Questions tagged [rioxarray]
geospatial xarray extension powered by rasterio. https://github.com/corteva/rioxarray
135
questions
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28
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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. ...
- 307
0
votes
0
answers
19
views
Reproject by Estimate_utm_crs()
If I am using function x.rio.reproject(x.rio.estimate_utm_crs()) then am I actually considering also parallels? The width and height of pixel changes with different longitude for me, however, The UTM ...
- 293
1
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1
answer
161
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Writing GeoTIFF from dask array using rioxarray in python results in "stripes" of no data
I am trying to write a large raster from a dask array to a GeoTIFF file, but am running into an issue where the resulting raster contains "stripes" of no data. The pixels that do contain ...
- 13
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0
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84
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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 ...
- 11
0
votes
1
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39
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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: ...
- 920
0
votes
1
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87
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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 ...
- 920
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1
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123
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Using xarray to write NetCDF4 to GeoTIFF, get AttributeError: 'DataArray' object has no attribute '_data'
I tried to convert GPM nc4 files from NASA into GeoTIFF, but I got an error. Here's my code:
import xarray
import rioxarray
import os
os.chdir(dir_path)
xds = xarray.open_dataset(
"3B-MO.MS....
1
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1
answer
72
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....
- 21
0
votes
0
answers
82
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Reprojecting NetCDF file from LCC to WGS84: 'Multiple grid mappings exist' error
I try to reproject a NetCDF file to WGS84 so I can clip it with a regional geometry for analysis. The file is a dataset with the CORDEX precipitation variable, climate change scenario rcp 2.6, years ...
- 1
0
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52
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Cordex precipatation values reproject to WGS84 from Lampert Conical
I have to calculate some precipitation indices for a region, and for this I have to reproject the dataset to WGS84. I have the following code to obtain the datasets:
import cdsapi
import rioxarray as ...
- 1
0
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0
answers
182
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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 ...
- 60
2
votes
2
answers
376
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
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1
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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:...
- 524
1
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1
answer
156
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Using coordinates to access GeoTIFF dataset
I'm trying to read a tile from the Sentinel1 SAR data collection. I'm using rioxarray to open the .tiff data file.
rioxarray.open_rasterio(
path_to_data,
overview_level=...
- 11
0
votes
0
answers
225
views
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
...
- 1
2
votes
1
answer
206
views
Converting NetCDF to GeoTIFF
I'm having trouble using rioxarray for converting one time layer of the .nc file to a GeoTIFF. I get the following error:
MissingSpatialDimensionError: y dimension not found. 'rio.set_spatial_dims()' ...
- 31
0
votes
1
answer
149
views
Rasterizing shapefiles using Geocube
I am trying to create a raster from a shapefile, with cells assigned a value from a specific column within the shapefile. I am using geocube below but am getting an error saying
AttributeError: '...
- 1
0
votes
0
answers
70
views
Using rioxarray to open netcdf output from polymer
I'm using rioxarray to clip some .nc files processed through Polymer (atmospheric processor). The issue I'm having is when I import the .nc file I get the following error:
The original file was in ...
1
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0
answers
189
views
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 ...
- 270
0
votes
1
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169
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
# ...
- 21
1
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1
answer
245
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Masking NetCDF data with a shapefile in that has more than one variable Python
I'm using NetCDF (TROPOSIF data) which i have been able plot and I now want to mask out my AOI with a shapefile.
I imported
import rioxarray
import geopandas as gpd
I opened the dataset using
ds = ...
- 21
0
votes
0
answers
208
views
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 ...
- 11
1
vote
1
answer
1k
views
Stack rioxarray DataArrays for output to GeoTIFF
I am trying to read a GeoTIFF, perform calculations (radiometric correction) on all bands, and then output back to GeoTIFF. Most of the code I have works fine, up until trying to output.
import os
...
- 459
1
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0
answers
134
views
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: ...
- 11
2
votes
0
answers
369
views
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-...
- 21
1
vote
1
answer
37
views
Estimating area from global raster datasets
I am trying to estimate how much area of emerged landmasses is covered by each of the 12 great groups of soils defined in the USDA Soil Taxonomy with rasterio/rioxarray. My results differ quite a bit ...
- 150
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1
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137
views
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 ...
- 524
0
votes
1
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596
views
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
1
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1
answer
585
views
How to fix CHECK_DISK_FREE_SPACE problem while writing a file with rioxarray?
