208 warnings and performance

src/grid/zgr.py

@@ -212,7 +212,6 @@ def fill_zgrid_vars(zgr_type, grid, hgr_type, e_dict, missing):
             grid (dict)          : vertical grid data dictionary
     """
     # gdep
-
     t_done = "gdept" not in missing
     if t_done is False:
         # Fill in the 3D gdept data from 1D gdept_0
@@ -248,10 +247,25 @@ def fill_zgrid_vars(zgr_type, grid, hgr_type, e_dict, missing):
     if w_done is False:
         if "e3w" not in missing:
             grid["gdepw"] = np.cumsum(grid["e3w"], axis=1)
+        elif zgr_type == "zco":
+            # Don't waste time calculating gdepw everywhere if it all the same.
+            gdepw_0 = calc_gdepw(
+                grid["gdept_0"][np.newaxis, :, np.newaxis, np.newaxis]
+            ).squeeze()
+            grid["gdepw"] = np.tile(
+                gdepw_0,
+                (
+                    grid["mbathy"].shape[0],
+                    grid["mbathy"].shape[1],
+                    grid["mbathy"].shape[2],
+                    1,
+                ),
+            )
+            grid["gdepw"] = np.transpose(grid["gdepw"], axes=[0, 3, 1, 2])
         else:
             # Fill in the 3D gdepw data from gdept
             grid["gdepw"] = calc_gdepw(grid["gdept"])
-            missing = sorted(list(set(missing) - set(["gdepw"])))
+        missing = sorted(list(set(missing) - set(["gdepw"])))
 
     # Calculate other gdep values
     gdep = horiz_interp_lev(grid["gdept"], grid["gdepw"], zgr_type, hgr_type)
@@ -264,7 +278,6 @@ def fill_zgrid_vars(zgr_type, grid, hgr_type, e_dict, missing):
                 grid[vi] = gdep[vi[4:]]
 
     # e3
-
     e3t_done = "e3t" not in missing
     if e3t_done is False:
         grid["e3t"] = vert_calc_e3(grid["gdept"], grid["gdepw"], "e3t")
@@ -301,8 +314,10 @@ def calc_gdepw(gdept):
     dep_out = np.zeros((gdept.shape))
     indxt = np.arange(gdept.shape[1])
     indxw = indxt[:-1] + 0.5
+
     for j in range(gdept.shape[2]):
         for i in range(gdept.shape[3]):
+            # dep_out[0, 1:, j, i] = np.interp(indxw, indxt, gdept[0, :, j, i])
             func = interp.interp1d(indxt, gdept[0, :, j, i], kind="cubic")
             # top gdepw is zero
             dep_out[0, 1:, j, i] = func(indxw)

src/pybdy/nemo_bdy_chunk.py

@@ -361,8 +361,8 @@ def chunk_large(ibdy, jbdy, chunk_number):
     for i in range(len(all_chunk)):
         i_chk = ibdy[chunk_number == all_chunk[i]]
         j_chk = jbdy[chunk_number == all_chunk[i]]
-        i_range = np.max(i_chk) - np.min(i_chk)
-        j_range = np.max(j_chk) - np.min(j_chk)
+        i_range = (np.max(i_chk) - np.min(i_chk)) + 1
+        j_range = (np.max(j_chk) - np.min(j_chk)) + 1
         ratio_box[i] = np.sum(chunk_number == all_chunk[i]) / (i_range * j_range)
 
     # Calculate which boundaries are too big

src/pybdy/nemo_bdy_setup.py

@@ -86,9 +86,9 @@ def _get_var_name_value(self, line):
         index = "-1"
         value = ""
         if name_prefix == "ln":
-            if value_str.find("true") is not -1:
+            if value_str.find("true") != -1:
                 value = True
-            elif value_str.find("false") is not -1:
+            elif value_str.find("false") != -1:
                 value = False
             else:
                 raise ValueError(
@@ -242,11 +242,11 @@ def _get_val(vars_dictionary, bool_vars_dictionary, line):
     value = line[1].strip()
 
     if name_prefix == "ln":
-        if value.find("true") is not -1:
+        if value.find("true") != -1:
             if (name in vars_dictionary) is not True:
                 vars_dictionary[name] = True
             bool_vars_dictionary[name] = True
-        elif value.find("false") is not -1:
+        elif value.find("false") != -1:
             if (name in vars_dictionary) is not True:
                 vars_dictionary[name] = False
             bool_vars_dictionary[name] = False

src/pybdy/profiler.py

@@ -90,7 +90,6 @@ def process_bdy(setup_filepath=0, mask_gui=False):
 
