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Xarray apply_ufunc with input of several 3D arrays

I have a function apply_dask_function() that I use to apply the function dask_function() on a xarray dataset (ds_example). dask_function() takes 3 inputs, which are two 1D arrays (length "time&...
vdc's user avatar
  • 149
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47views

Finding a way to iterate using the input of two xarray dataarrays when chunked

I am developing a relatively large model using xarray and therefore want to make use of chunks. Most of my operations run a lot faster when chunked but there is one that keeps running (a lot) slower ...
Rogier Westerhoff's user avatar
0votes
1answer
86views

Error when using xarray.apply_ufunc on a chunked xarray DataArray

Hello I am trying to sort the data inside some netCDF4 (.nc) files into bins as efficiently as possible. I am currently trying this with xarray and NumPy's digitize function. Since I want to process a ...
Innocuous Rift's user avatar
0votes
1answer
97views

Storing larger-than-memory xarray dataset to zarr using `dask.delayed` without blowing up memory

I'm trying to use dask to conduct larger-than-memory processing in xarray. Concretely, I'm trying to: Concatenate several NetCDF files (on the same geo grid, same variables) by time Regrid them to a ...
ks905383's user avatar
1vote
0answers
67views

How to make xarray.to_zarr write the same way as dask.array.to_zarr?

I have a 3D xarray DataArray that I've saved to to zarr using DataArray.to_zarr(). However, the resulting format is not readable by my tools, in this case napari. The structure of the zarr has one ...
user8188435's user avatar
0votes
0answers
31views

Run only a single chunk's worth of data without creating a Dask graph of all my chunks?

# Template xarray based on Earth Engine import numpy as np import pandas as pd import dask import xarray as xr # Define the dimensions time = pd.date_range("2020-12-29T18:57:32.281000", ...
Adriano Matos's user avatar
1vote
1answer
114views

In python xarray, how do I create and subset lazy variables without loading the whole dataarray?

I am trying to create a python function that opens a remote dataset (in a opendap server) using xarray and automatically creates new variables lazily. A use case would be to calculate magnitude and ...
Marcelo Andrioni's user avatar
2votes
1answer
144views

xarray and dask: efficiently processing a large netcdf file

I am trying to do a simple calculation on a very large netcdf file, and am struggling to speed it up -- probably because I program primarily in julia and R. I think xarray/dask are the best approach ...
j lev's user avatar
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0answers
183views

Progress bar on xarray.open_mfdataset?

I'm using xarray.open_mfdataset() to open tens of thousands of (fairly small) netCDF files, and it's taking quite some time. Being of an impatient nature, I would like to at least be assured that ...
Tor's user avatar
  • 785
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42views

Memory issues when using Dask

I have just started using 'dask', and I am running into some memory issues. I would like to share my problem along with a dummy code snippet that illustrates what I’ve done. My goal is to read a large ...
jei L's user avatar
2votes
1answer
482views

Is there a way to save into a zarr file an xarray, with the possibility of appending in multiple dimensions?

I'm currently doing an internship where I need to create large datasets, often hundreds of GB in size. I'm collecting temporal samples for cartography, where I collect 500 samples for each ...
Allan Delautre's user avatar
0votes
0answers
80views

Using stackstac, not able to mosaic all tiles/DataArray from the same date

I am trying to cloud access MODIS LST data through stackstac (code below). But, for my selected date range, in the output ds, I get lets say 5-6 different tiles (covering the entire bbox), which are ...
Arindan Mandal's user avatar
2votes
2answers
465views

How to handle large xarray/dask datasets to minimize computation time or running out of memory to store as yearly files (ERA5 dataset)

Currently, I am using ERA5-land data to calculate wind related variables. While I am able to calculate what I want, I do struggle with an efficient implementation to lift this heavy data in a feasible ...
Dominik N.'s user avatar
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0answers
56views

Optimal way to convert an xr.Dataset to a Dask DataFrame?

I am running a function in a Dask cluster to compute the normalized difference between two of my data variables in my xarray Dataset object. However, I need this to be in a Dask DataFrame format first ...
Adriano Matos's user avatar
0votes
0answers
29views

How can I speed up code when using climate data in Jupyter Notebook?

I am using climate data from the Levante Supercomputer in a JupyterNotebook, but I am having some problems regarding the computational time. Therefore, I was wondering if someone had some knowledge of ...
Gonquir's user avatar

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