Lionel GUEZ authored 9 months ago and GUEZ Lionel committed 8 months ago

Do not orient nor compute the area of `cont_list(n_cont)`. When the
area is too small, then we have one more copy than before, of
`cont_list(n_cont)` to `out_cont`, but, on the other hand, we have one
less call to `ccw_orient` than before. So this change should not
impact performance. Note that the orientation and area of
`cont_list(n_cont)` were not used after `get_1_outerm`.

Preparing to keep `cont_list` in projection coordinates.

Lionel GUEZ authored 9 months ago and GUEZ Lionel committed 8 months ago

Procedure `good_contour` now takes input in projection coordinates and
returns a contour in projection coordinates. The dummy argument step
of `good_contour` is thus removed.

It is `min_area` that we need in the code, in `get_1_outerm`. Instead
of computing it in the main program and trickling it down to
`get_1_outerm`, define it in `config_m`.

Follow commit d540a1f3.

This avoids copying `cont_list(n_cont)` to `out_cont` if it has
insufficient area.

Add dummy arguments `cont_list` and `n_cont` to `get_1_outerm`.

Because we are going to add another intent out argument.

Keep the good contours found when looking for the outermost contour,
subject to a maximum of `n_max_cont` contours. The idea is to use them
later when looking for the maximum-speed contour. Inside function
`get_1_outerm`, we temporarily store the good contours in a local
explicit-shape array, `cont_list`.

Rename dummy argument `innermost_level` to `innermost_level_2`.

Since `NR_util` has been integrated into Jumble.

Also split the tests, Fortran source files, Python files and JSon
files. Keep at the top level the files used in both `Inst_eddies` and
Overlap.

Motivations for the split:

- The top directory contained many files.

- It may be useful to compile only one of the two sub-projects. For
example, only `Inst_eddies` on Ciclad, where MPI 3 is not available.

Take into account new policy in `filter.py`: the names of the three
shapefiles are always the same and form a unit in a snaphot directory.

Rename `compil_prod_dir`to `build_dir` in JSON test files. Add a test
of `successive_overlap` with global grid, normal resolution.

Take into account new policy in `filter.py`: the names of the three
shapefiles are always the same and form a unit in a snaphot directory.

Rename `compil_prod_dir`to `build_dir` in JSON test files. Add a test
of `successive_overlap` with global grid, normal resolution.

spherical_polygon_area to spher_polygon_area.

In procedure max_speed_contour_ssh, instead of aborting when the speed
is not defined, continue with missing_ssh. Found such a case in
November 29th, 2015 data. Added corresponding test. In procedure
set_max_speed, if max_speed_contour_ssh returns missing_ssh then we
just take the outermost contour as max-speed contour.

values at longitude boundaries, in case of periodicity.

Add argument "periodic" to procedures get_snapshot and
set_all_outerm. Duplicate values at longitude boundaries in ssh, u, v
if periodic. set_all_outerm can now call local_extrema with periodic
true. In procedure set_all_outerm, we shift the longitudes of outside
points if necessary.

In program test_get_snapshot, define periodic from step and nlon.

internal procedure.

In procedure local_extrema, if periodic, pass arrays "field" and
"extr_map" with a duplicate column at each bound. Then there is no
need to copy to local 3x3 arrays. Add argument my_lbound.

reading and spares some disk space: we can reduce the size of the
field from 20 to 14 characters. We do not loose precision with this
reduction because the order of magnitude of the area is 1e3 km2 or
more so the decimal part of the field was 0. Accordingly, change the
are for a null contour from - 1 to - 1e6 m2.

Bug fix in program test_set_max_speed. No need for width 20 for field "speed".

amplitude min_amp if the difference between innermost level from
local_extrema and ssh extremum is smaller. This is not only a
performance improvement but also an improvement of results: the
algorithm sometimes finds a contour at just min_amp when before it did
not find any: the bisection algorithm converged just below
min_amp. Also, as a result, if an outermost contour is found, it is
now necessarily of sufficient amplitude.

Stdin to Input. Two input dir provided for in tests.json: $input_dir
and $large_input_dir.

Rename everywhere variable nearby_extr to outside_points to avoid
confusion with function nearby_extr. Rename file "nearby_extr.csv" to
"outside_points.csv".

In procedure nearby_extr, include in the selection extrema with
different sign, even if they do not have sufficient amplitude.

Bug fix in read_eddy: use the value of read attribute to define
e%interpolated.

procedure set_all_outerm. The idea is that, in this branch,
nearby_extr will eventually include extrema depending not only on them
having sufficient amplitude but also on their cyclonicity. Both pieces
of information cannot be simply encoded in extr_map.