netcdf-compare

Netcdf-compare is a netCDF comparison tool. It comes with a variety of command-line options to determine what exactly should be compared and how. For example, it is possible to compare only two specific variables, using specific absolute and/or relative tolerance limits.

Netcdf-compare is implemented in Python, using the numpy and netCDF4 libraries.

Installation

From Sources

> git clone https://github.com/stcorp/netcdf-compare.git
> pip install ./netcdf-compare

Then verify your installation with:

> netcdf-compare --help 

Usage

netcdf-compare [-h] [-a PATH] [-A PATH] [-v PATH] [-V PATH] [-g PATH]
                      [-G PATH] [-n] [-s] [-X] [-Y] [-W] [-q] [--atol FLOAT]
                      [--rtol FLOAT] [--combined_tolerance]
                      [--max-values NUMBER] [--verbose]
                      file1 file2

positional arguments:
  file1                 NetCDF file to compare
  file2                 NetCDF file to compare

optional arguments:
  -h, --help            show this help message and exit
  -a PATH, --attribute PATH
                        Attribute(s) to include
  -A PATH, --exclude-attribute PATH
                        Attribute(s) to exclude
  -v PATH, --variable PATH
                        Variable(s) to include
  -V PATH, --exclude-variable PATH
                        Variable(s) to exclude
  -g PATH, --group PATH
                        Group(s) to include
  -G PATH, --exclude-group PATH
                        Group(s) to exclude
  -n, --non-recursive   Non-recursively compare group(s)
  -s, --structure       Only compare structure (not content)
  -X, --skip-variables  Exclude all variables
  -Y, --skip-attributes
                        Exclude all attributes
  -W, --no-warnings     Hide warnings
  -q, --quiet           Do not show detailed differences.
  --atol FLOAT          Absolute tolerance (default 1e-6)
  --rtol FLOAT          Relative tolerance (default 1e-3)
  --combined_tolerance  Combine absolute/relative tolerance checking
  --max-values NUMBER   Number of example differences (default 1)
  --verbose             Verbose mode

Variables, groups and attributes can be referenced as follows:

-by name
-by absolute path, for example "/some/group" or "/group/group2/varname"
-by relative path, for example "group" or "group2/varname"

When not referenced by absolute path, there may be multiple matches.

Compound types and vlen/ragged arrays are not supported at the moment,

Output example

Comparing FCI data to a reference file may give the following output:

# command
> netcdf-compare fci-example.nc fci-reference.nc

# output
GROUP /
  VAR index_offset
    MAXIMUM ABSOLUTE VIOLATION: 65465
      (0,): 13, 84
    MAXIMUM RELATIVE VIOLATION: 5035.7692307692305
      (0,): 13, 84
    TOTAL NUMBER OF VIOLATIONS: 1
      FIRST 1 OCCURRENCE(S):
      (0,): 13, 84
  VAR index
    DIFFERENT SHAPE (FILE 1: (10,), FILE 2: (74,))

# --snip--

      GROUP quality_channel
        VAR number_of_noise_warning_pixels
          ATTRIBUTE long_name
            FILE 1: Number of pixels with noise_warning flag set
            FILE 2: Number of  pixels with noise_warning flag set
        VAR number_of_missing_warning_pixels
          MAXIMUM ABSOLUTE VIOLATION: 4294917908
            (0,): 0, 49388
          TOTAL NUMBER OF VIOLATIONS: 1
            FIRST 1 OCCURRENCE(S):
            (0,): 0, 49388
          ATTRIBUTE long_name
            FILE 1: Number of pixels with missing_warning flag set
            FILE 2: Number of  pixels with missing_warning flag set