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DOC: particlefile metadata (fixes #1701)
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@VeckoTheGecko
VeckoTheGecko committed Nov 20, 2024
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111 changes: 63 additions & 48 deletions docs/examples/tutorial_output.ipynb
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"- [**Plotting**](#Plotting)\n",
"- [**Animations**](#Animations)\n",
"\n",
"First we need to create some parcels output to analyze. We simulate a set of particles using the setup described in the [Delay start tutorial](https://docs.oceanparcels.org/en/latest/examples/tutorial_delaystart.html).\n"
"First we need to create some parcels output to analyze. We simulate a set of particles using the setup described in the [Delay start tutorial](https://docs.oceanparcels.org/en/latest/examples/tutorial_delaystart.html). We will also add some user defined metadata to the output file.\n"
]
},
{
Expand All @@ -30,7 +30,7 @@
"metadata": {},
"outputs": [],
"source": [
"from datetime import timedelta\n",
"from datetime import datetime, timedelta\n",
"\n",
"import numpy as np\n",
"\n",
Expand All @@ -41,16 +41,7 @@
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO: Output files are stored in Output.zarr.\n",
"100%|██████████| 86400.0/86400.0 [00:00<00:00, 93792.23it/s] \n"
]
}
],
"outputs": [],
"source": [
"example_dataset_folder = parcels.download_example_dataset(\"Peninsula_data\")\n",
"fieldset = parcels.FieldSet.from_parcels(\n",
Expand All @@ -68,8 +59,40 @@
" fieldset=fieldset, pclass=parcels.JITParticle, lon=lon, lat=lat, time=time\n",
")\n",
"\n",
"output_file = pset.ParticleFile(name=\"Output.zarr\", outputdt=timedelta(hours=2))\n",
"\n",
"output_file = pset.ParticleFile(name=\"Output.zarr\", outputdt=timedelta(hours=2))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Parcels saves some metadata in the output file with every simulation (Parcels version, CF convention information, etc.). This metadata is just a dictionary which is propogated to `xr.Dataset(attrs=...)` and is stored in the `.metadata` attribute. The user is free to manipulate this dictionary to add any custom, xarray-compatible metadata relevant to their simulation. Here we add a custom metadata field `date_created` to the output file."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"output_file.metadata[\"date_created\"] = datetime.now().isoformat()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO: Output files are stored in Output.zarr.\n",
"100%|██████████| 86400.0/86400.0 [00:01<00:00, 82356.55it/s]\n"
]
}
],
"source": [
"pset.execute(\n",
" parcels.AdvectionRK4,\n",
" runtime=timedelta(hours=24),\n",
Expand All @@ -85,35 +108,36 @@
"source": [
"## Reading the output file\n",
"\n",
"Parcels exports output trajectories in `zarr` [format](https://zarr.readthedocs.io/en/stable/). Files in `zarr` are typically _much_ smaller in size than netcdf, although may be slightly more challenging to handle (but `xarray` has a fairly seamless `open_zarr()` method).\n"
"Parcels exports output trajectories in `zarr` [format](https://zarr.readthedocs.io/en/stable/). Files in `zarr` are typically _much_ smaller in size than netcdf, although may be slightly more challenging to handle (but `xarray` has a fairly seamless `open_zarr()` method). Note when when we display the dataset we cam see our custom metadata field `date_created`.\n"
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<xarray.Dataset>\n",
"<xarray.Dataset> Size: 3kB\n",
"Dimensions: (trajectory: 10, obs: 12)\n",
"Coordinates:\n",
" * obs (obs) int32 0 1 2 3 4 5 6 7 8 9 10 11\n",
" * trajectory (trajectory) int64 0 1 2 3 4 5 6 7 8 9\n",
" * obs (obs) int32 48B 0 1 2 3 4 5 6 7 8 9 10 11\n",
" * trajectory (trajectory) int64 80B 0 1 2 3 4 5 6 7 8 9\n",
"Data variables:\n",
" lat (trajectory, obs) float32 dask.array<chunksize=(1, 1), meta=np.ndarray>\n",
" lon (trajectory, obs) float32 dask.array<chunksize=(1, 1), meta=np.ndarray>\n",
" time (trajectory, obs) timedelta64[ns] dask.array<chunksize=(1, 1), meta=np.ndarray>\n",
