init_shapefiles. This allows us to have variables for DBF field
numbers, as module variables. We avoid the burden of passing this
large number of variables as arguments to write_eddy. Safer to have
variables for DBF field numbers than relying on the order of those
fields.

Remove file_list. This was a duplication of information.

Use named constant for missing max speed value. It is used in two procedures.

to 1e4, safer too.

src_test_get_snapshot.

Move field speed from DBF file max_speed_contour to DBF file extremum
because it can be associated to either the contour in
outermost_contour or in max_speed_contour.

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.

of local variable radius in procedure set_max_speed. Add corresponding
column in outermost_contour DBF file. This is just a diagnostic of the
workings of get_snapshot. Clearer to have this output than having
special meaning in components ssh and area of speed_cont.

weight. So, in procedure set_max_speed, in case radius equals 1, set
e%max_speed to the speed on the outermost contour instead of zero.

In procedure set_max_speed, in case the highest speed is on the
outermost contour, set e%speed_cont%polyline to null_polyline instead
of e%out_cont%polyline. This saves main memory and there is less
copying to do.

speed_cont can now be null even if max_speed is not zero so change
test for null shape in procedure write_eddy.

It appears that the shapelib C library cannot write a NaN value to a
dbf file, so write 1e4 instead.

Bug fix in plot_snapshot.py.

to out_cont and speed_cont (shorter names).

Propagate change in shapelib_03: shp_append_simple_object_03 to
shp_append_object_03.

and signalling NaN so we cannot use the -ffpe-trap=invalid option.

Accept that we might not be able to compute the mean speed on the
outermost contour: there might be undefined values of velocity
around. In that case just use the contour coming from
max_speed_contour_ssh.

Add quiver_key in plot_snapshot.py.

New test for region 5.

procedure set_all_outerm. So do not define and output null max-speed
contours.

Bug fix in program test_set_all_outerm: take into account missing
values in ADT.

Make plot_snapshot.py work even if there is no max-speed contour
shapefile. So we can use plot_snapshot.py on results of program
test_set_all_outerm.

For ssh, missing value is huge(0.). We have to take a large value
because Contour_531 has an argument zmax for missing values. For
velocity, missing value is a quiet NaN. We have to take this because
we need to know if the interpolation procedure in mean_speed has not
used any missing value and we do not want to alter the interpolation
procedure itself.

In local_extrema, we accept as local extrema only points with 8 valid
values around them.

When we look for the maximum speed contour, we are hoping that good
contours do not englobe missing values. If this happens, the program
aborts.

When computing the mean speed on a contour, we are hoping that the
interpolation of speed on contour points does not use missing
values. If this happens, the program aborts.

Draw coastlines in plot_snaphot.py. At the same time, this allows the
use of any projection.

because the order is not obvious.

In test_mean_speed and test_set_max_speed, do not read primary
variables with nf95_gw_var so the primary variables are allowed to
have or not a degenerate dimension.

level max_speed_contour_ssh, take outermost contour as max-speed
contour.

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.

program behavior.

In plot_snapshot.py, no need to accumulate all content of shapefile
extremum_1, just process it record by record, as for other shapefiles.

remember the order of positional arguments so we rather use fixed
input file names and no arguments.

namelist input. Also, choose name of primary NetCDF variable in
namelist and read only this variable, not its coordinates. This makes
it easier to use an arbitrary NetCDF file.

In program test_set_outermost_contour, it is hard to remember the
order of positional arguments so we rather use fixed input file names
and no arguments.

In JSON input file for tests, it is simpler to use the "input" key
than creating a one-line input file, in some cases.

out-of-range index so add min when calculating urc.

Bug fix in procedure good_contour. polygon_contains_point should not
be called if polyline is not closed.

Procedure polygon_contains_point became unpure so remove pure for
procedure inside_4 too.

In program test_good_contour, read corner and step from namelist
rather than from coordinates in NetCDF file. Makes it possible to use
the same NetCDF file with different coordinates. Also read
outside_points from a file rather than standard input so there is no
need to specify in advance the number of outside points.

Take into account the possibility that no outermost contour was found
in program test_set_outermost_contour. Also, use fixed names for input
files because it is not convenient to require a particular order of
these two files on the command line.

defined. Also, allow test_set_outermost_contour to read ssh from a
NetCDF variable with a degenerate time coordinate or with no time
coordinante.

"stdout" key became optional in "tests.json" and "directory" key
became "title", with no indication of directory.

contour.

Read whole NetCDF files in program test_set_outermost_contour instead
of specifying a reading window. Simpler to prepare a file outside
the Fortran program, as in program test_local_extrema. Also, compute
step from read longitude and latitude.

contour no longer means that the eddy is interpolated.

acceptable. So define flat_extr by a strict inequality in procedure
get_snapshot.

Procedure set_outermost_contour no longer has a dummy argument
noise_around. We no longer call outermost_possible_level so we do not
have an artificial discontinuity of results with and without maximum
amplitude. We abandon the idea of reducing the amplitude of initial
level_good compared to innermost_level: problem of consistence with
get_snapshot, and it does not seem worth the trouble, just abandon
those problematic extrema. Allow for null outermost_contour instead of
aborting.

In procedure get_snapshot, s%list_vis(i)%suff_amp is first defined
only if flat_extr(i). Also we are no longer sure that
set_outermost_contour finds an outermost contour so we have to test
this to define s%list_vis(i)%suff_amp. noise_around is now defined
only for flat_extr(i) and s%list_vis(i)%suff_amp. Also, since we may
not find an outermost contour even if not flat_extr(i), we update
s%extr_map after the second call to set_outermost_contour.

In procedure local_extrema, we use the mask diff_center instead of
mask_center. So we no longer need procedure construct_mask_center. In
procedure local_extrema, we ignore one in two adjacent degenerate
extrema instead of aborting.

In plot_snapshot.py, color extrema and allow for null outermost
contour.

Synthesize output in test_local_extrema.py.

procedure inside was used in previous commits, but inside_4 is based
on polygon_contains_point.

In procedure set_max_speed, extend the search for radius beyond the
value provided by polygon_point_dist_2d. We are now certain that
ind_extr + radius is outside. We recover the value of radius that was
computed by inside assuming no degeneracy.

degenerate cases. Also, in procedure set_max_speed, I do not like
changing algorithms and results when going to min_amp = 0, and there
is no real meaning for this change.