     """
     # Start Logger
-
     logger.info("Start NRCT Logging: " + time.asctime())
     logger.info("============================================")
 
@@ -100,10 +99,11 @@ def process_bdy(setup_filepath=0, mask_gui=False):
     Setup = setup.Setup(setup_filepath)  # default settings file
     settings = Setup.settings
 
-    logger.info("Reading grid completed")
+    logger.info("Reading setup completed")
 
     bdy_msk = _get_mask(Setup, mask_gui)
     DstCoord.bdy_msk = bdy_msk == 1
+    logger.info("Reading mask completed")
 
     DstCoord.hgr = hgr.H_Grid(settings["dst_hgr"], settings["nme_map"], logger, dst=1)
     DstCoord.zgr = zgr.Z_Grid(
@@ -114,8 +114,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
         logger,
         dst=1,
     )
-
-    logger.info("Reading mask completed")
+    logger.info("Reading dst grid completed")
 
     bdy_ind = {}  # define a dictionary to hold the grid information
 
@@ -136,38 +135,11 @@ def process_bdy(setup_filepath=0, mask_gui=False):
         logger.info("File: coordinates.bdy.nc generated and populated")
 
     # Idenitify number of boundary points
-
     nbdy = {}
 
     for grd in ["t", "u", "v"]:
         nbdy[grd] = len(bdy_ind[grd].bdy_i[:, 0])
 
-    # Gather grid information
-
-    logger.info("Gathering grid information")
-    SourceCoord.hgr = hgr.H_Grid(
-        settings["src_hgr"], settings["nme_map"], logger, dst=0
-    )
-    SourceCoord.zgr = zgr.Z_Grid(
-        settings["src_zgr"],
-        settings["nme_map"],
-        SourceCoord.hgr.grid_type,
-        SourceCoord.hgr.grid,
-        logger,
-        dst=0,
-    )
-
-    # Fill horizontal grid information
-
-    try:  # if they are masked array convert them to normal arrays
-        SourceCoord.hgr.grid["glamt"] = SourceCoord.hgr.grid["glamt"].filled()  # lon
-    except Exception:
-        logger.debug("Not a masked array.")
-    try:
-        SourceCoord.hgr.grid["gphit"] = SourceCoord.hgr.grid["gphit"].filled()  # lat
-    except Exception:
-        logger.debug("Not a masked array.")
-
     # Assign horizontal grid data
 
     DstCoord.lonlat = {"t": {}, "u": {}, "v": {}}
@@ -196,6 +168,32 @@ def process_bdy(setup_filepath=0, mask_gui=False):
 
     logger.info("BDY lons/lats identified from %s", settings["dst_hgr"])
 
+    # Gather grid information
+
+    logger.info("Gathering src grid information")
+    SourceCoord.hgr = hgr.H_Grid(
+        settings["src_hgr"], settings["nme_map"], logger, dst=0
+    )
+    SourceCoord.zgr = zgr.Z_Grid(
+        settings["src_zgr"],
+        settings["nme_map"],
+        SourceCoord.hgr.grid_type,
+        SourceCoord.hgr.grid,
+        logger,
+        dst=0,
+    )
+
+    # Fill horizontal grid information
+
+    try:  # if they are masked array convert them to normal arrays
+        SourceCoord.hgr.grid["glamt"] = SourceCoord.hgr.grid["glamt"].filled()  # lon
+    except Exception:
+        logger.debug("Not a masked array.")
+    try:
+        SourceCoord.hgr.grid["gphit"] = SourceCoord.hgr.grid["gphit"].filled()  # lat
+    except Exception:
+        logger.debug("Not a masked array.")
+
     # Define z at t/u/v points
 
     DstCoord.depths = {"t": {}, "u": {}, "v": {}}