如何在 Python 中持久存储和有效访问非常大的 2D 列表？

Question

In Python, I'm reading in a very large 2D grid of data that consists of around 200,000,000 data points in total. Each data point is a tuple of 3 floats. Reading all of this data into a two dimensional list frequently causes Memory Errors. To get around this Memory Error, I would like to be able to read this data into some sort of table on the hard drive that can be efficiently accessed when given a grid coordinate ie harddrive_table.get(300, 42).

So far in my research, I've come across PyTables , which is an implementation of HDF5 and seems like overkill, and the built in shelve library, which uses a dictionary-like method to access saved data, but the keys have to be strings and the performance of converting hundreds of millions of grid coordinates to strings for storage could be too much of a performance hit for my use.

Are there any libraries that allow me to store a 2D table of data on the hard drive with efficient access for a single data point?

This table of data is only needed while the program is running, so I don't care about it's interoperability or how it stores the data on the hard drive as it will be deleted after the program has run.

Answer 1

1. HDF5 isn't really overkill if it works. In addition to PyTables there's the somewhat simpler h5py .

2. Numpy lets you mmap a file directly into a numpy array. The values will be stored in the disk file in the minimum-overhead way, with the numpy array shape providing the mapping between array indices and file offsets. mmap uses the same underlying OS mechanisms that power the disk cache to map a disk file into virtual memory, meaning that the whole thing can be loaded into RAM if memory permits, but parts can be flushed to disk (and reloaded later on demand) if it doesn't all fit at once.