diff --git a/Inst_eddies/Tests/long_tests.json b/Inst_eddies/Tests/long_tests.json
index ff33126b2a077fbe09712bf17611707e0cc81ba0..aef294ff51b3cdafe911fce695dc88abdffeac0e 100644
--- a/Inst_eddies/Tests/long_tests.json
+++ b/Inst_eddies/Tests/long_tests.json
@@ -75,7 +75,7 @@
"Extraction_eddies_region_2_noise": {
"create_file": [
"inst_eddies_nml.txt",
- "&config_nml /\n"
+ "&dates_nml slice=0/\n&config_nml /\n&input_ssh_nml /\n"
],
"commands":
[
@@ -83,7 +83,7 @@
"$build_dir/Inst_eddies/inst_eddies_Aviso.py",
"-b", "1.625", "15.625", "-38.375", "-30.375", "SHPC",
"$Aviso_DT_dir/dt_global_allsat_phy_l4_%Y%m%d_20210726.nc",
- "2006-01-01", "2006-01-15", "0", "f"
+ "2006-01-01", "2006-01-15"
],
"mv grid_nml.txt SHPC"
],
@@ -93,7 +93,7 @@
"Region_6": {
"create_file": [
"inst_eddies_nml.txt",
- "&config_nml /\n"
+ "&dates_nml date=20454 slice=0/\n&config_nml /\n&input_ssh_nml /\n"
],
"commands":
[
@@ -106,18 +106,17 @@
"mv grid_nml.txt SHPC"
],
"main_command": 0,
- "input": "20454\n0\nf\n",
"sel_diff_args": {"exclude": ["timings.txt", "perf_report.csv"]}
},
"Missing_file": {
"create_file": [
"inst_eddies_nml.txt",
- "&config_nml /\n"
+ "&dates_nml slice=0/\n&config_nml /\n&input_ssh_nml /\n"
],
"command": [
"$build_dir/Inst_eddies/inst_eddies_Aviso.py", "SHPC",
"$Eurec4A_NRT_dir/dataset-duacs-global-allsat-phy-%Y-%m-%d.nc",
- "2020-01-31", "2020-02-02", "0", "f"
+ "2020-01-31", "2020-02-02"
],
"description":
"Date 2020-02-01 is missing. Test of the script with a missing date.",
@@ -131,7 +130,7 @@
[
"$build_dir/Inst_eddies/inst_eddies_Aviso.py", "SHPC",
"$Aviso_DT_dir/dt_global_allsat_phy_l4_%Y%m%d_20210726.nc",
- "1993-01-01", "1993-03-31", "0", "f",
+ "1993-01-01", "1993-03-31",
"--bbox", "20", "30", "35", "42"
],
"mv grid_nml.txt SHPC"
@@ -139,7 +138,7 @@
"main_command": 0,
"create_file": [
"inst_eddies_nml.txt",
- "&config_nml /\n"
+ "&dates_nml slice=0/\n&config_nml /\n&input_ssh_nml /\n"
],
"sel_diff_args": {"exclude": ["timings.txt", "perf_report.csv"]}
},
@@ -150,7 +149,7 @@
[
"$build_dir/Inst_eddies/inst_eddies_Aviso.py", "SHPC",
"$Aviso_DT_dir/dt_global_allsat_phy_l4_%Y%m%d_20210726.nc",
- "2006-01-01", "2006-01-15", "0", "f",
+ "2006-01-01", "2006-01-15",
"--bbox", "0.125", "29.875", "-59.875", "-15.125"
],
"mv grid_nml.txt SHPC"
@@ -158,7 +157,7 @@
"main_command": 0,
"create_file": [
"inst_eddies_nml.txt",
- "&config_nml /\n"
+ "&dates_nml slice=0/\n&config_nml /\n&input_ssh_nml /\n"
],
"sel_diff_args": {"exclude": ["timings.txt", "perf_report.csv"]}
}
diff --git a/Inst_eddies/Tests/short_tests.json b/Inst_eddies/Tests/short_tests.json
index 8014b862f185f5b4231b595e2497550fd3e1e019..0eb43d37f1aa56ee5e07e977c35ffb959e240425 100644
--- a/Inst_eddies/Tests/short_tests.json
+++ b/Inst_eddies/Tests/short_tests.json
@@ -261,7 +261,7 @@
"description": "Part of the domain has missing values.",
"create_file": [
"inst_eddies_nml.txt",
- "&config_nml /\n"
+ "&dates_nml date=20454 slice=0/\n&config_nml /\n&input_ssh_nml /\n"
],
"commands":
[
@@ -275,34 +275,32 @@
"mv grid_nml.txt SHPC"
