Crop netcdf python open_dataset(SomeFile) SlicedData = data. The netcdf4 Python library allows Python users to easily read, write, and manipulate NetCDF4 files. 2 you will need convert the geometries to dict-like objects if the projection # of the geometries differ from the raster. Therefore I store the geometries (shapely. geometry import mapping # geometries = geodf. getlibversion() Optional Anaconda Environment YAML: This notebook can be run using the ‘nasa-gesdisc’ YAML file provided in the ‘environments’ subfolder. rio. Most tutorials in this repository take the form of python notebooks. geometric_transform() 1 Jan 1, 2024 · Addressing a pressing need for streamlined access to observed meteorological data in India, we present IMDLIB, an open-source Python library that oper… Visualize Himawari-8 satellite data. clip(geodf. Specifically designed to process high-resolution daily gridded rainfall datasets. I beg your pardon. NetCDFReader paraview. 5, indexes=None) Creates a masked or filled array using input shapes. In this lesson, you will learn how to crop a raster dataset in Python. to_netcdf(path = 'E:\PSU\CCAR REU\Python Codex\MASKS\Outputs\\NAfr. values, geodf. I have opened the netCDF using xarray. Sen4AgriNet: A Sentinel-2 multi-year, multi-country benchmark dataset for crop classification and segmentation with deep learning - Orion-AI-Lab/S4A You can extract the data from many netCDF files using for loop in python but I think the simple tools are GIS softwares like QGIS and ARCGIS. 5 for each city (as they might be in more than one 0. The clipping parameters can be specified as either a bounding box or another data layer. Oct 24, 2024 · Detailed tutorials for and examples of working with netCDF files using Python can be found on the PAVICS tutorial page, Pangeo Library, and xarray’s tutorials and videos page. 5 for 20 consecutive years stored in NetCDF files with a precision of 0. mask(dataset, shapes, all_touched=False, invert=False, nodata=None, filled=True, crop=False, pad=False, pad_width=0. ndimage. What are netCDF files? netCDF (network Common Data Form) is a format Oct 28, 2025 · What is NCO? The netCDF Operators (NCO) comprise about a dozen standalone, command-line programs that take netCDF, HDF, and/or DAP files as input, then operate (e. 7. 0. Sep 9, 2014 · Is there anyway I could in linux, with a simple nc-type command (without extracting the data in matlab/python to rewrite), crop this file to include a smaller region, subset of the above. interpolation. apply(mapping) May 7, 2015 · I need to subset data from a NetCDF using a specific shapefile. Reprojection Rasterio can map the pixels of a destination raster with an associated coordinate reference system and transform to the pixels of a source image with a different coordinate reference system and transform. import matplotlib. rasterio. . Here is my code: import numpy as np import pandas as pd import geopandas as gpd import… nctoolkit: Fast and easy analysis of netCDF data in Python ¶ nctoolkit is a comprehensive Python package for analyzing netCDF data on Linux and MacOS. This process is known as reprojection. show_versions ()” rioxarray rio accessors rioxarray extends xarray with the rio accessor. I need to obtain the precipitation data for a shapefile. 1Grid File Notes 3Running the Remapping (Conservative Method) 4Practical Examples of CDO and NCO Tools 4. HDF5 is a high-performance binary data format designed for storing and organizing large amounts of data, while NetCDF4 (based on HDF5) is widely used in atmospheric and oceanographic sciences for Feb 9, 2017 · I have a netCDF file with foll. The `netcdf4` Python library allows Python users to easily read, write, and manipulate NetCDF4 Sep 25, 2021 · I have a number of coordinates (roughly 20000) for which I need to extract data from a number of NetCDF files each comes roughly with 30000 timesteps (future climate scenarios). Mar 19, 2015 · With the netcdf4-python library the most straightforward way is creating a new netcdf file, adding dimensions, the variable name, its attributes and the save the array of data. NetCDF4 is an enhanced version of NetCDF that supports new data types and compression features. This reader will also look for meta information specified by the CF convention that specify things like topology and time. Here comes Xarray to the rescue. No need to convert between file formats (GRIB to netCDF and such) as Xarray gives similar Introductory level netCDF processing techniques will be demonstrated using netCDF Operators (NCO), Geospatial Data Abstraction Library (GDAL), and Python, including operations that are of interest to ecological applications. Example: Subset by Lat/Lon Bounds Crop to a region (e. py