Remove "_1" from the names of shapefiles. That only had sense when we

targetted a single main program.

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

Analysis/plot_snapshot.py

@@ -2,7 +2,9 @@
 
 """Plots outermost contours and max-speed contours.
 
-Red for anti-cyclones, blue for cyclones. Empty circles for extrema
+Red for anti-cyclones, blue for cyclones. 
+
+Without the --light option. Empty circles for extrema
 with a valid outermost contour, empty squares for other
 extrema. Squares on outermost contour for a well-defined but invalid
 outermost contour. Crosses on outermost contour for a valid outermost
@@ -10,6 +12,9 @@ contour but with no distinct max-speed contour. Filled circles on
 outermost contour and max-speed contour for a valid outermost contour
 with a distinct max-speed contour.
 
+With the --light option. Crosses for extrema with a valid outermost
+contour.
+
 This scripts takes about 30 s of CPU for a 90° by 90° window, about 4
 mn for a 180° by 180° window.
 
@@ -118,7 +123,8 @@ for shape_rec_extr, shape_outer, shape_m_s \
                                                    src_crs),
                         xytext = (3, 3), textcoords = "offset points")
 
-        if shape_outer.shapeType != shapefile.NULL:
+        if shape_outer.shapeType != shapefile.NULL and not args.light \
+           or shape_rec_extr.record.valid:
             points = np.array(shape_outer.points)
             lines = ax.plot(points[:, 0], points[:, 1], color = color,
                             transform = src_crs)

