added exception to catch bathymetries with zeros along boundaries as PyNEMO...

added exception to catch bathymetries with zeros along boundaries as PyNEMO mask generator doesn't support

pynemo/gui/nemo_bdy_mask.py

@@ -93,10 +93,12 @@ class Mask(object):
                     self.data = self.bathy_nc.variables['Bathymetry']
                 except:
                     self.data = self.bathy_nc.variables['deptho']
+                if sum(self.data[:, 0]) + sum(self.data[0, :]) + sum(self.data[:, -1]) + sum(self.data[-1, :]) == 0:
+                    raise BaseException('zeros around boundaries of bathymetry is not supported by PyNEMO mask generator')
                 self.data = np.asarray(self.data[:, :])
                 self.data = np.around((self.data + .5).clip(0, 1))
                 #apply default 1px border
-                self.apply_border_mask(1)            
+                self.apply_border_mask(1)
         except KeyError:
             self.logger.error('Bathymetry file does not have Bathymetry variable')
             raise
@@ -105,6 +107,7 @@ class Mask(object):
             raise
 
 
+
     def save_mask(self, mask_file):
         """Reads the mask data from the mask file"""
         if mask_file == None:

pynemo/profile.py

@@ -694,6 +694,9 @@ 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