Jun 11, 2021 · I've never really worked with netCDF files before, mainly much smaller pandas dataframes and CSVs. However, the data is currently not land-only (Figure 1) and I want it to only co If built with the netCDF-4 library, a netCDF classic file may be copied to a netCDF-4 file or to a netCDF-4 classic model file as well, permitting data compression, efficient schema changes, larger variable sizes, and use of other netCDF-4 features. The video shows how to mask and clip a netcdf file according to a desired shapefile. NetCDF is a standard format for storing multidimensional scientific data. This module nctoolkit: A Python package for netCDF analysis and post-processing # nctoolkit is a comprehensive and computationally efficient Python package for analyzing and post-processing netCDF data. Apr 11, 2024 · Good day, I am trying to create a spatial plot of gridded precipitation data. , 30°N–40°N, 100°W–90°W) using ncks: Read the contents of a netCDF file Read data with Python The easiest way to read a netCDF file is to use the xarray Python package. Matlab's current NetCDF reader should use the scale parameters (and missing value codes) from NetCDF-CF files without the need to apply scaling after the data have been loaded in Matlab. Would love to contribute it as method to this package Aug 19, 2023 · I have been trying to clip a global precipitation NetCDF file using a shape file of a basin I have. Please refer to the article on Visualising NetCDF data for a more general introduction to working with NetCDF files. Oct 28, 2020 · 2 I recommend to use xarray to handle netcdf data and geopandas + rasterio to handle your Shapefile. 1 Grid File Notes 2. Core abilities include: Contents 1Installing CDO 2CDO Grid Description Files 2. My mistake, I am in the wrong section but can't seem to delete my own post. If shapes do not overlap the raster Oct 6, 2025 · You can run this notebook in a live session or view it on Github. 01° square on the world map, there is an estimate of PM 2. 01°x0. 26. Contribute to ZPYin/Himawari-8_Visualizer development by creating an account on GitHub. warp. Here is the code: import xarray import rioxarray import geopandas from shapely. Aug 20, 2023 · The netCDF4 module in Python facilitates the reading and manipulation of NetCDF (Network Common Data Form) data files. Clipping by Bounding Box Clipping Vector Data by Polygon Clipping Raster Data by Polygon Batch Processing Clipping by Bounding Box Use gdal_translate with the -projwin flag to specify the coordinates of a clipping extent (ulx uly lrx lry). Star 23 Code Issues Pull requests ️ calculate polygon mask for netCDF/GRIB/raster python netcdf polygon shapefile masking crop-netcdf mask-netcdf crop-netcdf-shapefile polygon-mask Updated on Jul 22, 2023 Python Jun 23, 2021 · I have multiple global climate model (GCM) data files. You can control the format and engine used to write the file with the format and engine arguments. A toolbox to extract and wrangle daily gridded climate data from NETCDF objects available from the European Climate Assessement & Datasets (ECAD) for specific time period, compute summarized values and link them to set of spatial points. Dataset rather than a xr. Jul 16, 2020 · I have used xarray to clip my NetCDF file (it can be downloaded here) by a shapefile (it can be downloaded from here). It provides four key functions to process IMD NetCDF rainfall data and create rasters for various temporal scales, including annual, seasonal, monthly, and weekly Clipping Data Clipping is a method of subsetting data. Sep 4, 2019 · You will need the Python 3. This Python entry point script is written to be run via bash shell command, i. What Does Crop a Raster Mean? Cropping (sometimes also referred to as clipping), is when you subset or make a dataset smaller, by removing all data outside of the crop area or spatial extent. import rioxarray # for the extension to load import xarray import rasterio %matplotlib inline Regridding NetCDF data in Python This notebook tutorial was produced by the Knowledge Systems team at the Australian Institute of Marine Science to guide the reader through regridding NetCDF data in Python. After I run this code, I got the error: #AttributeError: module 'rasterio' has no Nov 9, 2020 · Sometimes a raster dataset covers a larger spatial extent than is needed for a particular purpose. By default, the file is saved as netCDF4 (assuming netCDF4-Python is installed). Print useful debugging information Example > python -c “import rioxarray; rioxarray. NetCDF files are a self-describing binary data format. nc') NC_NAfr = C_NAfr. format agnostic: It can read netCDF, GRIB, Zarr, raster files and also supports OPeNDAP. nc) geospatial files using python? If you can visualize the data, you can analyze the data. Jun 30, 2022 · A quick way to copy variables and metadata from one netcdf file to another using netcdf4-python - Converter. Others are appended as is. The similar posts are masking a netcdf file using a shapefile of points with rioxarray and h Jul 2, 2019 · I'm assuming that you know how to get a location as an XY pair out of your netCDF file, along with the velocity values at that location. 