Reading a large NetCDF file: Pixel by pixel or all at once?

I have a list of NetCDF files, which contain geospatial data.

From each file, I want to read just a few non-consecutive pixels. The number of pixels to read from each file is always different.

I'm wondering what the best practice for reading them is, especially when the number of pixels is very high. It seems that after a certain threshold, it's faster to read the entire file and then select the pixels I need, but I feel like this could take a toll in the RAM usage if I am reading many files in parallel.

Right now, I'm considering simply reading the entire file if npixels < threshold and reading one by one if npixels > threshold, but is there a better way?

Answer 1

[Shubham]

Hi Jose,

When deciding between reading individual pixels or entire datasets from large NetCDF files, the approach largely depends on the number of pixels you need and size of the files.

Here's a strategy to optimize performance while managing memory efficiently:

• Use "ncread" to read specific pixel values, minimizing memory usage.
• Employ the "setChunkCache" function for chunk caching to improve data access speed.
• You can use "parfor" for parallel processing and use indexing to efficiently manage data access and prevent memory bottlenecks, ensuring that your system's resources are not exceeded.

Refer to the following documentation links for more information on:

• ncread : https://mathworks.com/help/releases/R2024a/matlab/ref/ncread.html
• setChunkCache : https://mathworks.com/help/releases/R2024a/matlab/ref/netcdf.setchunkcache.html
• parfor : https://mathworks.com/help/releases/R2024a/parallel-computing/parfor.html

Hope this helps.