Awesome

Welcome to PyFVCOM!

Table of contents

• Introduction
• Installing
• Prerequisites
• Provides
• Examples

Introduction

PyFVCOM is a collection of various tools and utilities which can be used to extract, analyse and plot input and output files from FVCOM.

Installing

Easiest way is to install with pip/pip3:

pip install PyFVCOM

Prerequisites

• Python. This has been written against Python 2.7.11 and tentatively against Python 3.4.3, so in principle anything newer than those should be OK.

• numpy, again, this has been tested with numpy version 1.4.1 to 1.10.4.

• scipy, versions 0.7.2 to 0.14.1.

• matplotlib, versions 1.0.1 to 1.5.1.

• netCDF4, version 0.9.9 to 1.1.5.

• jdcal, version 1.0 to 1.2.

• pyshp, version 1.2.3.

Optionally:

• iPython, version 0.10.2 to 3.2.1. This makes for a good development environment, particularly when invoked with the -pylab argument, which automatically imports matplotlib.pylab and numpy, amongst others.

Provides

• buoy_tools - read data from an SQLite3 database of BODC buoy data.

  • get_buoy_metadata
  • get_buoy_data

• cst_tools - create coastline files for SMS from shapefiles or DHI MIKE arcs.

  • read_ESRI_shapefile
  • read_arc_MIKE
  • read_CST
  • write_CST

• ctd_tools - interrogate an SQLite data base of CTD casts.

  • get_CTD_metadata
  • get_CTD_data
  • get_ferrybox_data

• current_tools - convert from vector components to scalars and back.

  • scalar2vector
  • vector2scalar

• grid_tools - tools to parse SMS, DHI MIKE and FVCOM unstructured grids. Also provides functionality to add coasts and clip triangulations to a given domain. Functions to parse FVCOM river files are also included, as is a function to resample an unstructured grid onto a regular grid (without interpolation, simply finding the nearest point within a threshold distance).

  • read_sms_mesh
  • read_fvcom_mesh
  • read_mike_mesh
  • read_gmsh_mesh
  • write_sms_mesh
  • write_sms_bathy
  • write_mike_mesh
  • find_nearest_point
  • element_side_lengths
  • fix_coordinates
  • clip_triangulation
  • get_river_config
  • get_rivers
  • mesh2grid
  • line_sample
  • OSGB36_to_WGS84
  • connectivity
  • clip_domain
  • surrounders
  • get_area

• ll2utm - convert from spherical to cartesian UTM coordinates and back. Available from http://robotics.ai.uiuc.edu/~hyoon24/LatLongUTMconversion.py.

  • LL_to_UTM
  • UTM_to_LL

• ocean_tools - a number of routines to convert between combinations of temperature, salinity, pressure, depth and density.

  • pressure2depth
  • depth2pressure
  • dT_adiab_sw
  • theta_sw
  • cp_sw
  • sw_smow
  • sw_dens0
  • sw_seck
  • sw_dens
  • sw_svan
  • sw_sal78
  • sw_sal80
  • sw_salinity
  • dens_jackett
  • cond2salt
  • vorticity (currently empty)
  • zbar
  • pea
  • simpsonhunter
  • mixedlayerdepth
  • stokes
  • dissipation
  • calculate_rhum

• plot - plotting class for FVCOM outputs.

  • Plotter.plot_field
  • Plotter.plot_quiver
  • Plotter.plot_lines
  • Plotter.remove_line_plots
  • Plotter.plot_scatter

• process_results - perform some analyses on FVCOM data read in using read_FVCOM_results.

  • calculate_total_CO2
  • calculate_CO2_leak_budget
  • data_average
  • unstructured_grid_volume
  • residual_flow

• read_results - parse the netCDF model output and extract a subset of the variables.

  • ncwrite
  • ncread
  • read_probes
  • write_probes
  • elems2nodes
  • nodes2elems

• stats_tools - some basic statistics tools.

  • calculate_regression
  • calculate_polyfit
  • coefficient_of_determination
  • fix_range
  • rmse

• tidal_ellipse - Python version of the Tidal Ellipse MATLAB toolbox http://woodshole.er.usgs.gov/operations/sea-mat/tidal_ellipse-html/index.html.

  • ap2ep
  • ep2ap
  • cBEpm
  • get_BE
  • sub2ind
  • plot_ell
  • do_the_plot
  • prep_plot

• tide_tools - tools to use and abuse tidal data from an SQLite database of tidal time series.

  • julian_day
  • gregorian_date
  • add_harmonic_results
  • get_observed_data
  • get_observed_metadata
  • clean_observed_data
  • parse_TAPPY_XML
  • get_harmonics
  • read_POLPRED
  • grid_POLPRED
  • get_harmonics_POLPRED

Examples

The examples directory includes some Jupyter notebooks of some brief examples of how to use PyFVCOM. There are also sample scripts of those notebooks.