4. The rio accessor is activated by importing rioxarray like so: Feb 14, 2021 · When I attempt to clip it using xarray (in Python script) or nco (in the command line) by lat and lon coordinates, it is presumably not working as lat and lon are not dimensions. 5 Remove python netcdf polygon shapefile masking crop-netcdf mask-netcdf crop-netcdf-shapefile polygon-mask Updated on Jul 22, 2023 Python Dec 19, 2020 · I am trying to extract a geographic subregion from global NetCDF files available over opendap. nc4 or . How to read and plot . A place to find tutorials on how to use GES DISC tools, services, and data. Aug 30, 2024 · Discover how to clip and visualize NetCDF data using Python. pyplot as plt from netCDF4 import Nov 21, 2020 · I have a netcdf file that want to clip it based on my desired study area. Dataset`。我们所需要做的，只是依次定义维度、… To address this, a Python package, Iris, has been created to make loading and saving data from a variety of gridded datasets easier. Sep 23, 2023 · With the help of these libraries and Python’s adaptability, researchers and data scientists can readily browse complex multi-dimensional datasets, carry out geographical operations, and create Jun 10, 2022 · I have 7000 nc4 files and I need to clip netCDF files based on a shapefile, but I have a problem with rasterio. I'm also assuming that you're doing this in Python, since you put that tag on this question. mask. Apr 8, 2025 · I'm looking to use a shapefile to rio. HDF5 is a high-performance binary data format designed for storing and organizing large amounts of data, while NetCDF4 (based on HDF5) is widely used in atmospheric and oceanographic sciences for Oct 17, 2021 · 上一篇文章里我们学习了 如何读写NetCDF文件，今天我们将更进一步，学习使用xarray，从零写入一个NetCDF文件。 xarray支持我们使用字典结构的数据，创建一个`xarray. 3 Add an attribute to a variable in the NetCDF 4. Python package to automatically generate gridded climate data to be used as input for crop models - JJguri/bestiapop Oct 13, 2025 · Provides an object-oriented python interface to the netCDF version 4 library Nov 9, 2020 · Sometimes you will work with multiple rasters that are not in the same projections, and thus, need to reproject the rasters, so they are in the same coordinate reference system. Typically cropping of netCDF results in a rectangular box, but that's not what you want. 5 Improve this page Add a description, image, and links to the crop-netcdf topic page so that developers can more easily learn about it. reproject() is a geospatial-specific analog to SciPy’s scipy. , and usually, it is not an easy process for scholars and Aug 18, 2022 · NC_Aus = C_Aus. longitude) Read the contents of a netCDF file Read data with Python The easiest way to read a netCDF file is to use the xarray Python package. This script is process_climate_indices and is used to compute indices corresponding to gridded NetCDF datasets as well as US climate division NetCDF datasets. I think I have managed to do it and could get this plot with this script library (tidyverse) library (sf) l python mask netcdf data using shapefile Asked 7 years, 2 months ago Modified 7 years, 2 months ago Viewed 14k times Apr 18, 2022 · Currently the process to clip a netcdf4 file to a polygon is very lengthy. , derive new fields, compute statistics, print, hyperslab, manipulate metadata, regrid) and output the results to screen or files in text, binary, or netCDF formats. With some fiddling I was able to make a few world maps with the netCDF data, but I also started with monthly data so the amount of data is much greater with daily values. This information can cause the output to be a nonuniform Introduction **** The developed function is a comprehensive tool for the analysis of India Meteorological Department (IMD) NetCDF rainfall data. In other words, I'm hoping to "crop" a circle of a specified radius around a specified lat/lon. Working with Multidimensional Coordinates # Author: Ryan Abernathey Many datasets have physical coordinates which differ from their logical coordinates. Can read and write files in both the new netCDF 4 and the netCDF 3 format. With netCDF4, developers can access data stored in NetCDF files, making it a valuable tool for tasks involving climate data, geospatial information, and scientific research datasets. 