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175 changes: 175 additions & 0 deletions doc/getting-started-guide/faq.rst
Original file line number Diff line number Diff line change
Expand Up @@ -186,6 +186,181 @@ What other projects leverage xarray?

See section :ref:`ecosystem`.

How do I open format X file as an xarray.Dataset?
-------------------------------------------------

To open format X file in xarray, you need to know the `format of the data <https://docs.xarray.dev/en/stable/user-guide/io.html#csv-and-other-formats-supported-by-pandas/>`_ you want to read. If the format is supported, you can use the appropriate function provided by xarray. The following table provides links to the functions for different file formats in xarray, as well as links to other packages that can be used:

.. csv-table::
:header: "File Format", "xarray Backend", " Other Packages"
:widths: 15, 35, 15

"NetCDF (.nc, .nc4, .cdf)","xarray.open_dataset() OR xarray.open_mfdataset()", "`netCDF4 <https://pypi.org/project/netCDF4/>`_, `netcdf <https://pypi.org/project/netcdf/>`_ , `cdms2 <https://cdms.readthedocs.io/en/latest/cdms2.html>`_"
"HDF5 (.h5, .hdf5)","xarray.open_dataset() OR xarray.open_mfdataset()", "`h5py <https://www.h5py.org/>`_, `pytables <https://www.pytables.org/>`_ "
"GRIB1/GRIB2 (.grb, .grib)", "xarray.open_dataset()", "`cfgrib <https://pypi.org/project/cfgrib/>`_, `pygrib <https://pypi.org/project/pygrib/>`_"
"Zarr","xarray.open_zarr()","`zarr <https://zarr.readthedocs.io/en/stable/>`_ , `fsspec <https://filesystem-spec.readthedocs.io/en/latest/>`_"
"CSV (.csv)","xarray.open_dataset()<br>xarray.open_mfdataset()","`pandas <https://pandas.pydata.org/>`_ , `dask <https://www.dask.org/>`_ "
"Excel (.xls, .xlsx)","xarray.open_dataset()","`pandas <https://pandas.pydata.org/>`_, `openpyxl <https://pypi.org/project/openpyxl/>`_ "
"JSON (.json)","xarray.open_dataset()","`json <https://docs.python.org/3/library/json.html>`_, `pandas <https://pandas.pydata.org/>`_"

To use these backend functions in xarray, you can simply call them with the path to the file(s) you want to read as an argument.

NetCDF
------
Use xarray.open_dataset() to open a NetCDF file and return an xarray Dataset object.

.. code:: python

import xarray as xr

# use xarray to open the file and return an xarray.Dataset object
ds = xr.open_dataset("/path/to/my/file.nc")

# Print Dataset object
print(ds)

# Open multiple NetCDF files as a single dataset using xarray
ds = xr.open_mfdataset("/path/to/my/files/*.nc")

HDF5
----
Use xarray.open_dataset() to open an HDF5 file and return an xarray.Dataset object.

.. code:: python

import xarray as xr

# Open HDF5 file as an xarray Dataset
ds = xr.open_dataset("path/to/hdf5/file.h5", engine="h5netcdf")

# Print Dataset object
print(ds)

# Open a HDF5 file using h5py package
import h5py

f = h5py.File("/path/to/my/file.h5", "r")

# Open a HDF5 file using pytables package
import tables

f = tables.open_file("/path/to/my/file.h5", "r")

GRIB1/GRIB2
-----------
use the cfgrib.open_dataset() function from the cfgrib package to open a GRIB1 file as an xarray Dataset.

.. code:: python

import xarray as xr
import cfgrib

# Open GRIB1 file as an xarray Dataset
ds = xr.open_dataset(
"path/to/grib1/file.grb",
engine="cfgrib",
backend_kwargs={"filter_by_keys": {"typeOfLevel": "surface"}},
)

# OR open GRIB2 file as an xarray Dataset
ds = xr.open_dataset(
"path/to/grib2/file.grb2",
engine="cfgrib",
backend_kwargs={"filter_by_keys": {"typeOfLevel": "surface"}},
)

# Print Dataset object
print(ds)

The open_dataset() function reads the GRIB file and returns an xarray Dataset object, which can be used to access and manipulate the data in the file. Note that the backend_kwargs parameter is used to filter the GRIB messages in the file by their keys. In this example, only surface-level data is read from the GRIB file.

We recommend installing cfgrib via conda:
::
conda install -c conda-forge cfgrib


Zarr
----

.. code:: python

import xarray as xr

# Open the Zarr file and load it into an xarray dataset
dataset = xr.open_dataset("/path/to/file.zarr", engine="zarr")

# Print the dataset to see its contents
print(dataset)

CSV
---
.. code:: python

import xarray as xr

# Open a CSV file using xarray
ds = xr.open_dataset("/path/to/my/file.csv")

# Open a CSV file using pandas package
import pandas as pd

df = pd.read_csv("/path/to/my/file.csv")

Excel
-----
Excel files are not typically used for scientific data storage, and xarray does not have a built-in method to read Excel files. However, if your Excel file contains data that is organized in a way that can be converted to an xarray dataset, you can use the pandas and xarray packages in Python to read the file and convert it to an xarray object.

.. code:: python

import pandas as pd
import xarray as xr

# Open the Excel file and read the data into a pandas dataframe using the openpyxl engine
df = pd.read_excel(
"/path/to/your/file.xlsx", engine="openpyxl", sheet_name="Sheet1"
)

# Convert the pandas dataframe to an xarray dataset
dataset = xr.Dataset.from_dataframe(df)

# Print the dataset to see its contents
print(dataset)

JSON
----
JSON is not a file format that is commonly used for scientific data, and xarray does not have a built-in method to read JSON files. However, if your JSON file contains data that is organized in a way that can be converted to an xarray dataset, you can use the json and xarray packages in Python to read the file and convert it to an xarray object.

.. code:: python

import json
import xarray as xr

# Open the JSON file and read its contents
with open("/path/to/your/file.json", "r") as f:
data_dict = json.load(f)

# Convert the JSON data to an xarray dataset
dataset = xr.Dataset.from_dict(data_dict)

# Print the dataset to see its contents
print(dataset)

import pandas as pd
import xarray as xr

# Load JSON file as a pandas DataFrame
df = pd.read_json("path/to/json/file.json")

# Convert pandas DataFrame to xarray Dataset
ds = df.to_xarray()

# Print xarray Dataset object
print(ds)

Note that the structure of your JSON file needs to be compatible with the xarray data model for this approach to work. Specifically, your JSON data needs to be organized as a dictionary of arrays, where each key in the dictionary corresponds to a variable name and each value is an array of data.

These are just examples and may not cover all possible use cases. Some packages may have additional functionality beyond what is shown here. You can refer to the documentation for each package for more information.

How should I cite xarray?
-------------------------

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