gps2var 0.1.0a1

Fast reading of geospatial variables by GPS coordinates

gps2var

gps2var is a Python library providing fast loading of geospatial variables from raster files by GPS coordinates and with interpolation.

In particular, it allows parallel calls with coordinates specified as large NumPy arrays of arbitrary shapes, and is compatible with PyTorch data loaders.

Install with: pip install gps2var

See benchmark.ipynb for a performance benchmark.

Examples

Reading from a single file

PATH = "/vsizip/wc2.1_30s_bio.zip/wc2.1_30s_bio_1.tif"  # WorldClim annual mean temperature

with gps2var.RasterValueReader(PATH, interpolation='bilinear') as reader:
    lat, lon = 48.858222, 2.2945
    reader.get(lon, lat)  # [11.94036207]

Parallel reading from multiple files

MultiRasterValueReader reads from multiple raster files and concatenates the results.

# min and max temperature by month (averages for 1970-2000)
PATHS = [f"/vsizip/wc2.1_30s_{var}.zip/wc2.1_30s_{var}_{i:02}.tif"
         for var in ["tmin" , "tmax"] for i in range(1, 13)]

with gps2var.MultiRasterValueReader(PATHS, num_threads=len(PATHS)) as reader:
    lat, lon = 48.858222, 2.2945
    reader.get(lon, lat).reshape(2, 12)
    
# [[ 2.3  2.5  4.6  6.3 10.1 13.  15.  14.9 12.   8.8  5.   3.4]
#  [ 7.2  8.4 11.9 14.9 19.2 22.  24.7 24.8 20.9 15.9 10.6  8. ]]

Set use_multiprocessing=True to create a separate process for each raster. This is likely to be faster than the default (i.e. multithreading), at least if the number of rasters is large.

API

RasterValueReader

Can be created with a path to a file that can be read by Rasterio, or an open Rasterio DatasetReader. The behavior can be customized with keyword parameters; the most important ones are:

• crs: The coordinate reference system to use for querying. By default this is EPSG:4326, i.e. longitude and latitude (in this order) as used by GPS.
• interpolation: "nearest" (default) or "bilinear" (slower).
• fill_value: The value (scalar) with which to replace missing values. Defaults to np.nan.
• feat_dtype: The dtype to which to convert the result. Defaults to np.float32.
• feat_center: Center each of the features at the given value. Defaults to None (no centering).
• feat_scale: Scale each of the (centered) features by multiplying it by the given value. Defaults to None (no scaling).
• block_shape: The shape of the blocks read into memory (and stored in the GDAL block cache).
• preload_all: Indicates whether the whole dataset should be loaded into memory instead of loading one block at a time. Defaults to False.

Another option is to wrap all these arguments in a RasterReaderSpec (or simply a dictionary) and pass it as the first argument.

RasterValueReaderPool

Like RasterValueReader, but spawns num_workers worker processes that all read from the same file concurrently. Besides get() (which blocks until the result is ready), it provides async_get(), which returns a concurrent.futures.Future.

MultiRasterValueReader

Expects as the first argument a list of file paths, RasterReaderSpecs, or dicts, and reads from each file in a separate thread or process. Additional options to be applied to all items can be passed as keyword arguments. Additionally, the following parameters are accepted:

• use_multiprocessing: If True, each raster will be processed in a separate process.
• num_threads: The number of threads to use for parallel reading. By default, this is set to the number of rasters. Set to 0 to read in the main thread.

ProcessManager

A multiprocessing.BaseManager – a context manager that spawns a separate process. It provides RasterValueReader(), MultiRasterValueReader(), and RasterValueReaderPool() methods that create the corresponding reader in that process and return a proxy object that can be used in much the same way as the reader itself. A nice property of a proxy object is that it can be copied between processes without copying the underlying reader, so it works with PyTorch DataLoader.

PyTorch DataLoader and parallelism

Simply using a RasterValueReader with a PyTorch DataLoader with num_workers > 0 and with the "fork" start method (default on Unix) will not work.

Here are examples of usage that do work:

• Using multiprocessing.set_start_method("spawn"). This will create a copy of the reader in each worker process.

• Setting preload_all=True so that the whole raster is loaded into memory.

• Using MultiRasterValueReader as above, but with use_multiprocessing=True. This way, each raster wil be read in a separate process.

• Using ProcessManager, e.g.:

  # in __init__:
  self.manager = gps2var.ProcessManager()
  self.manager.start()  # start a new process
  self.reader = manager.RasterValueReader(path)  # proxy object
  
  # in __getitem__:
  self.reader.get(lon, lat)
  

  In this case, the reader is placed in a separate process and the workers connect to it using the proxy object.

Caveats and limitations

• gps2var reads the raster in windows, which is efficient if the locations requested in a single call tend to be close together. If this is not the case, better performance can be achieved using preload_all=True at the expense of loading the whole raster into memory.
• By default, the window shape used by gps2var is identical to the shape of the blocks in which the dataset is stored. This ensures the windows can be read efficiently, but it might mean reading a lot of data unnecessarily if the block size is large. Adjusting the window shape using the block_shape paramater might improve performance.