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Update README.md #35

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71 changes: 33 additions & 38 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -61,11 +61,11 @@ python fint.py ${FILE} ${MESH} ${INFL}
Currently it's just a list of help from `fint`. Later will expand each of the options with explination.

```shell
usage: pfinterp [-h] [--depths DEPTHS] [--timesteps TIMESTEPS] [--box BOX]
[--res N_POINTS_LON N_POINTS_LAT] [--influence INFLUENCE]
[--map_projection MAP_PROJECTION] [--interp {nn,mtri_linear,linear_scipy}]
[--mask MASK] [--ofile OFILE] [--odir ODIR] [--target TARGET] [--no_shape_mask]
[--rotate] [--no_mask_zero] [--timedelta TIMEDELTA]
usage: fint [-h] [--depths DEPTHS] [--timesteps TIMESTEPS] [--box BOX] [--res N_POINTS_LON N_POINTS_LAT] [--influence INFLUENCE]
[--map_projection MAP_PROJECTION]
[--interp {nn,mtri_linear,linear_scipy,cdo_remapcon,cdo_remaplaf,cdo_remapnn,cdo_remapdis,smm_con,smm_laf,smm_nn,smm_dis}]
[--mask MASK] [--ofile OFILE] [--odir ODIR] [--target TARGET] [--no_shape_mask] [--rotate] [--no_mask_zero] [--timedelta TIMEDELTA]
[--oneout] [--missing_value MISSING_VALUE]
data meshpath

Interpolates FESOM2 data to regular grid.
Expand All @@ -77,49 +77,44 @@ positional arguments:
optional arguments:
-h, --help show this help message and exit
--depths DEPTHS, -d DEPTHS
Depths in meters. Closest values from model levels will be taken. Several
options available: number - e.g. '100', coma separated list - e.g.
'0,10,100,200', slice 0:100 -1 - all levels will be selected.
Depths in meters. Closest values from model levels will be taken. Several options available: number - e.g. '100', coma
separated list - e.g. '0,10,100,200', slice 0:100 -1 - all levels will be selected.
--timesteps TIMESTEPS, -t TIMESTEPS
Explicitly define timesteps of the input fields. There are several options:
'-1' - all time steps, number - one time step (e.g. '5'), numbers - coma
separated (e.g. '0, 3, 8, 10'), slice - e.g. '5:10', slice with steps - e.g.
'8:120:12'. slice untill the end of the time series - e.g. '8:end:12'.
--box BOX, -b BOX Several options are available: - Map boundaries in -180 180 -90 90 format that
will be used for interpolation. - Use one of the predefined regions. Available:
gs (Golf Stream), trop (Atlantic Tropics), arctic, gulf (also Golf Stream, but
based on Mercator projection.)\))
Explicitly define timesteps of the input fields. There are several options: '-1' - all time steps, number - one time step (e.g.
'5'), numbers - coma separated (e.g. '0, 3, 8, 10'), slice - e.g. '5:10', slice with steps - e.g. '8:120:12'. slice untill the
end of the time series - e.g. '8:end:12'.
--box BOX, -b BOX Several options are available: - Map boundaries in -180 180 -90 90 format that will be used for interpolation. - Use one of the
predefined regions. Available: gs (Golf Stream), trop (Atlantic Tropics), arctic, gulf (also Golf Stream, but based on Mercator
projection.)))
--res N_POINTS_LON N_POINTS_LAT, -r N_POINTS_LON N_POINTS_LAT
Number of points along each axis that will be used for interpolation (for lon
and lat).
Number of points along each axis that will be used for interpolation (for lon and lat).
--influence INFLUENCE, -i INFLUENCE
Radius of influence for interpolation, in meters. Used for nearest neighbor
interpolation.
Radius of influence for interpolation, in meters. Used for nearest neighbor interpolation.
--map_projection MAP_PROJECTION, -m MAP_PROJECTION
Map projection. Available: mer, np
--interp {nn,mtri_linear,linear_scipy}
Interpolation method. Options are nn - nearest neighbor (KDTree implementation,
fast), mtri_linear - linear, based on triangulation information (slow, but more
precise)
--mask MASK File with mask for interpolation. Mask should have the same coordinates as
interpolated data. Usuall usecase is to use mtri_linear slow interpolation to
create the mask, and then use this mask for faster (nn) interpolation.
--interp {nn,mtri_linear,linear_scipy,cdo_remapcon,cdo_remaplaf,cdo_remapnn,cdo_remapdis,smm_con,smm_laf,smm_nn,smm_dis}
Interpolation method. Options are nn - nearest neighbor (KDTree implementation, fast), mtri_linear - linear, based on
triangulation information (slow, but more precise)
--mask MASK File with mask for interpolation. Mask should have the same coordinates as interpolated data. Usuall usecase is to use
mtri_linear slow interpolation to create the mask, and then use this mask for faster (nn) interpolation.
--ofile OFILE, -o OFILE
Path to the output file. Default is out.nc.
--odir ODIR Path to the output directory. Default is ./
--target TARGET Path to the target file, that contains coordinates of the target grid (as lon
lat variables)
--target TARGET Path to the target file, that contains coordinates of the target grid (as lon lat variables)
--no_shape_mask Do not apply shapely mask for coastlines. Useful for paleo applications.
--rotate Rotate vector variables to geographic coordinates. Use standard FESOM2 angles
(this should be fine in 99.99 percent of cases:)).
--no_mask_zero FESOM2 use 0 as mask value, which is terrible for some variables. Solution is
to create a mask using temperature or salinity, and then use this mask for
interpolation, applying this option.
--rotate Rotate vector variables to geographic coordinates. Use standard FESOM2 angles (this should be fine in 99.99 percent of
cases:)).
--no_mask_zero FESOM2 use 0 as mask value, which is terrible for some variables. Solution is to create a mask using temperature or salinity,
and then use this mask for interpolation, applying this option.
--timedelta TIMEDELTA
Add timedelta to the time axis. The format is number followed by unit. E.g.
'1D' or '10h'. Valid units are 'D' (days), 'h' (hours), 'm' (minutes), 's'
(seconds). To substract timedelta, put argument in quotes, and prepend ' -', so
SPACE and then -, e.g. ' -10D'.
Add timedelta to the time axis. The format is number followed by unit. E.g. '1D' or '10h'. Valid units are 'D' (days), 'h'
(hours), 'm' (minutes), 's' (seconds). To substract timedelta, put argument in quotes, and prepend ' -', so SPACE and then -,
e.g. ' -10D'.
--oneout Add timedelta to the time axis. The format is number followed by unit. E.g. '1D' or '10h'. Valid units are 'D' (days), 'h'
(hours), 'm' (minutes), 's' (seconds). To substract timedelta, put argument in quotes, and prepend ' -', so SPACE and then -,
e.g. ' -10D'.
--missing_value MISSING_VALUE
Missing value for the output file. Default is None.
```
# Containerized Usage

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