fixed start end date indexing

inputs/namelist_cmems.bdy

@@ -38,7 +38,7 @@
    sn_bathy   = 'http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_grid_C/NNA_R12_bathy_meter_bench.nc'
 
 !------------------------------------------------------------------------------
-!  I/O 
+!  I/O
 !------------------------------------------------------------------------------
    sn_src_dir      = '/Users/thopri/Projects/PyNEMO/inputs/CMEMS.ncml' ! src_files/'
    sn_dst_dir      = '/Users/thopri/Projects/PyNEMO/outputs'
@@ -49,7 +49,7 @@
    nn_fv      = -1e20                 !  set fill value for output files
    nn_src_time_adj = 0                ! src time adjustment
    sn_dst_metainfo = 'CMEMS example'
-   
+
 !------------------------------------------------------------------------------
 !  CMEMS Data Source Configuration
 !------------------------------------------------------------------------------
@@ -85,10 +85,10 @@
    nn_depth_max             = 5727.918000000001
 
 !------------------------------------------------------------------------------
-!  unstructured open boundaries                         
+!  unstructured open boundaries
 !------------------------------------------------------------------------------
     ln_coords_file = .true.               !  =T : produce bdy coordinates files
-    cn_coords_file = 'coordinates.bdy.nc' !  name of bdy coordinates files 
+    cn_coords_file = 'coordinates.bdy.nc' !  name of bdy coordinates files
                                           !  (if ln_coords_file=.TRUE.)
     ln_mask_file   = .false.              !  =T : read mask from file
     cn_mask_file   = 'mask.nc'            !  name of mask file
@@ -98,11 +98,11 @@
     ln_dyn3d       = .true.              !  boundary conditions for
                                           !  baroclinic velocities
     ln_tra         = .true.               !  boundary conditions for T and S
-    ln_ice         = .false.              !  ice boundary condition   
+    ln_ice         = .false.              !  ice boundary condition
     nn_rimwidth    = 9                    !  width of the relaxation zone
 
 !------------------------------------------------------------------------------
-!  unstructured open boundaries tidal parameters                        
+!  unstructured open boundaries tidal parameters
 !------------------------------------------------------------------------------
     ln_tide        = .false.              !  =T : produce bdy tidal conditions
     sn_tide_model  = 'fes'                !  Name of tidal model (fes|tpxo)
@@ -139,13 +139,13 @@
 	sn_tide_u      = '/Users/thopri/Projects/PyNEMO/DATA/TPXO/u_tpxo7.2.nc'
 	! location of FES data
 	sn_tide_fes      = '/Users/thopri/Projects/PyNEMO/DATA/FES/'
-	
+
 !------------------------------------------------------------------------------
 !  Additional parameters
 !------------------------------------------------------------------------------
-    nn_wei  = 1                   !  smoothing filter weights 
+    nn_wei  = 1                   !  smoothing filter weights
     rn_r0   = 0.041666666         !  decorrelation distance use in gauss
-                                  !  smoothing onto dst points. Need to 
+                                  !  smoothing onto dst points. Need to
                                   !  make this a funct. of dlon
     sn_history  = 'CMEMS test case'
                                   !  history for netcdf file
@@ -154,4 +154,4 @@
     nn_beta     = 0               !  Euler rotation angle
     nn_gamma    = 0               !  Euler rotation angle
 	rn_mask_max_depth = 100.0     !  Maximum depth to be ignored for the mask
-	rn_mask_shelfbreak_dist = 20000.0 !  Distance from the shelf break
+	rn_mask_shelfbreak_dist = 20000.0 !  Distance from the shelf break
\ No newline at end of file

pynemo/nemo_bdy_extr_tm3.py

@@ -473,13 +473,25 @@ class Extract:
         rev_seq = list(range(len(sc_time.time_counter)))
         rev_seq.reverse()
         for date in rev_seq:
-            if src_date_seconds[date] <= dst_start:
-                first_date = date
-                break
+            try:
+                if src_date_seconds[date-1] <= dst_start <= src_date_seconds[date]:
+                    first_date = date
+                    break
+            except IndexError:
+                if src_date_seconds[date] == dst_start:
+                    first_date = date
+                else:
+                    logging.error('Start date not found in source data')
         for date in range(len(sc_time.time_counter)):
-            if src_date_seconds[date] >= dst_end:
-                last_date = date
-                break
+            try:
+                if src_date_seconds[date] <= dst_end <= src_date_seconds[date+1]:
+                    last_date = date
+                    break
+            except IndexError:
+                if src_date_seconds[date] == dst_end:
+                    last_date = date
+                else:
+                    logging.error('End date not found in source data,')
 
         self.logger.info('first/last dates: %s %s', first_date, last_date)
 

pynemo/nemo_bdy_gen_c.py

@@ -78,7 +78,8 @@ class Boundary:
         try:
             msk = np.pad(bdy_msk,((1,1),(1,1)), 'constant', constant_values=(-1))
         except ValueError:
-            raise Exception('the ValueError above is commonly due to PyNEMO not finding the bathymetry/mask file')
+            raise Exception('the ValueError above is commonly due to PyNEMO not finding the bathymetry/mask file or '
+                            'in a incompatable format. E.g. there are zeros along all borders of bathy file...')
         # create index arrays of I and J coords
         igrid, jgrid = np.meshgrid(np.arange(bdy_msk.shape[1]), np.arange(bdy_msk.shape[0]))
 

pynemo/profile.py

@@ -722,9 +722,6 @@ def _get_mask(Setup, mask_gui):
                 mask = Mask_File(Setup.settings['bathy'])
                 mask.apply_border_mask(Constants.DEFAULT_MASK_PIXELS)
                 bdy_msk = mask.data
-        except BaseException:
-            raise Exception('PyNEMO mask generator does not support zeros along all '
-                            'boundaries please use valid bathymetry or mask file')
         except:
             return
     

test_scripts/bdy_coords_plot.py

@@ -15,7 +15,7 @@ from mpl_toolkits.basemap import Basemap
 
 from pynemo.tests import bdy_coords as bdc
 
-bdc.process_bdy('/Users/thopri/Projects/PyNEMO/inputs/namelist_cmems.bdy',False)
+bdc.process_bdy('/inputs/namelist_cmems.bdy', False)
 
 rootgrp = Dataset('/Users/thopri/Projects/PyNEMO/outputs/NNA_R12_bdyT_y1979m11.nc', "r", format="NETCDF4")
 bdy_msk = np.squeeze(rootgrp.variables['bdy_msk'][:]) - 1