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Created October 11, 2020 04:31
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intake-esm-multi-variables.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/glade/work/abanihi/softwares/miniconda3/envs/intake-dev/lib/python3.8/site-packages/fastprogress/fastprogress.py:102: UserWarning: Couldn't import ipywidgets properly, progress bar will use console behavior\n",
" warn(\"Couldn't import ipywidgets properly, progress bar will use console behavior\")\n"
]
}
],
"source": [
"import intake\n",
"import ast"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<p><strong>whp_test_collect_sim catalog with 2 dataset(s) from 4 asset(s)</strong>:</p> <div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>unique</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>path</th>\n",
" <td>4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>time</th>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>year</th>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>month</th>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>day</th>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>hour</th>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>file_type</th>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>variable</th>\n",
" <td>4</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"col = intake.open_esm_datastore(\"whp_test_collect_sim.json\", \n",
" csv_kwargs={'converters': {'variable': ast.literal_eval}})\n",
"col"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>path</th>\n",
" <th>time</th>\n",
" <th>year</th>\n",
" <th>month</th>\n",
" <th>day</th>\n",
" <th>hour</th>\n",
" <th>file_type</th>\n",
" <th>variable</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/...</td>\n",
" <td>2011-08-26T01:00</td>\n",
" <td>2011</td>\n",
" <td>8</td>\n",
" <td>26</td>\n",
" <td>1</td>\n",
" <td>CHRTOUT</td>\n",
" <td>(streamflow, nudge)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/...</td>\n",
" <td>2011-08-26T01:00</td>\n",
" <td>2011</td>\n",
" <td>8</td>\n",
" <td>26</td>\n",
" <td>1</td>\n",
" <td>GWOUT</td>\n",
" <td>(inflow, outflow)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/...</td>\n",
" <td>2011-08-26T02:00</td>\n",
" <td>2011</td>\n",
" <td>8</td>\n",
" <td>26</td>\n",
" <td>2</td>\n",
" <td>CHRTOUT</td>\n",
" <td>(streamflow, nudge)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/...</td>\n",
" <td>2011-08-26T02:00</td>\n",
" <td>2011</td>\n",
" <td>8</td>\n",
" <td>26</td>\n",
" <td>2</td>\n",
" <td>GWOUT</td>\n",
" <td>(inflow, outflow)</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" path time year \\\n",
"0 /glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/... 2011-08-26T01:00 2011 \n",
"1 /glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/... 2011-08-26T01:00 2011 \n",
"2 /glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/... 2011-08-26T02:00 2011 \n",
"3 /glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/... 2011-08-26T02:00 2011 \n",
"\n",
" month day hour file_type variable \n",
"0 8 26 1 CHRTOUT (streamflow, nudge) \n",
"1 8 26 1 GWOUT (inflow, outflow) \n",
"2 8 26 2 CHRTOUT (streamflow, nudge) \n",
"3 8 26 2 GWOUT (inflow, outflow) "
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"col.df.head()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'variable': {'count': 4,\n",
" 'values': ['inflow', 'nudge', 'outflow', 'streamflow']}}"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"col.unique(['variable'])"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['inflow', 'nudge', 'outflow', 'streamflow']"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"variables = col.unique(['variable'])['variable']['values']\n",
"variables"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(dict_keys(['2011.8.26.CHRTOUT', '2011.8.26.GWOUT']),\n",
" 'year.month.day.file_type')"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"col.keys(), col.key_template"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"def preprocess(ds):\n",
" \"\"\"Preprocess dataset\"\"\"\n",
" vars_to_set_to_coords = list(set(ds.data_vars).difference(set(variables)))\n",
" return ds.set_coords(vars_to_set_to_coords)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"--> The keys in the returned dictionary of datasets are constructed as follows:\n",
"\t'year.month.day.file_type'\n",
"█\r"
]
},
{
"data": {
"text/plain": [
"{'2011.8.26.GWOUT': <xarray.Dataset>\n",
" Dimensions: (feature_id: 185, reference_time: 1, time: 2)\n",
" Coordinates:\n",
" * time (time) datetime64[ns] 2011-08-26T01:00:00 2011-08-26T02:0...\n",
" * reference_time (reference_time) datetime64[ns] 2011-08-26\n",
" * feature_id (feature_id) int32 6212272 6212276 ... 6228424 6228442\n",