],
"main_command": 0,
- "input": "20454\n0\nf\n",
"sel_diff_args": {"exclude": ["timings.txt", "perf_report.csv"]}
},
"Inst_eddies_py": {
"description": "Like Extraction_eddies_region_4, but for a single date. This is a test of options of the wrapper script rather than a test of the Fortran executable.",
"create_file": [
"inst_eddies_nml.txt",
- "&config_nml /\n"
+ "&dates_nml date=20454 slice=0/\n&config_nml /\n&input_ssh_nml /\n"
],
"command": [
"$build_dir/Inst_eddies/inst_eddies.py",
"-b", "16.125", "20.875", "-38.875", "-34.125",
"SHPC", "$Aviso_DT_dir/dt_global_allsat_phy_l4_20060101_20210726.nc"
],
- "input": "20454\n0\nf\n",
"sel_diff_args": {"exclude": ["timings.txt", "perf_report.csv"]}
},
"Inst_eddies_loop": {
"create_file": [
"inst_eddies_nml.txt",
- "&config_nml /\n"
+ "&dates_nml slice=0/\n&config_nml /\n&input_ssh_nml /\n"
],
"commands":
[
[
"$build_dir/Inst_eddies/inst_eddies_Aviso.py", "SHPC",
"$src_dir/Inst_eddies/Tests/Input/Region_1/huv_region_1_%Y_%m_%d.nc",
- "2006-01-01", "2006-01-04", "0", "f"
+ "2006-01-01", "2006-01-04"
],
"mv grid_nml.txt SHPC"
],
@@ -386,13 +384,17 @@
[
"$build_dir/Inst_eddies/inst_eddies_Aviso.py", "SHPC",
"$Aviso_DT_dir/dt_global_allsat_phy_l4_%Y%m%d_20210726.nc",
- "2006-01-01", "2006-01-15", "0", "f",
+ "2006-01-01", "2006-01-15",
"--bbox", "16.125", "20.875", "-38.875", "-34.125"
],
"mv grid_nml.txt SHPC"
],
"main_command": 0,
- "create_file": ["inst_eddies_nml.txt", "&config_nml /\n"],
+ "create_file":
+ [
+ "inst_eddies_nml.txt",
+ "&dates_nml slice=0/\n&config_nml /\n&input_ssh_nml /\n"
+ ],
"sel_diff_args": {"exclude": ["timings.txt", "perf_report.csv"]}
},
"Complete_SSH":
diff --git a/Inst_eddies/inst_eddies.py.in b/Inst_eddies/inst_eddies.py.in
index 5dc6960ef6e1786a9817ce5f0252a5e1ec78aeac..205eda3756c55beb5f585df52461702ba2cf3187 100644
--- a/Inst_eddies/inst_eddies.py.in
+++ b/Inst_eddies/inst_eddies.py.in
@@ -21,12 +21,9 @@ def process_1_file(
nco_instance,
nc_file,
inst_eddies_exe,
- d,
- my_slice,
writer,
SHPC_dir,
inst_eddies_nml,
- periodic,
):
t0 = time.perf_counter()
@@ -55,22 +52,18 @@ def process_1_file(
subprocess.run(
[inst_eddies_exe, SHPC_dir, "unpacked.nc"],
check=True,
- input=f"&dates_nml date = {d}, slice = {my_slice}/\n"
- + str(inst_eddies_nml)
- + f"\n&input_ssh_nml periodic = {periodic}/\n",
+ input=str(inst_eddies_nml) + "\n",
text=True,
)
elapsed_Fortran = time.perf_counter() - t0
- writer.writerow([d, elapsed_NCO, elapsed_Fortran])
+ writer.writerow(
+ [inst_eddies_nml["dates_nml"]["date"], elapsed_NCO, elapsed_Fortran]
+ )
-def loop_inst_eddies(
- SHPC_dir, files, bbox, inst_eddies_nml, d, my_slice, periodic
-):
+def loop_inst_eddies(SHPC_dir, files, bbox, inst_eddies_nml):
"""`files` is an iterator of file paths. The first file must exist,
- others can be missing. bbox is a tuple of four real numbers. `d`
- is a date index (integer value) for the first date. my_slice is
- the slice index (integer value) in the SHPC.
+ others can be missing. bbox is a tuple of four real numbers.