Tests/short_tests.json

@@ -204,32 +204,32 @@
 	"args": "$compil_prod_dir/test_read_eddy",
 	"required":
 	[
-	    ["$input_dir/Region_4/extremum_1.dbf", "extremum_1_old.dbf"],
-	    ["$input_dir/Region_4/extremum_1.shp", "extremum_1_old.shp"],
-	    ["$input_dir/Region_4/extremum_1.shx", "extremum_1_old.shx"],
+	    ["$input_dir/Region_4/extremum.dbf", "extremum_old.dbf"],
+	    ["$input_dir/Region_4/extremum.shp", "extremum_old.shp"],
+	    ["$input_dir/Region_4/extremum.shx", "extremum_old.shx"],
 	    [
-		"$input_dir/Region_4/max_speed_contour_1.dbf",
-		"max_speed_contour_1_old.dbf"
+		"$input_dir/Region_4/max_speed_contour.dbf",
+		"max_speed_contour_old.dbf"
 	    ],
 	    [
-		"$input_dir/Region_4/max_speed_contour_1.shp",
-		"max_speed_contour_1_old.shp"
+		"$input_dir/Region_4/max_speed_contour.shp",
+		"max_speed_contour_old.shp"
 	    ],
 	    [
-		"$input_dir/Region_4/max_speed_contour_1.shx",
-		"max_speed_contour_1_old.shx"
+		"$input_dir/Region_4/max_speed_contour.shx",
+		"max_speed_contour_old.shx"
 	    ],
 	    [
-		"$input_dir/Region_4/outermost_contour_1.dbf",
-		"outermost_contour_1_old.dbf"
+		"$input_dir/Region_4/outermost_contour.dbf",
+		"outermost_contour_old.dbf"
 	    ],
 	    [
-		"$input_dir/Region_4/outermost_contour_1.shp",
-		"outermost_contour_1_old.shp"
+		"$input_dir/Region_4/outermost_contour.shp",
+		"outermost_contour_old.shp"
 	    ],
 	    [
-		"$input_dir/Region_4/outermost_contour_1.shx",
-		"outermost_contour_1_old.shx"
+		"$input_dir/Region_4/outermost_contour.shx",
+		"outermost_contour_old.shx"
 	    ]
 	],
 	"title": "Read_eddy"
@@ -238,32 +238,32 @@
 	"args": "$compil_prod_dir/test_read_snapshot",
 	"required":
 	[
-	    ["$input_dir/Region_4/extremum_1.dbf", "extremum_1_old.dbf"],
-	    ["$input_dir/Region_4/extremum_1.shp", "extremum_1_old.shp"],
-	    ["$input_dir/Region_4/extremum_1.shx", "extremum_1_old.shx"],
+	    ["$input_dir/Region_4/extremum.dbf", "extremum_old.dbf"],
+	    ["$input_dir/Region_4/extremum.shp", "extremum_old.shp"],
+	    ["$input_dir/Region_4/extremum.shx", "extremum_old.shx"],
 	    [
-		"$input_dir/Region_4/max_speed_contour_1.dbf",
-		"max_speed_contour_1_old.dbf"
+		"$input_dir/Region_4/max_speed_contour.dbf",
+		"max_speed_contour_old.dbf"
 	    ],
 	    [
-		"$input_dir/Region_4/max_speed_contour_1.shp",
-		"max_speed_contour_1_old.shp"
+		"$input_dir/Region_4/max_speed_contour.shp",
+		"max_speed_contour_old.shp"
 	    ],
 	    [
-		"$input_dir/Region_4/max_speed_contour_1.shx",
-		"max_speed_contour_1_old.shx"
+		"$input_dir/Region_4/max_speed_contour.shx",
+		"max_speed_contour_old.shx"
 	    ],
 	    [
-		"$input_dir/Region_4/outermost_contour_1.dbf",
-		"outermost_contour_1_old.dbf"
+		"$input_dir/Region_4/outermost_contour.dbf",
+		"outermost_contour_old.dbf"
 	    ],
 	    [
-		"$input_dir/Region_4/outermost_contour_1.shp",
-		"outermost_contour_1_old.shp"
+		"$input_dir/Region_4/outermost_contour.shp",
+		"outermost_contour_old.shp"
 	    ],
 	    [
-		"$input_dir/Region_4/outermost_contour_1.shx",
-		"outermost_contour_1_old.shx"
+		"$input_dir/Region_4/outermost_contour.shx",
+		"outermost_contour_old.shx"
 	    ]
 	],
 	"title": "Read_snapshot",
@@ -294,15 +294,15 @@
 	"required":
 	[
 	    [
-		"$tests_old_dir/Extraction_eddies_region_1_noise/extremum_1.shp",
+		"$tests_old_dir/Extraction_eddies_region_1_noise/extremum.shp",
 		"extremum.shp"
 	    ],
 	    [
-		"$tests_old_dir/Extraction_eddies_region_1_noise/extremum_1.shx",
+		"$tests_old_dir/Extraction_eddies_region_1_noise/extremum.shx",
 		"extremum.shx"
 	    ],
 	    [
-		"$tests_old_dir/Extraction_eddies_region_1_noise/extremum_1.dbf",
+		"$tests_old_dir/Extraction_eddies_region_1_noise/extremum.dbf",
 		"extremum.dbf"
 	    ],
 	    [
@@ -317,9 +317,9 @@
 	"description": "Same as Successive_overlap, but with larger domain: region 5 instead of region 4.",
 	"required":
 	[
-	    "$tests_old_dir/Extraction_eddies_region_5/extremum_1.*",
-	    "$tests_old_dir/Extraction_eddies_region_5/max_speed_contour_1.*",
-	    "$tests_old_dir/Extraction_eddies_region_5/outermost_contour_1.*"
+	    "$tests_old_dir/Extraction_eddies_region_5/extremum.*",
+	    "$tests_old_dir/Extraction_eddies_region_5/max_speed_contour.*",
+	    "$tests_old_dir/Extraction_eddies_region_5/outermost_contour.*"
 	],
 	"stdin_filename": "$input_dir/successive_overlap_region_5_nml.txt"
     },

Tests/test_read_eddy.f

@@ -14,16 +14,16 @@ program test_read_eddy
 
   type(eddy) e
   integer k, i
-  TYPE(shpfileobject) hshp_extremum ! shapefile extremum_1
-  TYPE(shpfileobject) hshp_outermost ! shapefile outermost_contour_1
-  TYPE(shpfileobject) hshp_max_speed ! shapefile max_speed_contour_1
+  TYPE(shpfileobject) hshp_extremum ! shapefile extremum
+  TYPE(shpfileobject) hshp_outermost ! shapefile outermost_contour
+  TYPE(shpfileobject) hshp_max_speed ! shapefile max_speed_contour
 