" z (trajectory, obs) float32 dask.array<chunksize=(1, 1), meta=np.ndarray>\n",
" lat (trajectory, obs) float32 480B dask.array<chunksize=(1, 1), meta=np.ndarray>\n",
" lon (trajectory, obs) float32 480B dask.array<chunksize=(1, 1), meta=np.ndarray>\n",
" time (trajectory, obs) timedelta64[ns] 960B dask.array<chunksize=(1, 1), meta=np.ndarray>\n",
" z (trajectory, obs) float32 480B dask.array<chunksize=(1, 1), meta=np.ndarray>\n",
"Attributes:\n",
" Conventions: CF-1.6/CF-1.7\n",
" date_created: 2024-11-20T11:07:47.494911\n",
" feature_type: trajectory\n",
" ncei_template_version: NCEI_NetCDF_Trajectory_Template_v2.0\n",
" parcels_kernels: JITParticleAdvectionRK4\n",
" parcels_mesh: flat\n",
" parcels_version: v2.4.2-367-gd9b7b447\n"
" parcels_version: 3.1.1.dev4\n"
]
}
],
Expand All @@ -126,17 +150,17 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<xarray.DataArray 'trajectory' (trajectory: 10)>\n",
"<xarray.DataArray 'trajectory' (trajectory: 10)> Size: 80B\n",
"array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])\n",
"Coordinates:\n",
" * trajectory (trajectory) int64 0 1 2 3 4 5 6 7 8 9\n"
" * trajectory (trajectory) int64 80B 0 1 2 3 4 5 6 7 8 9\n"
]
}
],
Expand Down Expand Up @@ -168,7 +192,7 @@
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{
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"metadata": {},
"outputs": [
{
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},
{
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{
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"execution_count": 10,
"metadata": {
"scrolled": true
},
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},
{
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"metadata": {},
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{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/erik/miniconda3/envs/parcels/lib/python3.11/site-packages/pandas/core/arrays/timedeltas.py:1093: RuntimeWarning: invalid value encountered in cast\n",
" data = (base * m + (frac * m).astype(np.int64)).view(\"timedelta64[ns]\")\n"
]
}
],
"outputs": [],
"source": [
"# Using xarray\n",
"mean_lon_x = []\n",
Expand All @@ -349,7 +364,7 @@
},
{
"cell_type": "code",
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"execution_count": 12,
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"<IPython.core.display.HTML object>"
]
},
"execution_count": 14,
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
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2 changes: 1 addition & 1 deletion docs/examples/tutorial_parcels_structure.ipynb
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Expand Up @@ -350,7 +350,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"The final part executes the simulation, given the `ParticleSet`, `FieldSet` and `Kernels`, that have been defined in the previous steps. If you like to store the particle data generated in the simulation, you define the `ParticleFile` to which the output of the kernel execution will be written. Then, on the `ParticleSet` you have defined, you can use the method `ParticleSet.execute()` which requires the following arguments:\n",
"The final part executes the simulation, given the `ParticleSet`, `FieldSet` and `Kernels`, that have been defined in the previous steps. If you like to store the particle data generated in the simulation, you define the `ParticleFile` to which the output of the kernel execution as well as - optionally - any user-specified metadata (see the [Working with Parcels output](https://docs.oceanparcels.org/en/latest/examples/tutorial_output.html) tutorial for more info) will be written. Then, on the `ParticleSet` you have defined, you can use the method `ParticleSet.execute()` which requires the following arguments:\n",
"\n",
"1. The kernels to be executed.\n",
"2. The `runtime` defining how long the execution loop runs. Alternatively, you may define the `endtime` at which the execution loop stops.\n",
Expand Down

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