Questions tagged [xarray]
xarray is a Python module for working with N-dimensional arrays
125
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Landsat from Planetary Computer unexpectedly turns up all no data in some regions
Using some code that gathers Landsat 8 collections from Microsoft Planetary Computer into Open Data Cube xarray using a stac search works fine in some regions but in others returns all nan values. ...
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75
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Randomly sample locations from a large xarray dataset
I want to create random sample locations on land (lat/lon), weighted by latitude, from a large xarray dataset. Currently, I am creating the lat/lon pairs from a land-sea-mask with the script below, ...
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Loading geospatial datasets with rioxarray
I'm using xarray to open and reproject some .grib files. The files have x, y, and time dimensions and contain several data variables. However, I have some issues with loading the data.
Loading them ...
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Extending raster after rasterizing geodataframe using geocube
I have created rasterized a geodataframe using geocube make_geocube.
The resulting xr.Dataset now has the extent of the underlying geodataframe vector data.
Say, the bounding box would be covering ...
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GeoTIFF from Dataset is very weight and with three bands instead of one
I need to compute the NDVI from an xarray Dataset created using this solution. I've used a for loop to read all the GeoTIFFs in my folder and the result is this:
<xarray.Dataset>
Dimensions: ...
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Memory filled with Xarray concat function
I'm facing in trouble related to the limit of my RAM. On my PC I have 32GB of RAM that is totaly filled from the concat of some DataArray.
I've create e simple function below to read a single band of ...
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Using Python (in Colab), how to convert a multiband ee.Image into an ee.ImageCollection?
I ultimately want to convert an ee.Image to an xarray object so I can further process the data.
I know the library wxee can do that with ee.ImageCollection.wx.to_xarray(). However, it requires an ee....
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Incorrect longitude coordinates on NetCDF from CAMS it can't allow masking
I've downloaded from Copernicus Atmosphere Monitoring Service some analysis about particulate matter in .nc file format.
I need to mask that data and save in the same file format.
Using Xarray library ...
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NetCDF time variable is missing a 'units' attribute
I have NetCDF files whose dates range from Jan 1850 to Dec 2014 (15th of each month). I need to extract data post Jan 1995. I am doing this:
start_time = datetime.datetime(1995, 1, 10, 0, 0)
times = ...
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Saving extracted array into new NetCDF file
I have a NetCDF file which looks like this:
<xarray.Dataset>
Dimensions: (time: 180, d2: 2, lat: 180, lon: 360)
Coordinates:
* time (time) object 2000-01-15 12:00:00 ... 2014-12-15 12:...
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Using rioxarray clip_box function does not return anything
I am trying to clip an xarray dataarray (or dataset, either one) to a bounding box using the rioxarray clip_box() function. My dataarray is 24 hours of temperature data for the continental US. My ...
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430
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Interpolate irregularly sampled data to a regular grid
I'm using .nc files with spatially referenced timeseries data in xarray, i.e. inherently 3-dimensional data (lat, lon, time). My issue is, that the dataset's coordinates lat and lon are merged to a ...
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241
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Saving plot from .nc file without showing the plot
I am trying to save the sequence of plots of 24 hours of ERA5 data from .nc file without plotting them. I am using xarray for reading .nc data. Here is my code:
import xarray as xr
import matplotlib....
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Convert the netcdf file to geotiff with chosen coordinate system
I have a nc file retrieved from the following link https://www.globsnow.info/swe/nrt/2020/data/GlobSnow_SWE_L3A_20200110_v.1.0.nc.gz. I am trying to convert this file to geotiff in wgs 1984 coordinate ...
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Error reading variables from NetCDF file with Xarray when there are multiple variable layers
I get an error reading variables from NetCDF file with Xarray when there are multiple variable layers
Data:
The netCDF file that I have has multiple layers:
/Geophysical_Data/...
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353
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Fixing the flipped/inverted Y axis in the xarray with rasterio
The data I read with xarray with rasterio engine is inverted along Y axis (This is SMAPL4 data). The correct dimension values are y=ds.y*(-1).
ds = xr.open_mfdataset(file_paths, engine="rasterio&...
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2
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376
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Is it possible to change a coordinate in an netCDF loaded with xarray?
I have a netCDF which is loaded in xarray with a dimension named bands (it was originally an import via rioxarray of ENVI data), but actually, I want to be able to parse the data by time. I have tried ...