   !-------------------------------------------------------------------------
 
-  call shp_open_03("extremum_1_old", pszaccess = "rb", hshp = hshp_extremum)
-  call shp_open_03("outermost_contour_1_old", pszaccess = "rb", &
+  call shp_open_03("extremum_old", pszaccess = "rb", hshp = hshp_extremum)
+  call shp_open_03("outermost_contour_old", pszaccess = "rb", &
        hshp = hshp_outermost)
-  call shp_open_03("max_speed_contour_1_old", pszaccess = "rb", &
+  call shp_open_03("max_speed_contour_old", pszaccess = "rb", &
        hshp = hshp_max_speed)
   call read_field_indices(hshp_extremum, hshp_outermost, hshp_max_speed)
   call read_eddy(e, k, i, hshp_extremum, hshp_outermost, hshp_max_speed, &
@@ -35,10 +35,10 @@ program test_read_eddy
   call init_shapefiles(hshp_extremum, hshp_outermost, hshp_max_speed)
   call write_eddy(e, k, i, hshp_extremum, hshp_outermost, hshp_max_speed)
   CALL shpclose(hshp_extremum)
-  print *, 'Created shapefile "extremum_1".'
+  print *, 'Created shapefile "extremum".'
   CALL shpclose(hshp_outermost)
-  print *, 'Created shapefile "outermost_contour_1".'
+  print *, 'Created shapefile "outermost_contour".'
   CALL shpclose(hshp_max_speed)
-  print *, 'Created shapefile "max_speed_contour_1".'
+  print *, 'Created shapefile "max_speed_contour".'
 
 end program test_read_eddy

Tests/test_read_snapshot.f

@@ -15,9 +15,9 @@ program test_read_snapshot
   implicit none
 
   type(snapshot) s
-  TYPE(shpfileobject) hshp_extremum ! shapefile extremum_1
-  TYPE(shpfileobject) hshp_outermost ! shapefile outermost_contour_1
-  TYPE(shpfileobject) hshp_max_speed ! shapefile max_speed_contour_1
+  TYPE(shpfileobject) hshp_extremum ! shapefile extremum
+  TYPE(shpfileobject) hshp_outermost ! shapefile outermost_contour
+  TYPE(shpfileobject) hshp_max_speed ! shapefile max_speed_contour
   integer i
 
   real:: corner(2) = [0.125, - 59.875]
@@ -33,10 +33,10 @@ program test_read_snapshot
   read(unit = *, nml = main_nml)
   write(unit = *, nml = main_nml)
 
-  call shp_open_03("extremum_1_old", pszaccess = "rb", hshp = hshp_extremum)
-  call shp_open_03("outermost_contour_1_old", pszaccess = "rb", &
+  call shp_open_03("extremum_old", pszaccess = "rb", hshp = hshp_extremum)
+  call shp_open_03("outermost_contour_old", pszaccess = "rb", &
        hshp = hshp_outermost)
-  call shp_open_03("max_speed_contour_1_old", pszaccess = "rb", &
+  call shp_open_03("max_speed_contour_old", pszaccess = "rb", &
        hshp = hshp_max_speed)
   call read_snapshot(s, hshp_extremum, hshp_outermost, hshp_max_speed, &
        corner * deg_to_rad, nlon, nlat)
@@ -54,11 +54,11 @@ program test_read_snapshot
 
   print *, "Number of extrema:", s%number_vis_extr
   CALL shpclose(hshp_extremum)
-  print *, 'Created shapefile "extremum_1".'
+  print *, 'Created shapefile "extremum".'
   CALL shpclose(hshp_outermost)
-  print *, 'Created shapefile "outermost_contour_1".'
+  print *, 'Created shapefile "outermost_contour".'
   CALL shpclose(hshp_max_speed)
-  print *, 'Created shapefile "max_speed_contour_1".'
+  print *, 'Created shapefile "max_speed_contour".'
 
   print *, "s%ind_extr:"
 

Tests/test_successive_overlap.f

@@ -16,9 +16,9 @@ program test_successive_overlap
 
   integer unit_edgelist, i
   type(snapshot) flow(2)
-  TYPE(shpfileobject) hshp_extremum ! shapefile extremum_1
-  TYPE(shpfileobject) hshp_outermost ! shapefile outermost_contour_1
-  TYPE(shpfileobject) hshp_max_speed ! shapefile max_speed_contour_1
+  TYPE(shpfileobject) hshp_extremum ! shapefile extremum
+  TYPE(shpfileobject) hshp_outermost ! shapefile outermost_contour
+  TYPE(shpfileobject) hshp_max_speed ! shapefile max_speed_contour
 
   real:: corner(2) = [huge(0.), huge(0.)]
   ! longitude and latitude of the corner of the whole grid, in degrees
@@ -33,10 +33,10 @@ program test_successive_overlap
   read(unit = *, nml = main_nml)
   write(unit = *, nml = main_nml)
 