" depth (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Data variables:\n",
" inflow (time, feature_id) float32 dask.array<chunksize=(1, 185), meta=np.ndarray>\n",
" outflow (time, feature_id) float32 dask.array<chunksize=(1, 185), meta=np.ndarray>\n",
" Attributes:\n",
" intake_esm_varname: ('inflow', 'outflow')\n",
" code_version: v5.1.0-beta2\n",
" model_initialization_time: 2011-08-26_00:00:00\n",
" station_dimension: gw_id\n",
" featureType: timeSeries\n",
" model_configuration: default\n",
" model_total_valid_times: 2\n",
" model_output_type: groundwater_rt\n",
" Conventions: CF-1.6\n",
" intake_esm_dataset_key: 2011.8.26.GWOUT,\n",
" '2011.8.26.CHRTOUT': <xarray.Dataset>\n",
" Dimensions: (feature_id: 185, reference_time: 1, time: 2)\n",
" Coordinates:\n",
" * time (time) datetime64[ns] 2011-08-26T01:00:00 2011-08-26T02:0...\n",
" * reference_time (reference_time) datetime64[ns] 2011-08-26\n",
" crs |S1 ...\n",
" * feature_id (feature_id) int32 6226932 6226946 ... 6226970 6226924\n",
" latitude (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" longitude (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" order (feature_id) int32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" elevation (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" q_lateral (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" velocity (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Head (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Data variables:\n",
" streamflow (time, feature_id) float32 dask.array<chunksize=(1, 185), meta=np.ndarray>\n",
" nudge (time, feature_id) float32 dask.array<chunksize=(1, 185), meta=np.ndarray>\n",
" Attributes:\n",
" dev: dev_ prefix indicates development/internal me...\n",
" intake_esm_varname: ('streamflow', 'nudge')\n",
" code_version: v5.1.0-beta2\n",
" dev_NOAH_TIMESTEP: 3600\n",
" model_initialization_time: 2011-08-26_00:00:00\n",
" station_dimension: feature_id\n",
" featureType: timeSeries\n",
" proj4: +proj=lcc +units=m +a=6370000.0 +b=6370000.0 ...\n",
" cdm_datatype: Station\n",
" dev_channel_only: 0\n",
" stream_order_output: 1\n",
" model_configuration: default\n",
" model_total_valid_times: 2\n",
" dev_channelBucket_only: 0\n",
" dev_OVRTSWCRT: 1\n",
" model_output_type: channel_rt\n",
" Conventions: CF-1.6\n",
" intake_esm_dataset_key: 2011.8.26.CHRTOUT}"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dsets = col.to_dataset_dict(preprocess=preprocess)\n",
"dsets"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"--> The keys in the returned dictionary of datasets are constructed as follows:\n",
"\t'year.month.day.file_type'\n",
"█\n",
"--> The keys in the returned dictionary of datasets are constructed as follows:\n",
"\t'year.month.day.file_type'\n",
"█\n",
"--> The keys in the returned dictionary of datasets are constructed as follows:\n",
"\t'year.month.day.file_type'\n",
"█\n",
"--> The keys in the returned dictionary of datasets are constructed as follows:\n",
"\t'year.month.day.file_type'\n",
"█\r"
]
}
],
"source": [
"# Collect datasets for all variables in a single dictionary. Since we are not grouping by `variable`, We modify the keys to include the variable\n",
"dsets = {}\n",
"for variable in variables:\n",
" v_dsets = col.search(variable=variable).to_dataset_dict(preprocess=preprocess)\n",
" keys = list(v_dsets.keys())\n",
" for key in keys:\n",
" # Modify keys\n",
" new_key = f'{key}{col.sep}{variable}'\n",
" v_dsets[new_key] = v_dsets.pop(key)\n",
" \n",
" dsets = {**dsets, **v_dsets}"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"dict_keys(['2011.8.26.GWOUT.inflow', '2011.8.26.CHRTOUT.nudge', '2011.8.26.GWOUT.outflow', '2011.8.26.CHRTOUT.streamflow'])"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dsets.keys()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'2011.8.26.GWOUT.inflow': <xarray.Dataset>\n",
" Dimensions: (feature_id: 185, time: 2)\n",
" Coordinates:\n",
" * feature_id (feature_id) int32 6212272 6212276 6212914 ... 6228424 6228442\n",
" depth (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Dimensions without coordinates: time\n",
" Data variables:\n",
" inflow (time, feature_id) float32 dask.array<chunksize=(1, 185), meta=np.ndarray>\n",
" Attributes:\n",
" intake_esm_varname: ['inflow']\n",
" code_version: v5.1.0-beta2\n",
" model_initialization_time: 2011-08-26_00:00:00\n",
" station_dimension: gw_id\n",
" featureType: timeSeries\n",
" model_configuration: default\n",
" model_total_valid_times: 2\n",
" model_output_type: groundwater_rt\n",
" Conventions: CF-1.6\n",
" intake_esm_dataset_key: 2011.8.26.GWOUT,\n",
" '2011.8.26.CHRTOUT.nudge': <xarray.Dataset>\n",
" Dimensions: (feature_id: 185, time: 2)\n",
" Coordinates:\n",
" crs |S1 ...\n",
" * feature_id (feature_id) int32 6226932 6226946 6228408 ... 6226970 6226924\n",
