🔀 Merge branch 'alongtrack_view' (#99)

Closes #99 Along track views of height change over time.
weiji14 · Jul 16, 2020 · 7872c27 · 7872c27
2 parents 89f2b29 + e4874b0
commit 7872c27
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Showing 6 changed files with 591 additions and 42 deletions.
diff --git a/atl11_play.ipynb b/atl11_play.ipynb
@@ -30,7 +30,7 @@
     "import hvplot.pandas\n",
     "import hvplot.xarray\n",
     "\n",
-    "# import intake\n",
+    "import intake\n",
     "import geopandas as gpd\n",
     "import numpy as np\n",
     "import pandas as pd\n",
@@ -123,6 +123,15 @@
    },
    "outputs": [],
    "source": [
+    "# Xarray open_dataset preprocessor to add fields based on input filename.\n",
+    "# Adapted from the intake.open_netcdf._add_path_to_ds function.\n",
+    "add_path_to_ds = lambda ds: ds.assign_coords(\n",
+    "    coords=intake.source.utils.reverse_format(\n",
+    "        format_string=\"ATL11.001z123/ATL11_{referencegroundtrack:04d}1x_{mincycle:02d}{maxcycle:02d}_{}_v{}.zarr\",\n",
+    "        resolved_string=ds.encoding[\"source\"],\n",
+    "    )\n",
+    ")\n",
+    "\n",
     "# Load dataset from all Zarr stores\n",
     "# Aligning chunks spatially along cycle_number (i.e. time)\n",
     "ds: xr.Dataset = xr.open_mfdataset(\n",
@@ -132,6 +141,7 @@
     "    combine=\"nested\",\n",
     "    concat_dim=\"ref_pt\",\n",
     "    parallel=\"True\",\n",
+    "    preprocess=add_path_to_ds,\n",
     "    backend_kwargs={\"consolidated\": True},\n",
     ")\n",
     "# ds = ds.unify_chunks().compute()\n",
@@ -306,11 +316,9 @@
    "source": [
     "# Save to Zarr/NetCDF formats for distribution\n",
     "ds_subset.to_zarr(\n",
-    "    store=f\"ATLXI/ds_subset_{placename}.zarr\", mode=\"w\", consolidated=True,\n",
+    "    store=f\"ATLXI/ds_subset_{placename}.zarr\", mode=\"w\", consolidated=True\n",
     ")\n",
-    "ds_subset.to_netcdf(\n",
-    "    path=f\"ATLXI/ds_subset_{placename}.nc\", engine=\"h5netcdf\",\n",
-    ")"
+    "ds_subset.to_netcdf(path=f\"ATLXI/ds_subset_{placename}.nc\", engine=\"h5netcdf\")"
    ]
   },
   {
@@ -324,7 +332,7 @@
     "    data=ds_subset.sel(cycle_number=7)[[*essential_columns]],\n",
     "    label=\"Cycle_7\",\n",
     "    kdims=[\"x\", \"y\"],\n",
-    "    vdims=[\"utc_time\", \"h_corr\", \"cycle_number\"],\n",
+    "    vdims=[\"utc_time\", \"h_corr\", \"cycle_number\", \"referencegroundtrack\"],\n",
     "    datatype=[\"xarray\"],\n",
     ")\n",
     "df_subset = points_subset.dframe()"
@@ -343,10 +351,12 @@
     "    title=f\"Elevation (metres) at Cycle 7\",\n",
     "    x=\"x\",\n",
     "    y=\"y\",\n",
-    "    c=\"h_corr\",\n",
-    "    cmap=\"Blues\",\n",
-    "    rasterize=True,\n",
+    "    c=\"referencegroundtrack\",\n",
+    "    cmap=\"Set3\",\n",
+    "    # rasterize=True,\n",
     "    hover=True,\n",
+    "    datashade=True,\n",
+    "    dynspread=True,\n",
     ")"
    ]
   },
@@ -726,13 +736,13 @@
     "    grid=agg_grid,\n",
     "    region=region.bounds(),\n",
     "    projection=f\"x1:{scale}\",\n",
-    "    frame=[\"afg\", f'WSne+t\"ICESat-2 Ice Surface Change over {region.name}\"',],\n",
+    "    frame=[\"afg\", f'WSne+t\"ICESat-2 Ice Surface Change over {region.name}\"'],\n",
     "    Q=True,\n",
     ")\n",
     "for subglacial_lake in subglacial_lakes:\n",
     "    fig.plot(data=subglacial_lake, L=True, pen=\"thinnest\")\n",
     "fig.colorbar(\n",
-    "    position=\"JCR+e\", frame=[\"af\", 'x+l\"Elevation Change from Cycle 5 to 6\"', \"y+lm\"],\n",
+    "    position=\"JCR+e\", frame=[\"af\", 'x+l\"Elevation Change from Cycle 5 to 6\"', \"y+lm\"]\n",
     ")\n",
     "fig.savefig(f\"figures/plot_atl11_dh56_{placename}.png\")\n",
     "fig.show(width=600)"
@@ -854,7 +864,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,

