allow __getattr__ to read in data arrays from disk (#23)

* include DataReader class

* within __getattr__ read data files

* bug

* update demo with plots

* typo

demos/reanalysis-forced.ipynb

@@ -225,7 +225,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Check out your domain:"
+    "### Check out your domain!\n",
+    "\n",
+    "Calling `expt.bathymetry` returns an xarray dataset, which can be plotted as usual. If you haven't yet run setup_bathymetry, calling `expt.bathymetry` will return `None` and prompt you to do so!"
    ]
   },
   {
@@ -309,6 +311,38 @@
     "        )"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Check out your initial condition data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "expt.init_tracers.salt.isel(zl = 0).plot()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### You can plot your segment data too"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "expt.segment_001.u_segment_001.isel(time = 5).plot()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

regional_mom6/regional_mom6.py

@@ -14,13 +14,8 @@
 import os
 import importlib.resources
 import datetime
-from .utils import (
-    quadrilateral_areas,
-    ap2ep,
-    ep2ap,
-)
+from .utils import quadrilateral_areas, ap2ep, ep2ap
 import pandas as pd
-import re
 from pathlib import Path
 import glob
 from collections import defaultdict
@@ -699,7 +694,7 @@ def __init__(
         depth,
         mom_run_dir,
         mom_input_dir,
-        toolpath_dir,
+        toolpath_dir=None,
         longitude_extent=None,
         latitude_extent=None,
         hgrid_type="even_spacing",
@@ -800,12 +795,66 @@ def __str__(self) -> str:
         return json.dumps(self.write_config_file(export=False, quiet=True), indent=4)
 
     def __getattr__(self, name):
+
+        ## First, check whether the attribute is an input file
+
+        if name == "bathymetry":
+            if (self.mom_input_dir / "bathymetry.nc").exists():
+                return xr.open_dataset(
+                    self.mom_input_dir / "bathymetry.nc",
+                    decode_cf=False,
+                    decode_times=False,
+                )
+            else:
+                print(
+                    f"bathymetry.nc file not found! Make sure you've successfully run the setup_bathmetry method, or copied your own bathymetry.nc file into {self.mom_input_dir}."
+                )
+                return None
+        elif name == "init_velocities":
+            if (self.mom_input_dir / "init_vel.nc").exists():
+                return xr.open_dataset(
+                    self.mom_input_dir / "init_vel.nc",
+                    decode_cf=False,
+                    decode_times=False,
+                )
+            else:
+                print(
+                    f"init_vel.nc file not found! Make sure you've successfully run the setup_initial_condition method, or copied your own init_vel.nc file into {self.mom_input_dir}."
+                )
+                return
+
+        elif name == "init_tracers":
+            if (self.mom_input_dir / "init_tracers.nc").exists():
+                return xr.open_dataset(
+                    self.mom_input_dir / "init_tracers.nc",
+                    decode_cf=False,
+                    decode_times=False,
+                )
+            else:
+                print(
+                    f"init_tracers.nc file not found! Make sure you've successfully run the setup_initial_condition method, or copied your own init_tracers.nc file into {self.mom_input_dir}."
+                )
+                return
+
+        elif "segment" in name:
+            try:
+                xr.open_mfdataset(
+                    str(self.mom_input_dir / f"*{name}*.nc"),
+                    decode_times=False,
+                    decode_cf=False,
+                )
+            except:
+                print(
+                    f"{name} files not found! Make sure you've successfully run the setup_ocean_state_boundaries method, or copied your own segment files file into {self.mom_input_dir}."
+                )
+                return None
+
+        ## If we get here, attribute wasn't found
+
         available_methods = [
             method for method in dir(self) if not method.startswith("__")
         ]
-        error_message = (
-            f"{name} method not found. Available methods are: {available_methods}"
-        )
+        error_message = f"{name} not found. Available methods and attributes are: {available_methods}"
         raise AttributeError(error_message)
 
     def _make_hgrid(self):
@@ -1067,7 +1116,6 @@ def write_config_file(self, path=None, export=True, quiet=False):
             "minimum_depth": self.minimum_depth,
             "vgrid": str(vgrid_path),
             "hgrid": str(hgrid_path),
-            "bathymetry": self.bathymetry_property,
             "ocean_state": self.ocean_state_boundaries,
             "tides": self.tides_boundaries,
             "initial_conditions": self.initial_condition,
@@ -1849,7 +1897,7 @@ def setup_bathymetry(
         tgrid = xr.Dataset(
             data_vars={
                 "depth": (
-                    ["nx", "ny"],
+                    ["ny", "nx"],
                     np.zeros(
                         self.hgrid.x.isel(
                             nxp=slice(1, None, 2), nyp=slice(1, None, 2)
@@ -1859,13 +1907,13 @@ def setup_bathymetry(
             },
             coords={
                 "lon": (
-                    ["nx", "ny"],
+                    ["ny", "nx"],
                     self.hgrid.x.isel(
                         nxp=slice(1, None, 2), nyp=slice(1, None, 2)
                     ).values,
                 ),
                 "lat": (
-                    ["nx", "ny"],
+                    ["ny", "nx"],
                     self.hgrid.y.isel(
                         nxp=slice(1, None, 2), nyp=slice(1, None, 2)
                     ).values,
@@ -3268,7 +3316,7 @@ def regrid_velocity_tracers(self):
         )
         segment_out[f"lat_{self.segment_name}"] = (
             [f"ny_{self.segment_name}", f"nx_{self.segment_name}"],
-            self.coords.lon.expand_dims(
+            self.coords.lat.expand_dims(
                 dim="blank", axis=self.coords.attrs["axis_to_expand"] - 2
             ).data,
         )