files, that make up a snapshot into a directory that contains only
these files. We hope that this will ease the handling of
snapshots. For now, this is useful in program
test_successive_overlap. So, in program extraction_eddies, create the
shapefiles in a directory called Snapshot. As we cannot create the
directory from Fortran (in Fortran 2003, it becomes possible in
Fortran 2008), we have to wrap the Fortran executable in a shell
script "extraction_eddies.sh". In the same way, read from a directory
Snapshot_old in programs test_read_eddy and test_read_snapshot and
create scripts "test_read_eddy.sh" and "test_read_snapshot.sh".

Reference the shell scripts "extraction_eddies.sh",
"test_read_eddy.sh" and "test_read_snapshot.sh" in JSON test files.

In program test_successive_overlap, finally read two snapshots, from
directories Snapshot_1 and Snapshot_2. Pass to successive_overlap the
date of the second snapshot. Use new variables corner_deg and step_deg
to avoid converting to rad twice.

Create directory Snapshot in Tests/Input/Region_4/2006_01_01.

overlap, we will have to read a set of three shapefiles, extremum,
outermost_contour and max_speed_contour, containing several
snapshots. We do not want to re-read field indices for each snapshot.

Rename u, v to ugos, vgos in NetCDF files.

vgos, lon to longitude, lat to latitude.

Add a test for successive_overlap with periodic grid.

Add snapshot for region 4 at a different date, in input files, for a
new test of successive_overlap.

read_snapshot and successive_overlap instead of a named constant of
module successive_overlap_m.

Bug fix in main programs test_read_snapshot and
test_successive_overlap: take into account that step is in degrees.

not sure about this. I will stay on the safe side for now.

Support periodic grid in successive_overlap.

eddies at date "j" in a new function candidate_overlap. This reduces
the number of nested constructs from 8 to 5. Incidentally, we can now
avoid defining needlessly polyline_1 if there is no candidate at date
"j". Also the function candidate_overlap should also be called by
non_successive_overlap.

Add argument periodic to procedure successive_overlap.

In main unit test_successive_overlap, pass to successive_overlap the
date subscript returned by read_snapshot instead of an arbitrary
value. Only print delta_in and delta_out if they are /= huge.

Tests/CMakeLists.txt. This is more concise since we can merge them
with target_sources.

Bug fix: missing source file successive_overlap.f90 for target
test_read_snapshot.

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.