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).

(instead of date_index = 1). This is the value read from the NetCDF
files. We have to increase the width of field date_index to 5 digits
(4 digits would only allow approximately 30 years since 1950).

In procedure read_snapshot, check that all input eddies have the same
date index, and return it as an additional argument.

Assume that the input NetCDF files contain a single date.

In program test_set_all_outerm, do not write file
"isolated_nodes_1.csv". Since s is defined by set_all_outerm only, all
the eddies are necessarily isolated.

targetted a single main program.

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

longer a test program).

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.

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.

order to take missing value attribute into account.

input NetCDF files rather than selecting a window. Clearer and easier
to set up new tests.

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.