Command Line Tools
sch
schimpy CLI tools for pre- and post- processing for SCHISM and data processing.
sch [OPTIONS] COMMAND [ARGS]...
Options
- -h, --help
Show this message and exit.
batch-metrics-cli
Command line interface for generating metrics plots.
MAIN_INPUTFILE: Path to the main input YAML file.
sch batch-metrics-cli [OPTIONS] MAIN_INPUTFILE
Options
- -h, --help
Show this message and exit.
Arguments
- MAIN_INPUTFILE
Required argument
clip-dems-cli
Trim each DEM on a prioritized list. The coordinates used for clipping is supplied either directly as an upper left and lower right coordinate or indirectly using the bounding coordinates of a sample image. In practice this script is usually used with images saved from SMS.
- Arguments:
DEMLIST file containing prioritized (high to low) list of dems.
sch clip-dems-cli [OPTIONS] DEMLIST
Options
- --coords <coords>
Bounding coordinates to which DEMs will be clipped (upper left x, y, lower right x, y).
- --image <infile>
Image or DEM used to infer bounding coordinates for clipping. Use jpeg for the image. This argument is mutually exclusive with –coords. If a sample is provided its upper left and lower right corner will be used.
- --prefix <prefix>
Prefix used for output file names.
- --outformat <outformat>
Output format, default is AAIGrid (ArcInfo ASCII).
- --verbose
Enable verbose output.
- --hshift
(Deprecated) Shift DEM by half cell for applications that incorrectly interpret the location of the origin and data centering of a DEM. This is a bug fix for SMS < 11.1
- -h, --help
Show this message and exit.
Arguments
- DEMLIST
Required argument
combine-consume-cli
sch combine-consume-cli [OPTIONS]
Options
- --start <start>
Required start date of simulation in format like yyyy-mm-dd
- --dir <dir>
directory in which output will be processed
- --fbase <fbase>
File base name. This will either be ‘schout.nc’ or a list of files like ‘elev.61,hvel.64,salt.63’.
- --hotstart
Combine hotstart in addition to fbase
- --hotstart_only
Only combine hotstart – avoids file search errors when nothing left to combine
- --consume
Delete combined files or unrequested files
- --assume_done
Assume that the simulation is finished, so incomplete blocks can be deleted
- --combiner <combiner>
Executable for combine_output.
- --hot_combiner <hot_combiner>
Executable for combine_output.
- --sndx <sndx>
First index to consider for processing.
- --endx <endx>
Last index to consider for processing.
- --sndx_hot <sndx_hot>
First index to consider for processing.
- --endx_hot <endx_hot>
Last index to consider for processing.
- --datefile <datefile>
File containing list of dates. Each line can have a single date or comma-separated pair indicating block start and end. Blank lines are ignored and # is comment character that can comment the entire line or be placed at the side of a line after the date(s).
- --blocks_per_day <blocks_per_day>
Blocks used to store 1 day worth of output.
contour-smooth-cli
Uses the min-max curvature flow algorithm of Malladi and Sethian to simplify DEM topography.
The script requires a subcommand like: $ contour_smooth.py smooth The most basic subcommand is smooth. Given limited efficiency at the moment, the script is generally run on a small area and dumps intermediate points in the processing as numpy arrays so you can view the differences using the contour_smooth.py view subcommand.
You can get subject-specific help on a subcommand by typing: $ contour_smooth.py subcommand –help
sch contour-smooth-cli [OPTIONS] COMMAND [ARGS]...
Options
- -h, --help
Show this message and exit.
save
Save dumped DEM based on .npy dump and the original DEM it came from.
sch contour-smooth-cli save [OPTIONS]
Options
- -h, --help
Show this message and exit.
- --dumpfile <dumpfile>
Required Dump file from smoothing (npy format).
- --original <original>
Required Original DEM (GeoTiff).
- --outfile <outfile>
Required Output file that will be saved (GeoTiff format).
smooth
Smooth the input DEM.
sch contour-smooth-cli smooth [OPTIONS]
Options
- -h, --help
Show this message and exit.
- --input <input>
Required Input file name, file in tiff format.
- --scales <scales>
Scales (in multiples of DEM side length) over which to smooth. The sequence [1,2,3,4] is an example, where the smoothing is gradually introduced at 10m, 20m, 30m and 40m for a 10m DEM.
- --nstep <nstep>
Number of pseudo time steps to resolve integration. Default is 40.
