unit test_get_snapshot. get_snapshot reads from shapefiles instead of
netCDF files.

Bug fix: programs test_get_snapshot and test_read_snapshot do not need
dispatch_snapshot.f and send_snapshot.f.

Procedures dispatch_snapshot, get_snapshot, send_snapshot and
receive_snapshot are no longer referenced, for now. They will be
called by the overlap program.

extraction of eddies and overlapping.

Procedure dispatch_snapshot will be called by the overlap program and
will not write eddies. So remove the calls to write_eddy from
dispatch_snapshot and move them to test_get_snapshot and
test_read_snapshot.

Do not create files isolated_nodes_1.csv and number_eddies_1.csv in
test_get_snapshot and test_read_snapshot, that will be done by the
overlap program.

distribution_function. This allows to plot comparisons of various
combinations of runs.

Update plot_snapshot.py to work with version 2 of pyshp.

script distribution_function.py. Return dictionary instead of tuple:
easier to use.

In script plot_snapshot.py, move definition of readers to the
beginning so there is no risk of entering the window for nothing if we
forgot the end_filename option. Also, enter the four values defining
the window in a single input: easier to copy and paste.

distribution_function.py. Plot two distribution functions and two
histograms for positive speed and absolute value of negative speed.

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.

and debugging options, short tests each take less than 10 s, while
long tests each take about one mn.

Bug fix in plot_snapshot.py. Slicing a multiple-dimension array with a
scalar logical does not produce an array with the same shape.

Removed computations of number of points per contour from program
test_get_snapshot. Created instead a post-processing script, stat.py,
computing these numbers of points and other stats.

plot the grid. Incorporate the functionality of script
plot_snapshot_light.py into script plot_snapshot.py, with option
--light, to avoid duplication of source code.

the possibility to restrict the plotted domain because the script
takes a very long time for a global domain.

known bug since three years for plots that go back and forth across
the map longitudinal boundary.

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.

longitude and latitude instead of second longitude and latitude to
compute step. This divides the rounding error on step by a factor nlon
or nlat.

and test_set_all_outerm.

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.

not six significant decimal digits.

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".

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.