2 Introduction netcdf4-python is a Python interface to the netCDF C library. mask module Mask the area outside of the input shapes with no data. nc files? The Network Common Data Format (NetCDF) is a self-describing scientific data access interface and library developed at the Unidata Program Center in Boulder. , global datasets) may need subsetting to reduce size before reprojection. open_dataset(file, group = ‘PRODUCT’) ds_ir = ds. Contribute to ZiluM/clip_code development by creating an account on GitHub. In these cases, you can crop a raster file to a smaller extent. Xarray provides several ways to plot and analyze such datasets. Casual users will appreciate the easy ability to do such as things as matching up point observation Jul 18, 2018 · 2 This question already has an answer here: Masking NetCDF time series data from shapefile using Python (1 answer) Oct 21, 2016 · However, I am hoping to filter the netCDF files so the max and min are found only within a certain distance of a given lat/lon. NCO can normal Added in version 0. Here I have completed the steps from downloading the data to clip 3 days ago · Units: dimensionless Step 2: (Optional) Subset the netCDF File Large netCDF files (e. Jul 9, 2022 · I have monthly estimates of PM 2. I successfully cropped one file but it takes time to crop one by one over thousand data files manually. NetCDFReader(*input, **params) Reads arrays from NetCDF files into structured VTK data sets. Xarray When working with higher dimensional data (3D or more), we can’t rely on Pandas. geometry. I'm using numpy and matplotlib right now, with Python on Windows. Nov 21, 2020 · I have a netcdf file that want to clip it based on my desired study area. 01° (i. RE: How to mask . The data are sea surface temperature and ocean color at 1/4 degree resolution. I have 4 polygons describing the US. 5 Remove Dec 19, 2020 · I am trying to extract a geographic subregion from global NetCDF files available over opendap. Feb 9, 2017 · I have a netCDF file with foll. $ process_climate_indices <options> The options for the entry point script are described below: Read the contents of a netCDF file Read data with Python The easiest way to read a netCDF file is to use the xarray Python package. Jul 9, 2020 · Read NetCDF Data with Python Access a slightly confusing, yet powerful, data format Network common data form (NetCDF) is commonly used to store multidimensional geographic data. nc') Read the contents of a netCDF file ¶ Read data with Python ¶ The easiest way to read a netCDF file is to use the xarray Python package. Sep 21, 2017 · I need to perform some geometric operations with geometries from another source on a netCDF-file. Let’s clip Jan 19, 2021 · I have a large collection of netcdf files which I need to crop with specific latitudes and longitudes and rewrite it as a new file. DataArray, rioxarray needs to guess which variables in the dataset should be clipped. 5 Dec 6, 2017 · The following is a similar question (Extract data from netcdf using a shapefile polygon in python) but the answer talks about running from command line but I'm using Spyder. crs, drop=False, invert=True) # Note: If you have rasterio < 1. I wish to clip the NetCDF files with a geodataframe containing the bounding boxes of the cities I am interested in and then make an average of the PM 2. It provides a self - describing, machine - independent way to store multi - dimensional arrays along with metadata. I'm using the polygon for the overlap (in operation it will be a state or county shapefile, this is simplified Aug 30, 2023 · cropping netcdf files using geo-coordinates. Learn how to crop raster data using a shapefile and export it as a new raster in open source Python nctoolkit: A Python package for netCDF analysis and post-processing # nctoolkit is a comprehensive and computationally efficient Python package for analyzing and post-processing netCDF data. The procedure is as follows: nctoolkit: A Python package for netCDF analysis and post-processing # nctoolkit is a comprehensive and computationally efficient Python package for analyzing and post-processing netCDF data. Thanks Mar 3, 2022 · NetCDF4 for Dummies A simplified guide to navigate and display NetCDF4 images in python Network Common Data Form (NetCDF) was something that I came across first time I wanted to plotsatellite Apr 3, 2024 · Can you clarify what you mean by "crop"? You have a gridded dataset. Jul 16, 2022 · Handling and Manipulating netCDF file in python July 16, 2022 NetCDF is a widely used data storage format, capable of storing high-dimensional, array-oriented data. In addition, the matplotlib library is used to make some plots. Read the contents of a netCDF file Read data with Python The easiest way to read a netCDF