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140
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When i save my xarray DataAarray the coordinates are wrong
I have three 3x3 arrays that are downsampled data from NOAA's Global Hydro Estimator (smaller to make it quicker for testing). One array is lats, one is lons, and one is rainfall. Here's a sample
lons:...
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225
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Clipping an xarray dataset with rio clip function produces empty xarray
I have an xarray dataset ds containing a variable 'pop'.
xarray.Dataset
Dimensions:
time: 1latitude: 5751longitude: 13197
Coordinates:
time
(time)
datetime64[ns]
2000-12-31
latitude
(latitude)
float64
...
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Interpolating a regular lat/lon grid with latitude line at Equator to a shifted grid using Python
I am very new to GIS and have to work with some precipitation data contained in two different datasets with comparable coordinate systems, but differently offset/shifted coordinates:
NASA GPM IMERG ...
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1
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Convert a multiband GeoTIFF to a timeseries NetCDF file in xarray
I am trying to create a time series object from extracted climate data (NEX-GDDP) using the Google Earth Engine (GEE). The data is daily meteorological data, and in the attached file, the data for ...
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189
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How to add additional bands to a TIFF using rioxarray
I'm trying to work out how to open a raster, determine the name of the existing band(s), then use that bands value in math to create a new band.
I believe the data is being loaded to a DataArray. I'm ...
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169
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Save multiple GeoTIFF files from a GRIB file, one file per day (time dimension)
I am trying to save multiple GeoTIFF files from a GRIB file I have elaborated.
Before converting to raster, the GRIB file I started with is a ERA5 2m hourly temperature over 3 days:
import iris
# ...
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1
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371
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Mask NetCDF data in Python with shapefile
Precursor to this question: Masking NetCDF data with a shapefile in that has more than one variable Python. Note: Data files are in the previous question.
I am trying to mask my polygon but I don't ...
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163
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y dimension not found while converting NetCDF to Raster with rasterio
So I have a NetCDF file from the TROPOSIF website and converted it to xarray dataset that looks like this:
And I'm trying to convert it to a tif file but while I'm trying to export the SIF_735 ...
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80
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Legend for gridded Holoviews visualization with categorical data
I'm using the holoviews extensions to visualize a gridded dataset with landcover classes. Plotting the data is straightforward with da.hvplot(). This results however in a continuous colormap with ...
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Using xarray and rioxarray for converting netCDF to GeoTIFF gives TypeError: cannot pickle '_thread.lock' object
I am trying to convert a netCDF file to GeoTIFF file using xarrray and rioxarray. But when I give the rio.to_raster command, it throws the TypeError: cannot pickle '_thread.lock' object. The NetCDF ...
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Georeference NetCDF using rioxarray
I have a NetCDF file with a lot of variables and an improperly set georeference. Loading using xarray works, using rioxarray.open_rasterio I get the following error: "NotGeoreferencedWarning: ...
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369
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Create an xarray dataset form a series of GeoTIFFs and clipping problem
I am trying to create a dataset from a series of GeoTIFFs (one .tiff file per day) and then clip it with a given geometry (shapefile).
The TIFF files, one per day, have this format: e.g. day 29-07-...
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Extract data for aoi from preprocessed Landsat CCDC ImageCollection using GEE Python API
I try to extract for a collection of 1 ha square polygons the bands coefficients from a preprocessed Landsat CCDC Google Earth Engine Asset ee.ImageCollection('projects/CCDC/v3').
My plan is the ...
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222
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Zonal stats from NetCDF for all time dimensions
I use the following code to get zonal stats of data for each time.
import xarray
import rasterstats
import geopandas
import numpy as np
nc_data = xarray.open_dataset(nc_file_path)
shp_prj = geopandas....
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GeoServer Java error when adding layer from NetCDF based store
Using xarray I have subsetted surface current data from the https://resources.marine.coperncus.eu OPeNDAP server. I save the subset as a NetCDF4 file. I am able to add the NetCDF file as a store in ...
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39
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Python, colorize raster randomly avoiding same color for adjacent cells
I'm processing GeoTIFF rasters with python and xarray. The file contains some cells with different values. It looks like that:
There are about 100 different values in the file and each value needs to ...
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1
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137
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Is there a way to limit the distance of rioxarray's interpolate_na()
I'm trying to run something similar to gdal's fillnodata command line tool in Xarray. Xarray has interpolate_na() that comes with an optional parameter limit where you can limit the number of ...
