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Along track views of height change over time #99

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merged 4 commits into from
Jul 16, 2020
Merged

Along track views of height change over time #99

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efe93e0
:children_crossing: Include referencegroundtrack via xarray preprocessor
weiji14 Jun 18, 2020
ee7685f
:chart_with_upwards_trend: Along track plots of height change over time
weiji14 Jun 19, 2020
984ac89
:twisted_rightwards_arrows: Merge branch 'master' into alongtrack_view
weiji14 Jun 24, 2020
e4874b0
:sparkles: Interactive ICESat-2 dhdt panel dashboard
weiji14 Jun 24, 2020
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34 changes: 22 additions & 12 deletions atl11_play.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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\")"
]
},
{
Expand All @@ -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()"
Expand All @@ -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",
")"
]
},
Expand Down Expand Up @@ -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)"
Expand Down Expand Up @@ -854,7 +864,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.2"
"version": "3.8.3"
}
},
"nbformat": 4,
Expand Down
34 changes: 22 additions & 12 deletions atl11_play.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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(
Expand All @@ -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()
Expand Down Expand Up @@ -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()
Expand All @@ -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,
)


Expand Down Expand Up @@ -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)
Expand Down
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