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Questions tagged [xarray]

xarray is a Python module for working with N-dimensional arrays

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1 answer
373 views

Polygon Drill on Open Data Cube

I face a crucial problem with ODC. I try to do a spatial join with a shapefile (polygon drill). I have followed the following steps: Read the shapefile and get the first polygon to test Ensure that ...
2 votes
1 answer
289 views

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 ...
0 votes
1 answer
782 views

How to extract exact values from a raster file (TIFF) using a shapefile, using xarray to open the raster

I have found a link online that extracts the values min mean max and median, this is using the zonal stats function. sjer_tree_heights = rs.zonal_stats(plot_buffer_path, ...
6 votes
1 answer
3k views

Using Rioxarray / QGIS Projection

For the past couple weeks I have been trying to view GOES17 data from netCDF files (converted to geotif) in QGIS 3.10 but cannot get the projection to work correctly. I have attempted numerous ...
-1 votes
1 answer
48 views

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 ...
0 votes
0 answers
22 views

Earth Engine client library not initialized when using a dask cluster and xarray?

I'm trying to test running a simple math operation client-side using xee, an xarray extension for the Google Earth Engine API. When I set up the Dask client and run the compute() method I keep getting ...
0 votes
0 answers
26 views

xee: Total request size (56623104 bytes) must be less than or equal to 50331648 bytes

I am using xee, an extension of xarray to work with data from Google Earth Engine. I am trying to test computing NDVI through an xarray of Landsat imagery, but I keep getting this error. EEException: ...
0 votes
1 answer
236 views

AttributeError: 'Dataset' object has no attribute 'rio' when using a LocalCluster from dask.distributed

I am trying to parallelize a function that uses a zarr datacube read from an s3 bucket to perform some calculations. However, when using a LocalCluster from dask.distributed, I lose the .rio accessor ...
2 votes
1 answer
27 views

Create .nc file from multiple tif files : metadata time

I'm trying to create a single .nc file with 3 dimensions : x,y and time. In order to do so I have multiple tif files named by their date : 2013-04-24_Turb.tif for the 24-04-2013. I would like to do ...
2 votes
1 answer
520 views

How to fix rioxarray.exceptions.DimensionMissingCoordinateError: x missing coordinates?

I'm trying to reproject a NetCDF file without an assigned projection. I was successful in assigning projection. But, while attempting to reproject the file, I receive the following error: rioxarray....
1 vote
1 answer
274 views

Accessing Numpy Array found within an XArray from Satpy

dask.array<shape=(76, 76), dtype=float32, chunksize=(76, 76)> Coordinates: crs object +proj=utm +datum=WGS84 +ellps=WGS84 +no_defs +units=m +zone=33.0 +type=crs * y (y) float64 ...
0 votes
1 answer
296 views

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 # ...
1 vote
0 answers
28 views

All-NaN slice encountered when apply xr_phenology function?

I want calculate vegetation phenology from ndvi netcdf dataset, I follow yours tutorials (DEA Australia and DEA Africa) to apply xr_phenology function , defined here. To avoid killed kernel of my ...
0 votes
1 answer
21 views

Invert latitude of NetCDF in Python / xarray

I thought it would be straight up, but I don't find a question like this one here. I created a NetCDF out of a GeoTIFF, but it did not have coordinates or CRS. I added it doing this: coords = { 'time' ...
1 vote
1 answer
188 views

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....
0 votes
1 answer
171 views

Plotting Open Data Cube xarray data with two or more measurement parameters in the same axis

How can I plot the two measurement parameters (seasonal cover and permanent water cover) in the same axis as I want to compare them? I have this code: #load the cgls product ds_cgls_builtcover = dc....
0 votes
0 answers
53 views

rioxarray.open_rasterio() won't close a file when using it with a context manager

I am writing some unit tests to test reading in raster data into an xr.Dataset data structure via the rioxarray.open_rasterio() method. The code creates a test raster to read into rioxarray....
0 votes
1 answer
56 views

QGIS crashes with "bad_alloc" when processing NetCDF file using xarray

I need to merge multiple NetCDF files in a QGIS plugin I am developing. I'm using xarray to do so, however, QGIS crashes with the error "Critical: Caught unhandled std::exception: std::bad_alloc&...
3 votes
1 answer
2k views

Value error when merging .nc files: xarray could not find any dimension coordinates to use to order the datasets for concatenation

I want to merge multiple .nc files into one. Each of the .nc files corresponds to a timestep which should be added together to have one .nc file with all data for all dates. When I execute the ...
2 votes
1 answer
449 views

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 ...
0 votes
0 answers
55 views

Performance difference between xarray open_mfdataset and open_dataset

I'm dealing with CMIP6 Scenariomip data, I have eight ESMs precipitation grid that each one is composed by multiple netcdf files. There is one ESMs's netcdf files are seperately reserved every decade, ...
0 votes
0 answers
91 views