diff --git a/atl11_play.py b/atl11_play.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: hydrogen
 #       format_version: '1.3'
-#       jupytext_version: 1.4.2
+#       jupytext_version: 1.5.0
 #   kernelspec:
 #     display_name: deepicedrain
 #     language: python
@@ -34,7 +34,7 @@
 import hvplot.pandas
 import hvplot.xarray
 
-# import intake
+import intake
 import geopandas as gpd
 import numpy as np
 import pandas as pd
@@ -63,6 +63,15 @@
 print(f"{len(stores)} reference ground track Zarr stores")
 
 # %%
+# Xarray open_dataset preprocessor to add fields based on input filename.
+# Adapted from the intake.open_netcdf._add_path_to_ds function.
+add_path_to_ds = lambda ds: ds.assign_coords(
+    coords=intake.source.utils.reverse_format(
+        format_string="ATL11.001z123/ATL11_{referencegroundtrack:04d}1x_{mincycle:02d}{maxcycle:02d}_{}_v{}.zarr",
+        resolved_string=ds.encoding["source"],
+    )
+)
+
 # Load dataset from all Zarr stores
 # Aligning chunks spatially along cycle_number (i.e. time)
 ds: xr.Dataset = xr.open_mfdataset(
@@ -72,6 +81,7 @@
     combine="nested",
     concat_dim="ref_pt",
     parallel="True",
+    preprocess=add_path_to_ds,
     backend_kwargs={"consolidated": True},
 )
 # ds = ds.unify_chunks().compute()
@@ -178,19 +188,17 @@
 # %%
 # Save to Zarr/NetCDF formats for distribution
 ds_subset.to_zarr(
-    store=f"ATLXI/ds_subset_{placename}.zarr", mode="w", consolidated=True,
-)
-ds_subset.to_netcdf(
-    path=f"ATLXI/ds_subset_{placename}.nc", engine="h5netcdf",
+    store=f"ATLXI/ds_subset_{placename}.zarr", mode="w", consolidated=True
 )
+ds_subset.to_netcdf(path=f"ATLXI/ds_subset_{placename}.nc", engine="h5netcdf")
 
 # %%
 # Look at Cycle Number 7 only for plotting
 points_subset = hv.Points(
     data=ds_subset.sel(cycle_number=7)[[*essential_columns]],
     label="Cycle_7",
     kdims=["x", "y"],
-    vdims=["utc_time", "h_corr", "cycle_number"],
+    vdims=["utc_time", "h_corr", "cycle_number", "referencegroundtrack"],
     datatype=["xarray"],
 )
 df_subset = points_subset.dframe()
@@ -201,10 +209,12 @@
     title=f"Elevation (metres) at Cycle 7",
     x="x",
     y="y",
-    c="h_corr",
-    cmap="Blues",
-    rasterize=True,
+    c="referencegroundtrack",
+    cmap="Set3",
+    # rasterize=True,
     hover=True,
+    datashade=True,
+    dynspread=True,
 )
 
 
@@ -359,13 +369,13 @@
     grid=agg_grid,
     region=region.bounds(),
     projection=f"x1:{scale}",
-    frame=["afg", f'WSne+t"ICESat-2 Ice Surface Change over {region.name}"',],
+    frame=["afg", f'WSne+t"ICESat-2 Ice Surface Change over {region.name}"'],
     Q=True,
 )
 for subglacial_lake in subglacial_lakes:
     fig.plot(data=subglacial_lake, L=True, pen="thinnest")
 fig.colorbar(
-    position="JCR+e", frame=["af", 'x+l"Elevation Change from Cycle 5 to 6"', "y+lm"],
+    position="JCR+e", frame=["af", 'x+l"Elevation Change from Cycle 5 to 6"', "y+lm"]
 )
 fig.savefig(f"figures/plot_atl11_dh56_{placename}.png")
 fig.show(width=600)