ANHALIZE is an analysis tool for the ANHA configuration of the NEMO model.

ANHALIZE is an analysis tool for the Arctic and Northern Hemisphere Atlantic (ANHA) configuration of the NEMO model. The focus is on data manipulation, analysis, and visualization.

This tool has been originally developed to support ocean modeling research at the Centre for Earth Observation Science (CEOS), at the University of Manitoba.

NOTE: This code is stable, but new features are currently under development.

• Python (> 3.10.0)

1. Clone this repository with:

   git clone [email protected]:PORTAL-CEOS/ANHALYZE.git
   

   Additional Notes

   To learn about what this means, and how to use Git, see this w3 tutorial,
   this datacamp tutorial, this NHS Git guide, or this git tutorial.

2. Install the dependencies in your python environment with:

   cd ANHALYZE/
   python3 -m pip install -r requirements.txt
   

   Then install the package with:

   python3 -m pip install .
   

   If you want to install the package in development mode, you can do:

   python3 -m pip install  --editable .
   

   Additional Notes

   • Note1: If you are managing multiple venvs, you could use virtualenvwrapper as an organizing tool.

   • Note2: The minimum libraries required for this project are listed in requirements.in which was created automatically with

     pip install pipreqs
     pipreqs <project-directory> --savepath requirements.in --scan-notebooks    
     

     Additionally, the jupyter library was added manually.

     The required libraries including their dependencies are listed in requirements.txt. This was created automatically from requirements.in by using

     pip install pip-tools
     pip-compile    
     

   Additional Help

   Set up your environment using pip. For more information on how to use virtual environments and why they are important, see this Real Python tutorial, or see the NHS virtual environments guide.

   If you are using Linux/MacOS you can use this simple example, or for more information about setting your venv look here.

   ```
   python3 -m venv <venv-directory>
   source <venv-directory>/bin/activate
   python3 -m pip install -r requirements.txt 
   ```
   

Once installed you can import the library like this:

import anhalyze as ah

This example requires an ANHA*_gridT.nc file.

import anhalyze as ah

filename = 'ANHA*gridT.nc'

# Open file
aa = ah.AnhaDataset(filename)

# Do selection of lat_range, lon_range, and depth_range.
aaa = aa.sel(lat_range=[50,65],lon_range=[-93,-75],depth_range=[0,300])

# Plot region for a selected variable.
aaa.show_var_data_map(var='votemper')

Masking is done internally. The default mask file will be automatically downloaded here <package root path>/anhalyze/package_data/, the default mask name is ANHA4_mask.nc.

There are two alternate options for providing your own mask file:

You can add the following environmental variable(s) to your .bash_profile (or .bashrc, etc..), and edith paths to your needs:

#------------------------------------------------------------- 
#ANHALIZE setup
#-------------------------------------------------------------
export MASK_FILENAME='/root_path/user/../your_mask_location/mask_name.nc'
#-------------------------------------------------------------

You can provide your mask filename with full path when opening an ANHA*.nc file, as follows:

import anhalyze as ah

# Open file
aa = ah.AnhaDataset(filename, mask_filename='mask_full_filename')

Anhalize will first try to find your own mask, if none is provided, it will attempt to download the default mask and use that. If you don't want this behaviour then edit the configuration file package_data.toml, located in <package root path>/anhalyze/config/. In the [mask] section, change variable autodownload_file from 'true' to 'false'. This will prevent the file to be downloaded. If you don't provide a valid mask alternative, the code will return an error message. This assumes the default mask has not been downloaded already. If that is the case, you will need to delete it manually.

• 0.7 (planned)
  • To release AnhalyzeLocation class.
  • pip install functionality
• 0.6 (planned)
  • To release AnhalyzeProject class.
• 0.5 (upcoming)
  • First main release, includes:
    • AnhaDataset class
    • Basic functionality of single ANHA nc files.
      • data reading/writing
      • region selection
      • map plotting
  • See commit change or See release history
• 0.0.1 (current)
  • Beta version, initial development.

MIT license, see LICENSE.

-------------------- Deprecated below this line. --------------------

Need to add the following environmental variables to your .bash_profile (or .bashrc, etc..), and edith paths to your needs:

#------------------------------------------------------------- 
#ANHALIZE setup
#-------------------------------------------------------------
export DATA_PATH='/root_path/user/NEMO/ANHA4/ANHA4-Wxx000-S/'
#-------------------------------------------------------------