquisition. The project should be organised as a standard UVP6 project, with a "raw" folder that includes different data.txt and associated vignettes. The user will then chose when he wants to start the split/merge operation.

Split your raw folder into different raw folders depending on acquisition configuration

One important prerequisite of merging and splitting acquisition is to make sure that we merge data that have been acquired with the same method. The package is thus designed to split your original raw folder in as much raw folders as there is unique acquisition configuration. Each new folder will be name "raw_a", "raw_b" etc... The original datatxt will be copied in the new project.

Merge and/or split the data

Once we are sure that our raw folders have the same acquisition parameters we can proceed to data manipulation. The user will input a time step on which he want to reshape the new raw folders (one per acq conf). The new datatxt will be name like "'%Y%m%d-%H%M%S_Merged_data.txt".

Moving vignette to new raw folder

Finally, the vig will be copied from the old raw folder, based on the different dates of the merged_data.txt dates.

UVP6_create_meta

What does it do ?

create metadata for a UVP MOORING project by processing data files stored in a specified folder. Here's a breakdown of what the script does:

Invite the user to specify the project, the latitude, longitude to execute

When you will execute UVP6_create_meta.py a message will prompt you to provide the path of a UVP project with the longitude and latitude acquisition. The project should be organised as a standard UVP6 project, with a "raw" folder that includes different Merged.txt created from the script above UVP6_time_merge. The project metadata and the UVP6 HW_conf must be present in the config folder of the project.

Extracting Depth and Station ID

we will extract depth and station ID from the folder path, or with user input. The user should make sure that all the information needed are in the path or in the *.txt of folder config of the UVP

Processing Data Files

The script searches for data files (*Merged_data.txt) in the specified folder, parses these files to extract relevant information like the filename, profile ID, and sample datetime. It also calculates the number of images in each .txt (end image number). In the end, it will create a DataFrame with this information, and classify it based on the datetime.

Storing the meta file

The new datatxt will be named like "'uvp6_header_NAMEOFTHEPROJECT.txt". For now it is stored in your home repository and should be then moved manually to your project, in the meta file (this feature will be updated soon).