Merge pull request #124 from ec-jrc/development

Coords from netcdf template

VERSION

@@ -1 +1 @@
-4.1.1
+4.1.2

src/lisflood/__init__.py

@@ -10,7 +10,7 @@
 
 __version__ = version
 __authors__ = "Ad de Roo, Emiliano Gelati, Peter Burek, Johan van der Knijff, Niko Wanders"
-__date__ = "09/06/2022"
-__copyright__ = "Copyright 2019-2022, European Commission - Joint Research Centre"
+__date__ = "22/03/2023"
+__copyright__ = "Copyright 2019-2023, European Commission - Joint Research Centre"
 __maintainer__ = "Stefania Grimaldi, Cinzia Mazzetti, Carlo Russo, Damien Decremer, Corentin Carton De Wiart, Valerio Lorini, Ad de Roo"
 __status__ = "Operation"

src/lisflood/global_modules/netcdf.py

@@ -10,25 +10,14 @@
 from pyproj import Proj
 
 from .settings import (calendar_inconsistency_warning, get_calendar_type, calendar, MaskAttrs, CutMap, NetCDFMetadata,
-                       LisSettings, MaskInfo)
+                       get_core_dims, LisSettings, MaskInfo)
 from .errors import LisfloodWarning, LisfloodError
 from .decorators import Cache, cached
 from .zusatz import iterOpenNetcdf
 # from .add1 import *
 from .add1 import nanCheckMap, decompress
 
 
-def get_core_dims(dims):
-    if 'x' in dims and 'y' in dims:
-        core_dims = ('y', 'x')
-    elif 'lat' in dims and 'lon' in dims:
-        core_dims = ('lat', 'lon')
-    else:
-        msg = 'Core dimension in netcdf file not recognised! Expecting (y, x) or (lat, lon), have '+str(dims)
-        LisfloodError(msg)
-    return core_dims
-
-
 def mask_array_np(data, mask, crop):
     data_cut = data[:, crop[2]:crop[3], crop[0]:crop[1]]
     return data_cut[:, mask]
@@ -331,18 +320,24 @@ def read_lat_from_template(binding):
     return lat_deg
 
 
-def get_space_coords(nrow, ncol, dim_lat_y, dim_lon_x):
+def get_space_coords(template, dim_lat_y, dim_lon_x):
+    cutmap = CutMap.instance()
+    crop = cutmap.cuts
+    coordinates = {}
+    coordinates[dim_lat_y] = template.coords[dim_lat_y][crop[2]:crop[3]]
+    coordinates[dim_lon_x] = template.coords[dim_lon_x][crop[0]:crop[1]]
+    return coordinates
+
+
+def get_space_coords_pcraster(nrow, ncol, dim_lat_y, dim_lon_x):
     cell = pcraster.clone().cellSize()
     xl = pcraster.clone().west() + cell / 2
     xr = xl + ncol * cell
     yu = pcraster.clone().north() - cell / 2
     yd = yu - nrow * cell
-    #lats = np.arange(yu, yd, -cell)
-    #lons = np.arange(xl, xr, cell)
     coordinates = {}
     coordinates[dim_lat_y] = np.linspace(yu, yd, nrow, endpoint=False)
     coordinates[dim_lon_x] = np.linspace(xl, xr, ncol, endpoint=False)
-
     return coordinates
 
 
@@ -386,18 +381,18 @@ def write_header(var_name, netfile, DtDay,
     ncol = np.abs(cutmap.cuts[1] - cutmap.cuts[0])
 
     dim_lat_y, dim_lon_x = get_core_dims(meta_netcdf.data)
-    latlon_coords = get_space_coords(nrow, ncol, dim_lat_y, dim_lon_x)
+    latlon_coords = get_space_coords(meta_netcdf, dim_lat_y, dim_lon_x)
 
     if dim_lon_x in meta_netcdf.data:
-        lon = nf1.createDimension(dim_lon_x, ncol)  # x 1000
+        nf1.createDimension(dim_lon_x, ncol)  # x 1000
         longitude = nf1.createVariable(dim_lon_x, 'f8', (dim_lon_x,))
         valid_attrs = [i for i in meta_netcdf.data[dim_lon_x] if i not in not_valid_attrs]
         for i in valid_attrs:
             setattr(longitude, i, meta_netcdf.data[dim_lon_x][i])
     longitude[:] = latlon_coords[dim_lon_x]
 
     if dim_lat_y in meta_netcdf.data:
-        lat = nf1.createDimension(dim_lat_y, nrow)  # x 950
+        nf1.createDimension(dim_lat_y, nrow)  # x 950
         latitude = nf1.createVariable(dim_lat_y, 'f8', (dim_lat_y,))
         valid_attrs = [i for i in meta_netcdf.data[dim_lat_y] if i not in not_valid_attrs]
         for i in valid_attrs:

src/lisflood/global_modules/settings.py

@@ -43,6 +43,7 @@
 from .decorators import cached
 from .default_options import default_options
 
+
 project_dir = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), '../../..'))
 
 
@@ -189,6 +190,17 @@ def __iter__(self):
         return iter(self.info)
 
 
+def get_core_dims(dims):
+    if 'x' in dims and 'y' in dims:
+        core_dims = ('y', 'x')
+    elif 'lat' in dims and 'lon' in dims:
+        core_dims = ('lat', 'lon')
+    else:
+        msg = 'Core dimension in netcdf file not recognised! Expecting (y, x) or (lat, lon), have '+str(dims)
+        LisfloodError(msg)
+    return core_dims
+
+
 @nine
 class NetCDFMetadata(with_metaclass(Singleton)):
     def __init__(self, uid):
@@ -203,6 +215,10 @@ def __init__(self, uid):
             nf1 = iterOpenNetcdf(filename, "Trying to get metadata from netcdf template \n", 'r')
             for var in nf1.variables:
                 self.data[var] = {k: v for k, v in iteritems(nf1.variables[var].__dict__) if k != '_FillValue'}
+            core_dims = get_core_dims(self.data)
+            self.coords = {}
+            for dim in core_dims:
+                self.coords[dim] = nf1.variables[dim][:]
             nf1.close()
             return
         except (KeyError, IOError, IndexError, Exception):
@@ -212,6 +228,10 @@ def __init__(self, uid):
         nf1 = iterOpenNetcdf(filename, "Trying to get metadata from E0 maps \n", 'r')
         for var in nf1.variables:
             self.data[var] = {k: v for k, v in iteritems(nf1.variables[var].__dict__) if k != '_FillValue'}
+        core_dims = get_core_dims(self.data)
+        self.coords = {}
+        for dim in core_dims:
+            self.coords[dim] = nf1.variables[dim]
         nf1.close()
 
 @nine