file is to use the xarray Python package. Climatic variables such as precipitation, temperature , soil moisture, atmospheric concentrations and many more that are produced from sources like satellite observations, reanalysis, climate models etc. Casual users will appreciate the easy ability to do such as things as matching up point observation Jan 28, 2021 · Sometimes you may want to spatially clip a vector data layer to a specified boundary for easier plotting and analysis of smaller spatial areas. Improve this page Add a description, image, and links to the crop-netcdf topic page so that developers can more easily learn about it. 2 Copy variables from one NetCDF file to another 4. structure: <xarray. Do you want everything outside the shapefile to become nan? In Python, you can read and edit NetCDF data using the xarray module and shapefiles with the geopandas package. Learn how to clip a vector data layer in Python using GeoPandas and Shapely. Its capacities to store multiple geospatial raster layers over time allow another level of abstraction on data analysis, however the format is of limited use on normal desktop applications and most times we are required to use a programming language such as Python or R. Pixels are masked or set to nodata outside the input shapes, unless invert is True. Mar 23, 2020 · I have a 3-D time-series precipitation data (187 x 1800 x 3600), stored in a NetCDF file. In NetCDF file we can apply bilinear interpolation to have data for any latitude and longitude within India by taking 4 grids adjoining the particular latitude and longitude. Hello! My goal is to mask a NetCDF file with a shapefile. For reading and plotting data of a NetCDF file, you should work with different programming languages such as MATLAB, NCL, R, Python, and etc. pyplot as plt from netCDF4 import rasterio. RE: Clipping a NetCDF file with mask and Python - Added by Muhammad Ramzan almost 3 years ago Hello Benoît are you able to crop the NetCDF files based on your study area. ds = xr. Once you've got an XY pair, you just need a function (with a bunch of parameters) to transform it to lon/lat. requires spatio-temporal Use python, shp_file to clip netcdf data. simple. We would like to show you a description here but the site won’t allow us. For example: # # from shapely. How can I do multiple crops? Thanks May 12, 2022 · When you call the rioxarray accessor ds. 5GB with latitude values ranging from [-90, 90] and longitude values ranging from [-180, 180]. Jupyter is a very popular version of python notebooks, and is used extensively by the GES DISC team. Learn how to open and process MACA version 2 climate data for the Continental United States using the open source python package, xarray. Using the solution clipped = xds. where((44 < ds. Crop a NetCDF file by XY, Z, and Time with CDO + python bindings - subset_examples. Polygon) from the other source in a geopandas. x Anaconda distribution, git and bash to set things up. Northeast conti Their problem is related to one shapefile and cropping the netcdf accordingly. This is the code: import geopandas as gpd import rioxarray import xarray as xr import matplotlib. Rasterio’s rasterio. paraview. Some of the following examples make use of the Iris loading capabilities, while others use the netCDF4 Python package so as to show a range of different approaches to data loading. This guide covers the full process from data manipulation to visualizing results before and after clipping. Given that the netcdf4 files are huge, the process often leads to Memory issues. nc, but I don't know how to extract the file's date. NCO can normal This video explains how to read, clip and save a raster by using an specific shapefile. Use ncks (from the netcdf4-python package) or gdal_translate to crop by spatial extent. The required region runs from 13 degrees west to 10 degrees east: longitudes -13 to 10. clip a raster so I can find where they overlap. In the absence of any other information, the files will be read as image data. That is around 4~5 lines of code. Relies on NumPy arrays. g. Nov 19, 2021 · Historic and projected climate data are most often stored in netcdf 4 format. e. Dataset> Dimensions: (latitude: 94, longitude: 192, time: 366) Coordinates: * longitude (longitude) float32 Jun 11, 2020 · How to read and visualize netCDF (. Learn how to reproject raster data in Python using Rasterio. Converting NetCDF dataset array to GeoTiff How do I add projection to this NetCDF file? (Satellite) Create a new raster TIFF file which is masked based on the GeoJSON file How to mask NetCDF time series data from a shapefile in Python? Extract data from raster at a point Convert raster to CSV with lat, lon, and value columns Feb 14, 2021 · When I attempt to clip it using xarray (in Python script) or nco (in the command line) by lat and lon coordinates, it is presumably not working as lat and lon are not dimensions. py Sep 26, 2022 · I have a NetCDF file with 2. 