-  call shp_open_03("extremum_1", pszaccess = "rb", hshp = hshp_extremum)
-  call shp_open_03("outermost_contour_1", pszaccess = "rb", &
+  call shp_open_03("extremum", pszaccess = "rb", hshp = hshp_extremum)
+  call shp_open_03("outermost_contour", pszaccess = "rb", &
        hshp = hshp_outermost)
-  call shp_open_03("max_speed_contour_1", pszaccess = "rb", &
+  call shp_open_03("max_speed_contour", pszaccess = "rb", &
        hshp = hshp_max_speed)
   call read_snapshot(flow(1), hshp_extremum, hshp_outermost, hshp_max_speed, &
        corner * deg_to_rad, nlon, nlat)

extraction_eddies.f

@@ -91,8 +91,6 @@ program extraction_eddies
   call nf95_get_var(ncid, varid, lat_min)
   call nf95_get_var(ncid, varid, lat_max, start = [nlat])
 
-  call nf95_close(ncid)
-
   call assert(lon_max > lon_min .and. lat_max > lat_min, &
        "extraction_eddies coordinate order")
   step = [(lon_max - lon_min) / (nlon - 1), (lat_max - lat_min) / (nlat - 1)]  &
@@ -112,7 +110,6 @@ program extraction_eddies
 
   ! Read ssh, u and v at date k:
 
-  call nf95_open("h.nc", nf90_nowrite, ncid)
   call get_var(periodic, max_radius(1), ssh, ncid, nlon, k, name = "adt", &
        new_fill_value = huge(0.))
   ! (We cannot keep the original fill value because Contour_531

init_shapefiles.f

@@ -28,7 +28,7 @@ contains
 
     !---------------------------------------------------------------------
 
-    call shp_create_03("extremum_1", shpt_point, hshp_extremum)
+    call shp_create_03("extremum", shpt_point, hshp_extremum)
     call dbf_add_field_03(ifield_extr_ssh, hshp_extremum, 'ssh', ftdouble, &
          nwidth = 13, ndecimals = 6)
     call dbf_add_field_03(ifield_extr_date, hshp_extremum, 'date_index', &
@@ -44,7 +44,7 @@ contains
     call dbf_add_field_03(ifield_extr_speed, hshp_extremum, 'speed', ftdouble, &
          nwidth = 13, ndecimals = 6)
 
-    call shp_create_03("outermost_contour_1", shpt_polygon, hshp_outermost)
+    call shp_create_03("outermost_contour", shpt_polygon, hshp_outermost)
     call dbf_add_field_03(ifield_out_r_eq_area, hshp_outermost, &
          'r_eq_area', ftdouble, nwidth = 10, ndecimals = 4)
     call dbf_add_field_03(ifield_out_ssh, hshp_outermost, 'ssh', ftdouble, &
@@ -56,7 +56,7 @@ contains
     call dbf_add_field_03(ifield_out_radius4, hshp_outermost, 'radius4', &
          ftinteger, nwidth = 2, ndecimals = 0)
 
-    call shp_create_03("max_speed_contour_1", shpt_polygon, hshp_max_speed)
+    call shp_create_03("max_speed_contour", shpt_polygon, hshp_max_speed)
     call dbf_add_field_03(ifield_max_speed_r_eq_area, hshp_max_speed, &
          'r_eq_area', ftdouble, nwidth = 10, ndecimals = 4)
     call dbf_add_field_03(ifield_max_speed_ssh, hshp_max_speed, 'ssh', &

set_all_outerm.f

@@ -141,6 +141,7 @@ contains
        if (abs(s%list_vis(i)%ssh_extr - innermost_level(i)) < min_amp) &
             innermost_level(i) = s%list_vis(i)%ssh_extr &
             + merge(min_amp, - min_amp, s%list_vis(i)%cyclone)
+       
        outside_points = nearby_extr(s%extr_map(llc(1):urc(1), llc(2):urc(2)), &
             s%list_vis, i)
        if (periodic) outside_points(1, :) = outside_points(1, :) &