- --max_time <max_time>
Pseudo time representing final time step. Default is 4.0.
- --report_interval <report_interval>
Intermediate interval at which integration will be segmented and smoothed DEMs will be dumped. For example, if –max_time is 2.0 and –report_interval is 0.1, you will get 20 intermediate reports.
view
View two versions of the smoothed DEM based on their .npy dump.
sch contour-smooth-cli view [OPTIONS] FILE0 FILE1
Options
- -h, --help
Show this message and exit.
- --levels <levels>
Contour levels.
- --vmin <vmin>
Minimum elevation in color bar.
- --vmax <vmax>
Maximum elevation in color bar.
Arguments
- FILE0
Required argument
- FILE1
Required argument
convert-linestrings-cli
Convert SCHISM line strings between YAML and Shapefile formats.
sch convert-linestrings-cli [OPTIONS]
Options
- -h, --help
Show this message and exit.
- --input <input>
Required Input file (YAML or Shapefile).
- --output <output>
Required Output file (YAML or Shapefile).
convert-mesh-cli
Convert a mesh from one format to another. The format is decided by the extensions automatically.
sch convert-mesh-cli [OPTIONS]
Options
- --input <input>
Required Input mesh file.
- --output <output>
Required Output mesh file.
- --crs <crs>
CRS string for the projection.
- -h, --help
Show this message and exit.
convert-points-cli
Convert SCHISM points (source and sink) between YAML and Shapefile formats.
sch convert-points-cli [OPTIONS]
Options
- -h, --help
Show this message and exit.
- --input <input>
Required Input file (YAML).
- --output <output>
Required Output file (Shapefile).
- -h, --help
Show this message and exit.
convert-polygons-cli
Convert SCHISM polygons between YAML and Shapefile formats.
sch convert-polygons-cli [OPTIONS]
Options
- -h, --help
Show this message and exit.
- --input <input>
Required Input file (YAML or Shapefile).
- --output <output>
Required Output file (YAML or Shapefile).
- -h, --help
Show this message and exit.
model-time-cli
Convert elapsed model seconds to or from dates
sch model-time-cli [OPTIONS] COMMAND [ARGS]...
Options
- -h, --help
Show this message and exit.
clip
Clip (subset) an input file in elapsed time to a new, later, start date
sch model-time-cli clip [OPTIONS] ELAPSED_INPUT...
Options
- --start <start>
Required Start time in ISO-like format 2009-03-12T00:00:00. Time part is optional.
- --clip_start <clip_start>
Required Starting date for output.
- --out <out>
Name of output file. If input is a *.th file the file will be converted and output to this file, otherwise printed to screen
- -h, --help
Show this message and exit.
Arguments
- ELAPSED_INPUT
Required argument(s)
to-date
Convert input elapsed seconds or *.th file with elapsed seconds as the time column to equivalent output with a datetime or annotated with datetimes.
sch model-time-cli to-date [OPTIONS] ELAPSED_INPUT...
Options
- --start <start>
Required Start time in ISO-like format 2009-03-12T00:00:00. Time part is optional.
- --step <step>
Model time step in seconds. If given, answer will be the integer time step.
- --elapsed_unit <elapsed_unit>
Time unit of input file. Must be either ‘s’ for seconds or ‘d’ for days. Only used for files
- --time_format <time_format>
Time format for output, e.g. the default is %%Y-%%m-%%dT%%H:%%M:%%S for 2009-03-14T22:40:00. Only used when converting fields.
- --annotate
Annotate output.
- --out <out>
Name of output file. If input is a *.th file the file will be converted and output to this file, otherwise printed to screen
- -h, --help
Show this message and exit.
Arguments
- ELAPSED_INPUT
Required argument(s)
to-elapsed
Interpret model times in elapsed seconds and translate between calendar time and elapsed. The script requires a subcommand like: $ model_time.py to_elapsed. You can also get subject-specific help on a subcommand by typing $ model_time.py subcommand –help
sch model-time-cli to-elapsed [OPTIONS] DATED_INPUT...
Options
- --start <start>
Starting date and time basis for output if the input is a file.
- --annotate
Annotate output.
- --step <step>
Model time step. If given, answer will be the integer time step.
- --out <out>
Name of output file. If input is a *.th file the file will be converted and output to this file, otherwise printed to screen
- --skip_nan
Skip a record with nan if True
- -h, --help
Show this message and exit.
Arguments
- DATED_INPUT
Required argument(s)