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stitchee, a python package for concatenating netCDF data along an existing dimension

Project Status: Active – The project has reached a stable, usable state and is being actively developed Documentation Status Mypy checked Python Versions Package version Code coverage

Overview

STITCHEE (STITCH by Extending a dimEnsion) is used for concatenating netCDF data along an existing dimension, and it is designed as both a standalone utility and for use as a service in Harmony.

Getting started, with poetry

  1. Follow the instructions for installing poetry here.
  2. Install stitchee, with its dependencies, by running the following from the repository directory:
poetry install

How to test stitchee locally

poetry run pytest tests/

Usage

$ poetry run stitchee --help
usage: stitchee [-h] -o OUTPUT_PATH [--no_input_file_copies] [--keep_tmp_files] [--concat_method {xarray-concat,xarray-combine}] [--concat_dim CONCAT_DIM]
                [--xarray_arg_compat XARRAY_ARG_COMPAT] [--xarray_arg_combine_attrs XARRAY_ARG_COMBINE_ATTRS] [--xarray_arg_join XARRAY_ARG_JOIN] [-O]
                [-v]
                path/directory or path list [path/directory or path list ...]

Run the along-existing-dimension concatenator.

options:
  -h, --help            show this help message and exit
  --no_input_file_copies
                        By default, input files are copied into a temporary directory to avoid modification of input files. This is useful for testing,
                        but uses more disk space. By specifying this argument, no copying is performed.
  --keep_tmp_files      Prevents removal, after successful execution, of (1) the flattened concatenated file and (2) the input directory copy if created
                        by '--make_dir_copy'.
  --concat_method {xarray-concat,xarray-combine}
                        Whether to use the xarray concat method or the combine-by-coords method.
  --concat_dim CONCAT_DIM
                        Dimension to concatenate along, if possible. This is required if using the 'xarray-concat' method
  --sorting_variable SORTING_VARIABLE
                        Name of a variable to use for sorting datasets before concatenation by xarray. E.g., 'time'.
  --xarray_arg_compat XARRAY_ARG_COMPAT
                        'compat' argument passed to xarray.concat() or xarray.combine_by_coords().
  --xarray_arg_combine_attrs XARRAY_ARG_COMBINE_ATTRS
                        'combine_attrs' argument passed to xarray.concat() or xarray.combine_by_coords().
  --xarray_arg_join XARRAY_ARG_JOIN
                        'join' argument passed to xarray.concat() or xarray.combine_by_coords().
  --group_delim GROUP_DELIM
                        Character or string to use as group delimiter
  -O, --overwrite       Overwrite output file if it already exists.
  -v, --verbose         Enable verbose output to stdout; useful for debugging

Required:
  path/directory or path list
                        Files to be concatenated, specified via (1) multiple paths of the files to be concatenated, (2) single path to text
                        file containing linebreak-separated paths of files to be concatenated, (3) single path to netCDF file to be copied to
                        output path, or a (4) single directory containing the files to be concatenated.
  -o OUTPUT_PATH, --output_path OUTPUT_PATH
                        The output filename for the merged output.

For example:

poetry run stitchee /path/to/netcdf/directory/ -o /path/to/output.nc

This package is NASA Software Release Authorization (SRA) # LAR-20433-1