I get this warning when I try to write out a raster using rioxarray:
Free disk space available is 0 bytes, whereas 1152072000 are at least necessary. You can disable this check by defining the ...
- 679
5
votes
1
answer
311
views
MissingCRS error while opening MODIS data using rioxarray
I have a MODIS data. It is a hdf file (not hdf5). I can open it using ArcGIS and QGIS with no crs. When I use the following script, I get MissingCRS: CRS not found. Please set the CRS with 'rio....
- 74.7k
1
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1
answer
218
views
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 ...
- 15.4k
0
votes
1
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225
views
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 ...
- 481
5
votes
3
answers
302
views
Raster Statistics of Fire Driven Forest Loss within shapefile
I have two inputs,
a) shapefile, which I am reading in as a geodataframe, download here: https://we.tl/t-QxfgtLWOVN
b) raster data from - GFW Fire Driven Forest Loss dataset, download here: https://...
- 199
0
votes
1
answer
56
views
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 ...
- 35
2
votes
1
answer
372
views
Clip using geodataframe and rioxarry.clip not clipping xarray dataset
I am trying to clip an xarray dataset using rioxarray.clip with geometry from a geodataframe. I am running the code on a cloud platform built on kubernetes clusters in a distributed manner using Dask. ...
2
votes
1
answer
293
views
How to use Python packages (GeoPandas, rioxarray) inside GRASS Python scripts?
I want to combine the functionality of GRASS GIS with other Python packages such as GeoPandas and rioxarray. My OS is Windows. It is possible to import other standard packages such as numpy and Pandas....
1
vote
1
answer
1k
views
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 ...
- 33
0
votes
0
answers
533
views
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
1
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1
answer
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 ...
- 838
4
votes
2
answers
2k
views
Vectorizing a raster containing holes using rasterio
I want to vectorize raster that contains holes (nodata) in the areas with valid data.
My current version uses rasterio.features.shapes:
shape_list = list(shapes(raster.values, mask=raster.values !=...
- 367
1
vote
1
answer
139
views
RuntimeWarning when I try to plot a raster
I'm using JupyterNotebook to analyze some GIS data. I need to clip a raster and plot the result but I've a strange problem. Folder with data is here; the raster size is 1MB.
I'm be able to plot the ...
- 920
1
vote
1
answer
354
views
How to convert crs_wkt starting with GEOGCRS to a ogc_wkt string (to use rioxarray.reproject_match)
I have two xarray data arrays (1. land_data, 2. climate_data) that I want to reproject and match (rio.reproject_match()):
climate_data_matched = climate_data.rio.reproject_match(land_data)
Land data ...
- 33
0
votes
1
answer
890
views
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....
- 524
1
vote
1
answer
581
views
Extract by polygon from a rioxarray's raster
I'm attempting to extract NBR mean value from MODIS data based on a set of polygons. The polygon set has overlapping everywhere (don't blame me, it's not my work nor my idea). The shapefile is ...
- 13.1k
1
vote
2
answers
529
views
Add projection to rioxarray dataset in Python
I've downloaded a netcdf from the Climate Data Store and would like to write a CRS to it, so I can clip it for a shapefile. However, I get an error when assigning a CRS. Below my script and what is ...
- 215
0
votes
2
answers
680
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 ...
- 1,084
0
votes
1
answer
1k
views
Converting raster GeoTIFF or NetCDF to image in Google Earth Engine
I try to convert raster tif or netcdf file to ee.Image Google Earth Engine object in Python. The netcdf raster testing data (5-bands) is in this link. Here I converted the first band from raster file ...
- 209
1
vote
0
answers
29
views
Polygon clipping with percentage tile membership
Let me setup the problem: I have a tiled world map (0.1° x 0.1°) with values assigned to each tile. I want to assign the values to each country, and I'm doing so by clipping to their ZEE mask. But ...
0
votes
0
answers
351
views
Xarray to NetCDF with transform applied
I have a process that uses rioxarray to crop GeoTIFFs and create a nice xarray dataset. This works well. When I export to new GeoTIFFs they are perfect, coordinates and data are fine. When I try to ...
0
votes
1
answer
194
views
Wrong results using xarray groupby to calculte anomalies
I want to compute ten days anomalies based on MODIS NDSI. The data is stored as a GeoTIFF. For this task I have two folders, one with the reference period of 2001-2020 and one with 2001-2022 for which ...
