import click
import os
[docs]
def visit_list(
output_dir,
var,
start,
end,
filename,
overwrite
):
"""Generate a file containing a list of SCHISM output files to be visualized on VisIt.
Parameters
----------
output_dir : str
Outputs directory containing SCHISM output files.
var: str
variable name for SCHISM output files (e.g., horizontalVelX).
start : int
Starting index for the file list.
end : int
Ending index for the file list.
filename : str
Filename for the list of SCHISM output files.
"""
# Check if the output file already exists
if os.path.exists(filename) and overwrite == False:
print(f"File already exists: {filename}. Use --overwrite to overwrite the file.")
return
# Make sure output_dir exists
try:
assert os.path.exists(output_dir)
except AssertionError:
print(f"Path does not exist: {output_dir}")
# Make sure var is a SCHISM output variable
valid_vars = ["horizontalVelX", "horizontalVelY", "zCoordinates", "out2d", "salinity",
"sedConcentration_1", "sedConcentration_2", "sedConcentration_3", "GEN_1", "GEN_2", "GEN_3", "temperature", "verticalVel"]
try:
assert var in valid_vars
except AssertionError:
print(f"Invalid SCHISM output variable: {var}")
print(f"Valid SCHISM output variables are: {', '.join(valid_vars)}")
# start should be less than end
try:
assert start <= end
except AssertionError:
print(f"Invalid start and end indices: start ({start}) should be less than or equal to end ({end})")
# filename should have .visit extension
try:
assert filename.endswith(".visit")
except AssertionError:
print(f"File being generated should have .visit extension: {filename}")
# Generate file list. Use absolute paths to avoid issues with VisIt not being able to find files.
file_list = []
for i in range(start, end + 1):
file_name = f"{var}_{i}.nc"
file_path = os.path.abspath(os.path.join(output_dir, file_name))
if os.path.exists(file_path):
file_list.append(file_path)
else:
print(f"Warning: File does not exist and will be skipped: {file_path}")
# Write to file
with open(filename, "w") as f:
for file_path in file_list:
f.write(f"{file_path}\n")
if len(file_list) > 0:
print(f"File list generated: `{os.path.abspath(filename)}` with {len(file_list)} files:")
for file_path in file_list:
print(f" {file_path}")
else:
print(f"No file list was generated.")
@click.command(help="Generates a file list for visualizaing multiple, consecutive files in VisIt. \n Example: visit_list --output_dir . --var horizontalVelX --start 1 --end 10 --filename list_winter.visit")
@click.option(
"--output_dir",
default=None,
required=True,
type=click.Path(exists=True),
help="Path to the `outputs` directory containing SCHISM output files.",
)
@click.option(
"--var",
default=None,
required=True,
type=str,
help="variable name for SCHISM output files (e.g., horizontalVelX).",
)
@click.option(
"--start",
default=None,
required=True,
type=int,
help=(
"Starting index for the file list."
),
)
@click.option(
"--end",
default=None,
required=True,
type=int,
help="Ending index for the file list.",
)
@click.option(
"--filename",
default=None,
required=True,
type=str,
help=("Filename for the list of SCHISM output files."
),
)
@click.option(
"--overwrite",
is_flag=True,
default=False,
required=False,
help="Overwrite the output file if it already exists.",
)
@click.help_option("-h", "--help")
def visit_list_cli(
output_dir,
var,
start,
end,
filename,
overwrite
):
"""
Command-line interface to create a file containing a list of SCHISM output files to be visualized on VisIt.
"""
visit_list(
output_dir,
var,
start,
end,
filename,
overwrite
)
if __name__ == "__main__":
visit_list_cli()