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Add lat and lon to DataArray read in by rioxarray
I downloaded a GeoTIFF from here: https://www.nass.usda.gov/Research_and_Science/Crop_Progress_Gridded_Layers/index.php
(file also available: https://drive.google.com/file/d/1XcfEw-...
- 115
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Rasterising GOES-R Derived Motion Winds
I have CONUS Derived Motion Winds netCDF data from the GOES-R 17 satellite, retrieved from the AWS repository (specifically OR_ABI-L2-DMWC). I am trying to rasterise this into a GeoTiff (specifically ...
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1
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218
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Changes to GDAL NetCDF driver between 3.2 and 3.4
I am preparing data in python using xarray and rioxarray, then exporting to NetCDF. On one machine with
micha@RMS:Kinneret$ gdalinfo --version
GDAL 3.2.2, released 2021/03/05
the extent of the ...
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Looking up whole time-series for specific point from 45 GB file
I want to look-up 8760 times for a single lat/lon combo in less than a second from 43.82 GB file of wind data containing:
8760 times (every hour in a year)
721 latitudes (every 0.25° from -90.0° to ...
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225
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How to apply a function on two rasters in Python?
I would like to cell-wise function operation on two rasters. While I saw some examples of adding or subtracting two rasters, I'm yet to come across a complex example of how to manipulate rasters using ...
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1k
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Xarray computing of a new variable on the basis of the existing one
I have netcdf file with calculated average temperature (°F). My goal is to create new data variable within the same file with cooling / heating degree days using that average. This format is totally ...
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1
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56
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NetCDF stretched along Y (latitude) axis
I'm working with NOAA temperature NetCDF files and trying limit area of interest to the US area only using bounding box.
In Jupyter Notebook I wrote few lines to do it and on the plot everything looks ...
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1
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2k
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Create one NetCDF file from multiple NetCDF files using Python [closed]
I am downloading climate data in NetCDF format. For each variable (e.g. 'precipitation'), I need to merge 9 NetCDFs, each belonging to an unique climate model. Each NetCDF has the same size (time, lat,...
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How to deal with Nan value when using rioxarray rio.reproject()?
I was trying to use rio.reproject_match() to match the resolution of two xarray datasets. However, when I used resample methods like Resampling.bilinear or Resampling.average, a large area would ...
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216
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Pixel-based regression using xarray has incorrect P-value, but everything else is correct
I am using the code from this website to perform a regression on each pixel of an image time-series of rain and NDVI. The code works for everything, that is the outputs match the outputs of scipy, for ...
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1
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434
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Convert GeoTIFF to Zarr Store using Xarray
I am trying to convert my 3-band GeoTIFF to Zarr store. I am able to read in the GeoTIFF from xarray with rasterio backend.
In [1]: import xarray as xr
In [2]: xtci = xr.open_dataset('tci.tif', ...
- 995
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533
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Combine two raster datasets from different areas - xarray
I simply wish to combine two raster datasets from different spatial extents and with different coordinate reference systems using python. Eventually, I wish to combine enumerable datasets, but ...
- 168
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1
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1k
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Xarray Dataset to raster - ValueError: failed to prevent overwriting existing key grid_mapping in attrs
I have a netcdf file located here http://thredds.northwestknowledge.net:8080/thredds/catalog/TERRACLIMATE_ALL/data/catalog.html?dataset=TERRACLIMATE_ALL_SCAN/data/TerraClimate_tmin_1958.nc.
I am ...
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1
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1k
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Increase map size with subplots and Cartopy
I try to make subplot maps with Cartopy using data from xarray tutorial and increase each map in vertical size, but failed. Also making colorbar at each specific subplots.
import matplotlib.pyplot as ...
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1
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308
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Unable to convert Sentinel-5P NetCDF file to GeoTIFF using xarray python
I am trying to convert Sentinel-5P NetCDF file (available at https://drive.google.com/file/d/1dJdhQspdI3p5YyyiBBiNxUPCCOU91QrU/view?usp=sharing) to GeoTIFF using the following code:
import xarray
...
- 606
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1
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890
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Why do rioxarray reprojection and pyproj transform give different values when selecting a pixel by point coordinates?
I'm opening this grib file using rioxarray and reprojecting to WGS84 in the following manner with the goal of grabbing pixel values by coordinates.
import rioxarray
url = 'https://noaa-hrrr-bdp-pds....
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