.. _sec-unit-conversion: =============== Unit Conversion =============== The ``sdf-xarray`` package automatically extracts the units for each coordinate/variable/constant from an SDF file and stores them as an :class:`xarray.Dataset` attribute called ``"units"``. Sometimes we want to convert our data from one format to another, e.g. converting the grid coordinates from meters to microns, time from seconds to femto-seconds or particle energy from Joules to electron-volts. .. ipython:: python from sdf_xarray import open_mfdataset import matplotlib.pyplot as plt plt.rcParams.update({ "axes.labelsize": 16, "xtick.labelsize": 14, "ytick.labelsize": 14, "axes.titlesize": 16 }) ===================== Rescaling Coordinates ===================== For simple scaling and unit relabeling of coordinates (e.g., converting meters to microns), the most straightforward approach is to use the ``rescale_coords()`` method via the custom ``xarray.Dataset.epoch`` dataset accessor. This method scales the coordinate values by a given multiplier and updates the ``"units"`` attribute in one step. Rescaling Grid Coordinates ~~~~~~~~~~~~~~~~~~~~~~~~~~ We can use the ``xarray.Dataset.epoch.rescale_coords()`` method to convert X, Y, and Z coordinates from meters (m) to microns (µm) by applying a multiplier of ``1e6``. .. ipython:: python fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(16, 6)) with open_mfdataset("tutorial_dataset_2d/*.sdf") as ds: ds_in_microns = ds.epoch.rescale_coords( multiplier=1e6, unit_label="µm", coord_names=["X_Grid_mid", "Y_Grid_mid"] ) derived_number_density = ds["Derived_Number_Density_Electron"].isel(time=0).compute() derived_number_density_microns = ds_in_microns["Derived_Number_Density_Electron"].isel(time=0).compute() derived_number_density.plot(ax=ax1, x="X_Grid_mid", y="Y_Grid_mid") ax1.set_title("Original X Coordinate (m)") derived_number_density_microns.plot(ax=ax2, x="X_Grid_mid", y="Y_Grid_mid") ax2.set_title("Rescaled X Coordinate (µm)") @savefig coordinate_conversion.png width=9in fig.tight_layout() Rescaling Time Coordinate ~~~~~~~~~~~~~~~~~~~~~~~~~ We can also use the ``xarray.Dataset.epoch.rescale_coords()`` method to convert the time coordinate from seconds (s) to femto-seconds (fs) by applying a multiplier of ``1e15``. .. ipython:: python with open_mfdataset("tutorial_dataset_2d/*.sdf") as ds: ds_time_in_femto = ds.epoch.rescale_coords( multiplier=1e15, unit_label="fs", coord_names="time" ) print(f"[Original] units: {ds['time'].attrs['units']}, values: {ds['time'].values}") print(f"[Rescaled] units: {ds_time_in_femto['time'].attrs['units']}, values: {ds_time_in_femto['time'].values}") ================================ Unit Conversion with pint-xarray ================================ While this is sufficient for most use cases, we can enhance this functionality using the `pint `_ library. Pint allows us to specify the units of a given array and convert them to another, which is incredibly handy. We can take this a step further, however, and utilize the `pint-xarray `_ library. This library allows us to infer units directly from an `xarray.Dataset.attrs` while retaining all the information about the `xarray.Dataset`. This works very similarly to taking a NumPy array and multiplying it by a constant or another array, which returns a new array; however, this library will also retain the unit logic (specifically the ``"units"`` information). .. note:: Unit conversion is not supported on coordinates in ``pint-xarray`` which is due to an underlying issue with how ``xarray`` implements indexes. Installation ~~~~~~~~~~~~ To install the pint libraries you can simply run the following optional dependency pip command which will install both the ``pint`` and ``pint-xarray`` libraries. You can install these optional dependencies via pip: .. code:: console $ pip install "sdf_xarray[pint]" .. note:: Once you install ``pint-xarray`` it is automatically picked up and loaded by the code so you should have access to the ``xarray.Dataset.pint`` accessor. Quantifying Arrays ~~~~~~~~~~~~~~~~~~ When using ``pint-xarray``, the library attempts to infer units from the ``"units"`` attribute on each `xarray.DataArray`. Alternatively, you can also specify the units yourself by passing a string into the ``xarray.Dataset.DataArray.pint.quantify()`` function call. Once the type is inferred the original `xarray.DataArray` will be converted to a `pint.Quantity` and the ``"units"`` attribute will be removed. In the following example we will extract the time-resolved total particle energy of electrons which is measured in Joules and convert it to electron volts. .. ipython:: python with open_mfdataset("tutorial_dataset_1d/*.sdf") as ds: total_particle_energy = ds["Total_Particle_Energy_Electron"] total_particle_energy total_particle_energy = ds["Total_Particle_Energy_Electron"].pint.quantify() total_particle_energy Now that this dataset has been converted a `pint.Quantity`, we can check it's units and dimensionality .. ipython:: python total_particle_energy.pint.units total_particle_energy.pint.dimensionality Converting Units ~~~~~~~~~~~~~~~~ We can now convert it to electron volts utilising the `pint.Quantity.to` function .. ipython:: python total_particle_energy_ev = total_particle_energy.pint.to("eV") Unit Propagation ~~~~~~~~~~~~~~~~ Suppose instead of converting to ``"eV"``, we want to convert to ``"W"`` (watts). To do this, we divide the total particle energy by time. However, since coordinates in `xarray.Dataset` cannot be directly converted to `pint.Quantity`, we must first extract the coordinate values manually and create a new Pint quantity for time. Once both arrays are quantified, Pint will automatically handle the unit propagation when we perform arithmetic operations like division. .. note:: Pint does not automatically simplify ``"J/s"`` to ``"W"``, so we use `pint.Quantity.to` to convert the unit string. Since these units are the same it will not change the underlying data, only the units. This is only a small formatting choice and is not required. .. ipython:: python import pint time_values = total_particle_energy.coords["time"].data time = pint.Quantity(time_values, "s") total_particle_energy_w = total_particle_energy / time total_particle_energy_w.pint.units total_particle_energy_w = total_particle_energy_w.pint.to("W") total_particle_energy_w.pint.units Dequantifying and Restoring Units ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. note:: If this function is not called prior to plotting then the ``units`` will be inferred from the `pint.Quantity` array which will return the long name of the units. i.e. instead of returning ``"eV"`` it will return ``"electron_volt"``. The ``xarray.Dataset.DataArray.pint.dequantify`` function converts the data from `pint.Quantity` back to the original `xarray.DataArray` and adds the ``"units"`` attribute back in. It also has an optional ``format`` parameter that allows you to specify the formatting type of ``"units"`` attribute. We have used the ``format="~P"`` option as it shortens the unit to its "short pretty" format (``"eV"``). For more options, see the `Pint formatting documentation `_. .. ipython:: python total_particle_energy_ev = total_particle_energy_ev.pint.dequantify(format="~P") total_particle_energy_w = total_particle_energy_w.pint.dequantify(format="~P") total_particle_energy_ev To confirm the conversion has worked correctly, we can plot the original and converted `xarray.Dataset` side by side: .. ipython:: python fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2, figsize=(16,8)) ds["Total_Particle_Energy_Electron"].plot(ax=ax1) total_particle_energy_ev.plot(ax=ax2) total_particle_energy_w.plot(ax=ax3) ax4.set_visible(False) fig.suptitle("Comparison of conversion from Joules to electron volts and watts", fontsize="18") @savefig unit_conversion.png width=9in fig.tight_layout()