1 Do a conservative regridding of a grid from one resolution to another. Dataset> Dimensions: (latitude: 94, longitude: 192, time: 366) Coordinates: * longitude (longitude) float32 Read the contents of a netCDF file Read data with Python The easiest way to read a netCDF file is to use the xarray Python package. sel(lat= Mar 7, 2022 · I'm trying to crop a netcdf file with a polygon with stars package from daily netcdf data. Aug 1, 2024 · NetCDF has become a popular choice for storing and delivering precipitation and water resources related data. Jun 11, 2020 · How to read and visualize netCDF (. What I'm having trouble to do is: when writing this new netcdf file I want to name it with its respective date and time, something like "yyyymmddhhmm". If the shapefile contained countries, with a unique country ID and the netCDF file contained global weather data what would the easiest way be to extract the weather data by country? The obvious answer would be a big for loop of code generating a file per country. netCDF version 4 has many features not found in earlier versions of the library and is implemented on top of HDF5. Package netCDF4 Version 1. The API modelled after In this tutorial, I have demonstrated how to clip multiple netcdf files by study area shapefile or country shapefile in python. 4 Remove unwanted Variables 4. I want to split my netcdf file into smaller ones. for each 0. Read the contents of a netCDF file ¶ Read data with Python ¶ The easiest way to read a netCDF file is to use the xarray Python package. If you are comfortable with Python language and would like to integrate this conversion in a manipulation script process, here is a method to convert NetCDF file to GeoTIFF using a Python routine. #pytho However, for a more recent version of the NetCDF standard and additional features, please consider the permissively-licensed netcdf4-python. Dec 15, 2020 · My question is similar to what others have already asked but the posted solutions haven't worked for me. py Is there anyone who can provide assistance in using Python code or R to clip NetCDF data with a shapefile? Apr 11, 2025 · NetCDF4 is an enhanced version of NetCDF that supports new data types and compression features. 01° square). netcdf file from shape file? - Added by Karin Meier-Fleischer about 7 years ago Add a description, image, and links to the crop-netcdf-shapefile topic page so that developers can more easily learn about it Jul 9, 2025 · To check the version of your library, call the following function after importing netCDF4-python: netCDF4. I have written a two-step function that does this on Python pretty quickly. For do that I used xarray as follow. Casual users will appreciate the easy ability to do such as things as matching up point observation netcdf4-python: python/numpy interface to the netCDF C library - Unidata/netcdf4-python Python interface to the netCDF version 4 library. NCO aids analysis of gridded and unstructured scientific data 3 days ago · If you’re working with scientific data, climate models, or large datasets in Python, chances are you’ve encountered **HDF5** (Hierarchical Data Format) and **NetCDF4** (Network Common Data Form). This module can read and write files in both the new netCDF 4 and the old netCDF 3 format, and can create files that are readable by HDF5 clients. Learn more about cropping, netcdf, geo-coordinates MATLAB Jan 7, 2022 · I am writing a program that will open Meteorological NetCDF data, slice it for a given region and then do some calculations, for example: data =xr. clip using a xr. Who is nctoolkit for? # Everyone from casual to regular users of netCDF data will find nctoolkit useful. The method docstring gives the following warning: Warning: Clips variables that have dimensions ‘x’/’y’. to_netcdf(path = 'E:\PSU\CCAR REU\Python Codex\MASKS\Outputs\Aus. longitude) Jul 10, 2022 · I have monthly estimates of PM 2. It has Pandas like syntax, so if you know Pandas you will find yourself at home with Xarray. So the issue you're running into is that rioxarray sees four variables in your dataset: IMD Gridded data has two formats (NetCDF and Binary file), always prepare NetCDF format because we can easily convert through programming applications like Python, Matlab. Can create files that are readable by HDF5 utilities. Apr 11, 2025 · NetCDF (Network Common Data Form) is a widely used format for storing scientific data. mgsrq btwk gqpimv mmmmt jphuvx ahqmi yiixrns hcry ngt czbhs auvgee roeuwu kfnwsj crymt gkdbm