"""
@@ -84,6 +77,7 @@ def loop_inst_eddies(
)
nco_instance = nco.Nco()
+ my_slice = inst_eddies_nml["dates_nml"]["slice"]
if os.access(f"{SHPC_dir}/Slice_{my_slice}", os.F_OK):
shutil.rmtree(f"{SHPC_dir}/Slice_{my_slice}")
@@ -103,24 +97,27 @@ def loop_inst_eddies(
# First file is out of the loop because it must be present:
nc_file = next(files)
- print("inst_eddies.loop_inst_eddies: Date:", d)
+ print(
+ "inst_eddies.loop_inst_eddies: Date:",
+ inst_eddies_nml["dates_nml"]["date"],
+ )
print("inst_eddies.loop_inst_eddies: Input file:", nc_file, flush=True)
process_1_file(
bbox,
nco_instance,
nc_file,
inst_eddies_exe,
- d,
- my_slice,
writer,
SHPC_dir,
inst_eddies_nml,
- periodic,
)
- d += 1
+ inst_eddies_nml["dates_nml"]["date"] += 1
for nc_file in files:
- print("inst_eddies.loop_inst_eddies: Date:", d)
+ print(
+ "inst_eddies.loop_inst_eddies: Date:",
+ inst_eddies_nml["dates_nml"]["date"],
+ )
print("inst_eddies.loop_inst_eddies: Input file:", nc_file, flush=True)
if os.access(nc_file, os.F_OK):
@@ -129,12 +126,9 @@ def loop_inst_eddies(
nco_instance,
nc_file,
inst_eddies_exe,
- d,
- my_slice,
writer,
SHPC_dir,
inst_eddies_nml,
- periodic,
)
else:
print("inst_eddies.loop_inst_eddies: Missing file:", nc_file)
@@ -148,7 +142,7 @@ def loop_inst_eddies(
n_shapes = len(shpr)
ishape_last.write(str(n_shapes - 1) + "\n")
- d += 1
+ inst_eddies_nml["dates_nml"]["date"] += 1
perf_report.close()
os.remove("unpacked.nc")
@@ -186,22 +180,12 @@ if __name__ == "__main__":
sys.exit(args.file[0] + " not found")
if os.access("inst_eddies_nml.txt", os.R_OK):
- print("Will use inst_eddies_nml.txt.")
+ print(
+ "Will use inst_eddies_nml.txt, using date in dates_nml as first "
+ "date..."
+ )
else:
sys.exit('"inst_eddies_nml.txt" not found -- Aborting')
inst_eddies_nml = f90nml.read("inst_eddies_nml.txt")
- d = input("Enter first date index (integer value): ")
- d = int(d)
- my_slice = input("Enter slice index (integer value): ")
- my_slice = int(my_slice)
- periodic = input("periodic (t/f)? ")
- loop_inst_eddies(
- args.SHPC_dir,
- iter(args.file),
- args.bbox,
- inst_eddies_nml,
- d,
- my_slice,
- periodic,
- )
+ loop_inst_eddies(args.SHPC_dir, iter(args.file), args.bbox, inst_eddies_nml)
diff --git a/Inst_eddies/inst_eddies_Aviso.py b/Inst_eddies/inst_eddies_Aviso.py
index 75d53784f5cf7bb171a29dc36abb4137b454bdfe..37760b8dee99f3d5a2ebbcd63be5e6e4b4336c37 100644
--- a/Inst_eddies/inst_eddies_Aviso.py
+++ b/Inst_eddies/inst_eddies_Aviso.py
@@ -53,8 +53,6 @@ argparser.add_argument(
)
argparser.add_argument("first_date", help="%%Y-%%m-%%d")
argparser.add_argument("last_date", help="%%Y-%%m-%%d")
-argparser.add_argument("slice", type=int, help="slice number to create")
-argparser.add_argument("periodic", choices=["t", "f"])
argparser.add_argument(
"-b",
"--bbox",
@@ -68,19 +66,18 @@ last_date = parser.parse(args.last_date).date()
d = (first_date - datetime.date(1950, 1, 1)).days
if os.access("inst_eddies_nml.txt", os.R_OK):
- print("Will use inst_eddies_nml.txt.")
+ print("Will use inst_eddies_nml.txt, ignoring date in dates_nml...")
else:
sys.exit('"inst_eddies_nml.txt" not found -- Aborting')
inst_eddies_nml = f90nml.read("inst_eddies_nml.txt")
# We choose to use d as the first date index. We could choose anything.
+inst_eddies_nml["dates_nml"]["date"] = d
+
inst_eddies.loop_inst_eddies(
args.SHPC_dir,
filename_generator(args.template, first_date, last_date),
args.bbox,
inst_eddies_nml,
- d,
- my_slice=args.slice,
- periodic=args.periodic,
)