" latitude (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" longitude (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" order (feature_id) int32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" elevation (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" q_lateral (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" velocity (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Head (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Dimensions without coordinates: time\n",
" Data variables:\n",
" nudge (time, feature_id) float32 dask.array<chunksize=(1, 185), meta=np.ndarray>\n",
" Attributes:\n",
" dev: dev_ prefix indicates development/internal me...\n",
" intake_esm_varname: ['nudge']\n",
" code_version: v5.1.0-beta2\n",
" dev_NOAH_TIMESTEP: 3600\n",
" model_initialization_time: 2011-08-26_00:00:00\n",
" station_dimension: feature_id\n",
" featureType: timeSeries\n",
" proj4: +proj=lcc +units=m +a=6370000.0 +b=6370000.0 ...\n",
" cdm_datatype: Station\n",
" dev_channel_only: 0\n",
" stream_order_output: 1\n",
" model_configuration: default\n",
" model_total_valid_times: 2\n",
" dev_channelBucket_only: 0\n",
" dev_OVRTSWCRT: 1\n",
" model_output_type: channel_rt\n",
" Conventions: CF-1.6\n",
" intake_esm_dataset_key: 2011.8.26.CHRTOUT,\n",
" '2011.8.26.GWOUT.outflow': <xarray.Dataset>\n",
" Dimensions: (feature_id: 185, time: 2)\n",
" Coordinates:\n",
" * feature_id (feature_id) int32 6212272 6212276 6212914 ... 6228424 6228442\n",
" depth (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Dimensions without coordinates: time\n",
" Data variables:\n",
" outflow (time, feature_id) float32 dask.array<chunksize=(1, 185), meta=np.ndarray>\n",
" Attributes:\n",
" intake_esm_varname: ['outflow']\n",
" code_version: v5.1.0-beta2\n",
" model_initialization_time: 2011-08-26_00:00:00\n",
" station_dimension: gw_id\n",
" featureType: timeSeries\n",
" model_configuration: default\n",
" model_total_valid_times: 2\n",
" model_output_type: groundwater_rt\n",
" Conventions: CF-1.6\n",
" intake_esm_dataset_key: 2011.8.26.GWOUT,\n",
" '2011.8.26.CHRTOUT.streamflow': <xarray.Dataset>\n",
" Dimensions: (feature_id: 185, time: 2)\n",
" Coordinates:\n",
" crs |S1 ...\n",
" * feature_id (feature_id) int32 6226932 6226946 6228408 ... 6226970 6226924\n",
" latitude (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" longitude (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" order (feature_id) int32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" elevation (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" q_lateral (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" velocity (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Head (feature_id) float32 dask.array<chunksize=(185,), meta=np.ndarray>\n",
" Dimensions without coordinates: time\n",
" Data variables:\n",
" streamflow (time, feature_id) float32 dask.array<chunksize=(1, 185), meta=np.ndarray>\n",
" Attributes:\n",
" dev: dev_ prefix indicates development/internal me...\n",
" intake_esm_varname: ['streamflow']\n",
" code_version: v5.1.0-beta2\n",
" dev_NOAH_TIMESTEP: 3600\n",
" model_initialization_time: 2011-08-26_00:00:00\n",
" station_dimension: feature_id\n",
" featureType: timeSeries\n",
" proj4: +proj=lcc +units=m +a=6370000.0 +b=6370000.0 ...\n",
" cdm_datatype: Station\n",
" dev_channel_only: 0\n",
" stream_order_output: 1\n",
" model_configuration: default\n",
" model_total_valid_times: 2\n",
" dev_channelBucket_only: 0\n",
" dev_OVRTSWCRT: 1\n",
" model_output_type: channel_rt\n",
" Conventions: CF-1.6\n",
" intake_esm_dataset_key: 2011.8.26.CHRTOUT}"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dsets"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
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Raw
whp_test_collect_sim.json
{
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Raw
whp_test_collect_sim_assets.csv
path time year month day hour file_type variable
/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/wrfhydropy/tests/data/collection_data/simulation/201108260100.CHRTOUT_DOMAIN1 2011-08-26T01:00 2011 8 26 1 CHRTOUT ['streamflow', 'nudge']
/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/wrfhydropy/tests/data/collection_data/simulation/201108260100.GWOUT_DOMAIN1 2011-08-26T01:00 2011 8 26 1 GWOUT ['inflow', 'outflow']
/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/wrfhydropy/tests/data/collection_data/simulation/201108260200.CHRTOUT_DOMAIN1 2011-08-26T02:00 2011 8 26 2 CHRTOUT ['streamflow', 'nudge']
/glade/u/home/jamesmcc/WRF_Hydro/wrf_hydro_py/wrfhydropy/tests/data/collection_data/simulation/201108260200.GWOUT_DOMAIN1 2011-08-26T02:00 2011 8 26 2 GWOUT ['inflow', 'outflow']
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