Low performance when writing a large xarray.DataArray with dask

I'm preprocessing HMASR data, the data contains multiple data files with format of netcdf, and each tile (1X1 degree) is a nc file. So I read it through xarray open_mfdataset() to mosaic it spatially ...
1 vote
1 answer
219 views

Exporting NetCDF file in MODIS sinusoidal grid with xarray

I have 18 TIFF files in the MODIS sinusoidal grid I would like to convert to one file in NetCDF format. I have converted the tifs to an xarray xarray.core.dataset.Dataset format called stacked. At ...
1 vote
1 answer
63 views

While exporting the rasters using rioxarray, nodata value is undefined after the mask

I have used xarray to open the netcdf file, and using rioxarray exported the raster as a .tif file. However, the exported raster doesn't have definition for nodata value, and hence, the GIS software ...
6 votes
1 answer
11k views

Indexing coordinates in order to get a value by coordinates from xarray

Firstly, I am a super rookie and just recently started working with GIS. Therefore I am not sure how to ask/word the question, or even if it makes sense. So bear with me. I have some NetCDF files, ...
0 votes
0 answers
97 views

xarray : no such file directory

I'm trying to transform a .nc file in .tiff using this code : import xarray as xr import rioxarray as rio nc_file = xr.open_dataset("C:/Users/aurel/OneDrive/Documents/Mémoire/Datasets/CCI_lake/...
0 votes
0 answers
48 views

How can I extract the array indices from a xarray.rio.clip operation?

I have a line of code that clips a Dataset from a larger xarray.core.dataset.Dataset. clipped = ds.rio.clip([user_polygon], crs=4326, all_touched=True) I need to process many of these large datasets (...
1 vote
0 answers
22 views

Buffer Error when using xarray

When I tried to using python package "xarray" to read grib files, I got an error. It's quite weird, because I had did it successfully yesterday. This is my code: import xarray as xr import ...
0 votes
1 answer
44 views

Gridworkflow intersection with other spatial objects such as a geodataframe

I am working with a large GridWorkFlow object; I am not able to load all the tiles due to in-memory compute resources (24.00 GB mem 8 CPU) and do not need to either. I am interested in intersecting ...
3 votes
1 answer
303 views

How to write CRS info to NetCDF in a way QGIS can read? (Python/Xarray)

I have a NetCDF file I have subset by geometry and time, and now I need to save it as a new NetCDF file. The original file does not have the CRS set, thus I am setting it in this one. The problem is ...
0 votes
1 answer
487 views

Extract nearest values from NetCDF file in Python

I have a NetCDF database (link to file) obtained from Copernicus Climate Data of ~43k unevenly spaced values around the world. Instead of being indexed using (lat, lon) it uses a sequence of 'stations'...
0 votes
0 answers
31 views

Change dtype of coordinates NetCDF

I was wondering how to change the dtype from float32 to float64 of coordinates. I can run the following code in the terminal ncap2 -s 'lat=double(lat); lon=double(lon)' infile.nc outfile.nc How ever ...
0 votes
1 answer
242 views

Transform ee.ImageCollection to xr.Dataset in Python (via Colab)

I am trying to transform an ee.ImageCollection (Landsat) for a Region of Interest into an xr.Dataset so I can further process the data and ultimately export as a .csv. I have tried using the library ...
0 votes
0 answers
43 views

How to open NetCDF4-CF files from SMAP in xarray

I've downloaded a list of netCDF4-CF files from SMAP (Following this guide in jupyter notebook) to get daily soil moisture data over 2020 in South Sudan. The result is a series of .nc files that I ...
1 vote
0 answers
96 views

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. ...
0 votes
1 answer
75 views

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: ...
0 votes
2 answers
896 views

How to stack list of Xarrays

I have a folder with 4 .tiff (GeoTiff) files. Each of these contains two layers (the spectral band and a mask). I'm able to create a list containig each image using xarray.open_rasterio. Now I need to ...
6 votes
1 answer
10k views

Using rioxarray to assign spatial reference (EPSG:4326) to NetCDF built from CSV with lat long columns

I am trying to create a NetCDF from a CSV file. The idea comes from the fact that the original CSV comes with many columns, three of these representing: a specific year ("time") the Y ...
0 votes
0 answers
258 views

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, ...
1 vote
0 answers
360 views

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 ...
0 votes
1 answer
317 views

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 ...
1 vote
0 answers
153 views

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:...
0 votes
0 answers
347 views

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 ...
1 vote
2 answers
938 views

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&...
0 votes
1 answer
355 views

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/...
1 vote
1 answer
1k views

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 ...
0 votes
1 answer
542 views

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....
1 vote
0 answers
152 views

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 ...
2 votes
2 answers
995 views

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 ...
0 votes
1 answer
228 views

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:...