0ce6b1b4.

Write extr_map in test_read_snapshot since extr_map has been
defined. So create a procedure write_extr_map because now we want to
write extr_map both in test_local_extrema and in test_read_snapshot.

Preparing to take into account periodicity in successive_overlap: add
argument periodic to read_snapshot and extend s%extr_map in longitude
if periodic.

In program extraction_eddies, constraint on max_radius(1) is necessary
only if periodic.

Make read_snapshot more general: add argument step.

In procedure get_snapshot, remove definition of s%number_eddies
because this is already done in read_snapshot.

Promote dist_lim from local constant of successive_overlap to constant
of module successive_overlap_m because we need it in read_snapshot
(and test_successive_overlap and test_read_snapshot).

targetted a single main program.

In script plot_snapshot.py, with option --light, do not plot invalid
outermost contours.

after its initial computation and show more directly the consequence
of a NaN value. The drawback is the repetition of one line of code. As
for performance, one less test is performed in the case of a NaN
value.

In script stat.py, add stats for cases when speed is missing.

outside_points(1, :) if necessary in procedure get_snapshot; read
max_radius at run-time. Add a corresponding test.

procedure so it can be used by program test_set_all_outerm.

Move dummy argument corner of set_all_outerm to last position.

Bug fix in procedure get_snapshot: urc(2) must always be lower than
nlat, even if periodic is true. Fix the same bug in procedure
set_all_outerm: llc(2) >= 1 and urc(2) <= nlat even if periodic is true.

Bug fix in procedure set_all_outerm: the lower bound of dummy argument
ssh is not always 1.

Make script examine_ssh_values.py work for a periodic domain.

Make program test_set_all_outerm work for a periodic
domain. max_radius is now chosen at run-time (we must change it for
a very coarse grid). Add a corresponding test.

In written shapefiles, replace field "area" by field "r_eq_area",
that is radius of disk of equal area. This is a smaller number so it
needs fewer characters, especially for a global coarse grid.

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.

first dimension of input field. So there may be extrema on the borders
and we have to create a private procedure local_extremum.

Added scale option to script plot_snapshot.py.

validity of an eddy depending not only on its amplitude but also its
surface. (Note that, in this version, the component valid is redundant: one
can simply test the component out_cont%n_points.)

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.

corner_window for all eddies in a two-dimensional array.

hard-coding them.

Remove component twice of type eddy, no longer needed.

the logic with flat_extr and noise_around is no longer needed.

set_all_outerm: the value of component suff_amp is modified inside the
first batch of get_1_outerm.

>= 0 everywhere outside of procedure local_extrema.

In test Nearby_extr, use output from Get_snapshot_region_1_noise since
we now use suff_amp in extremum shapefile.

than extr_map /= i.

Preparing to remove the coding of sufficient amplitude in extr_map: do
not use anywhere the sign of extr_map, use the component suff_amp of
the type eddy instead.

In program test_successive_overlap, I would rather not use default
values for namelist variables.

Add a larger test for successive_overlap, to have eddies wih
insufficient amplitude in the region.

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.

instead of defining the component ssh to the ssh of the extremum or to
the ssh of the outermost contour, use a missing value flag
(1e4). Also, when radius4 >= 2 and the max speed contour is the
outermost contour, use missing value flag in the ssh component of max
speed contour instead of ssh on outermost contour. This makes clearer
output.

Add function null_ssh_contour.

In procedure get_1_outerm, simplify the comparison of level_try and
level_good. So we do not need any longer the dummy argument
ssh_extremum.

to out_cont and speed_cont (shorter names).

set_all_outerm. Thus, we have the clearer intent(out) for argument s
of set_all_outerm. Also, this prepares a possible replacement of
set_all_outerm by a procedure from the Topology toolkit.

Create test program for procedure set_all_outerm.

with some components intent(in) and one component intent(out) was less
clear. Also, replace argument ind_targ_extr by argument i. This is
simpler both in get_1_outerm and in set_all_outerm.

There is now no need to use an eddy in test_get_1_outerm.

set_all_outerm, for clarity.