Patch for errors in NASA OceanColor L3 nc files. Specially fix the UD…

… flip issue. (#8380)

NASA MODIS L3 grids are a mess, with wrong coordinates and the valid_min/max attributes in opposite order of that of the lat vector. That is, the lat vector is top-down but valid_min = -90 and valid_max = 90. Furthermore, the grid is grid-registered and the start lat should be -90 + 180/4321/2 = -89.97917148808146 but it wrongly starts at -89.979171752929688 (well ends at this number because the vec is top-down). Same mess with the lon vector.

src/gmt_gdalread.c

@@ -446,6 +446,9 @@ GMT_LOCAL int gmtgdalread_populate_metadata (struct GMT_CTRL *GMT, struct GMT_GD
 
  Ctrl->RasterCount = raster_count = GDALGetRasterCount(hDataset);
 
+ if (raster_count == 0)
+ GMT_Report(GMT->parent, GMT_MSG_ERROR, "No layers found in this file. Likely data is stored in SUBDATASETS\n.Must provide the SUBDATASET name.\n");
+
  /* ------------------------------------------------------------------------- */
  /* Get some metadata for each band. */
  /* ------------------------------------------------------------------------- */

src/gmt_nc.c

@@ -688,6 +688,19 @@ GMT_LOCAL int gmtnc_grd_info (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *head
  nc_get_att_double (ncid, ids[HH->xy_dim[0]], "valid_max", &dummy[1])));
 
  if (has_vector && has_range) { /* Has both so we can do a basic sanity check */
+
+ if ((strstr(HH->name, ".L3m.") != NULL) && ((strstr(HH->name, "_MODIS") != NULL) || (strstr(HH->name, "_VIIRS") != NULL))) {
+ /* Patch for the OceanColor level 3 gids that have WRONG coordinates, and advertize a PIXEL registration
+ valid_min|max whilst their lon vector is GRID registered.
+ */
+ double inc;
+ dummy[0] = -180.0 + 180.0 / (header->n_columns + 1); xy[0] = dummy[0];
+ dummy[1] = 180.0 - 180.0 / (header->n_columns + 1);
+ inc = gmt_M_get_inc(GMT, dummy[0], dummy[1], header->n_columns, registration);
+ for (unsigned k = 1; k < header->n_columns; k++)
+ xy[k] = xy[0] + k * inc;
+ }
+
  threshold = (0.5+GMT_CONV5_LIMIT) * dx;
  min = xy[0]; max = xy[header->n_columns-1];
  if (min > max) gmt_M_double_swap (min, max); /* Got it backwards in the array */
@@ -743,13 +756,6 @@ GMT_LOCAL int gmtnc_grd_info (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *head
  if (gmt_M_is_dnan(header->inc[GMT_X]) || gmt_M_is_zero (header->inc[GMT_X])) header->inc[GMT_X] = 1.0;
  if (header->n_columns == 1) registration = GMT_GRID_PIXEL_REG; /* The only way to have a grid like that */
 
-#ifdef NC4_DEBUG
- GMT_Report (GMT->parent, GMT_MSG_WARNING, "x registration: %u\n", header->registration);
- GMT_Report (GMT->parent, GMT_MSG_WARNING, "x dummy: %g %g\n", dummy[0], dummy[1]);
- GMT_Report (GMT->parent, GMT_MSG_WARNING, "x[0] x[nx-1]: %g %g\n", xy[0], xy[header->n_columns-1]);
- GMT_Report (GMT->parent, GMT_MSG_WARNING, "xinc: %g %g\n", header->inc[GMT_X]);
-#endif
-
  /* Extend x boundaries by half if we found pixel registration */
  if (registration == GMT_GRID_NODE_REG && header->registration == GMT_GRID_PIXEL_REG)
  header->wesn[XLO] = dummy[0] - header->inc[GMT_X] / 2.0,
@@ -786,6 +792,14 @@ GMT_LOCAL int gmtnc_grd_info (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *head
  if (has_vector && has_range) { /* Has both so we can do a basic sanity check */
  threshold = (0.5+GMT_CONV5_LIMIT) * dy;
  min = xy[0]; max = xy[header->n_rows-1];
+
+ /* Need to do this here because NASA MODIS L3 grids are a mess, with wrong coordinates and the valid_min/max attributes 
+ in opposite order of that of the lat vector. That is, the lat vector is top-down but valid_min = -90 and valid_max = 90.
+ Furthermore, the grid is grid-registered and the start lat should be -90 + 180/4321/2 = -89.97917148808146 but it wrongly
+ starts at -89.979171752929688 (well ends at this number because the vec is top-down). Same mess with the lon vector.
+ */
+ if (min > max) HH->row_order = k_nc_start_north;
+
  if (min > max) gmt_M_double_swap (min, max); /* Got it backwards in the array */
  if (fabs (dummy[0] - min) > threshold || fabs (dummy[1] - max) > threshold) {
  if (gmtnc_not_obviously_polar (dummy)) {
@@ -807,7 +821,19 @@ GMT_LOCAL int gmtnc_grd_info (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *head
  }
  }
  else {
- GMT_Report (GMT->parent, GMT_MSG_WARNING, "The y-coordinates and range attribute are in conflict but range is exactly 180; we rely on this range\n");
+ if ((strstr(HH->name, ".L3m.") != NULL) && ((strstr(HH->name, "_MODIS") != NULL) || (strstr(HH->name, "_VIIRS") != NULL))) {
+ /* Patch for the OceanColor level 3 gids that have WRONG coordinates, and advertize a PIXEL registration
+ valid_min|max whilst their lat vector is GRID registered.
+ */
+ double inc;
+ dummy[0] = -90.0 + 180.0 / (header->n_rows + 1); xy[0] = dummy[0];
+ dummy[1] = 90.0 - 180.0 / (header->n_rows + 1);
+ inc = gmt_M_get_inc(GMT, dummy[0], dummy[1], header->n_rows, registration);
+ for (unsigned int k = 1; k < header->n_rows; k++)
+ xy[k] = xy[0] + k * inc;
+ }
+ else
+ GMT_Report (GMT->parent, GMT_MSG_WARNING, "The y-coordinates and range attribute are in conflict but range is exactly 180; we rely on this range\n");
  if ((header->n_rows%2) == 1 && header->registration == GMT_GRID_NODE_REG) /* Pixel registration? */
  GMT_Report (GMT->parent, GMT_MSG_WARNING, "Guessing of registration in conflict between x and y, using %s\n", regtype[header->registration]);
  else