GPSat

Quick Start

Run an example notebook in colab:

Documentation

can be found at: GPSat Documentation

Environment setup

from the top level directory, e.g. the one containing this file, create a virtual environment named venv

python -m venv venv

activate virtual environment with

source venv/bin/activate

It's recommend to use a recent version of python, e.g. >= 3.10

Install requirements with

python -m pip install -r requirements.txt

Inline Example

Simple example of running optimal interpolation, includes binning raw data, predicting at multiple locations using many local experts

python script: examples/inline_example.py notebook: notebooks/inline_example.ipynb

Read Raw Data and Store to HDF5

NOTE: Running python scripts must be done in the top directory of this repository

See (out of date): notebooks/read_raw_data_and_store.ipynb

or run

python -m GPSat.read_and_store <input_config.json>

If <input_config.json> not supplied an example config (configs/example_read_and_store_raw_data.json.json) will be used, paths will be changed to the package location. Will create data/example/ABC.h5

Bin Data

python -m GPSat.bin_data <input_config.json>

If <input_config.json> not supplied an example config (configs/example_bin_raw_data.json) will be used, paths will be changed to the package location. Requires data/example/ABC.h5 exists and will create data/example/ABC_binned.h5

see (currently out of date): notebooks/bin_raw_data.ipynb

(Optional) Plot Observations

It can be useful to visualise before processing it further. This can be done with

python -m examples.plot_observations <input_config.json>

If <input_config.json> not supplied an example config (configs/example_plot_observations.json) will be used, paths will be changed to the package location. Requires data/example/ABC.h5 exists.

Run Local Expert OI

python -m examples.local_expert_oi <input_config.json>

If <input_config.json> not supplied an example config will be used (configs/example_local_expert_oi.json.json). Requires data/example/ABC_binned.h5 exists and will create results/example/ABC_binned_example.h3

NOTE: to use a GPU with TensorFlow LD_LIBRARY_PATH may need to specified in Environment Variables. An example of such a path is /path/to/conda/envs/<env_name>/lib/

A work in progress plotting script is available (python -m examples.local_expert_plot_obs <input_config.json>) that will plot the expert locations and observations used in OI. The input_config is the same used for local_expert_oi.

Post-Process HyperParameters

Provide the results file to apply some post-processing of hyperparameters, e.g. smooth with a kernel

python -m GPSat.postprocessing <input_config.json>

if <input_config.json> not supplied an example config (example_postprocessing.json) will be used, which requires results/example/ABC_binned_example.h5 exists and the results will be written to the same file to table _SMOOTHED.

Post-processing (smoothing) hyperparameters will write a config to file that can be used to generate predictions using the newly smoothed hyperparameters via examples.local_expert_oi.

Generate Predictions using Post-Processed Hyper Parameters

Run local_expert_oi again this time using the configuration file generate from the post-processing step, e.g.:

python -m examples.local_expert_oi results/example/ABC_binned_example_SMOOTHED.json

The post-processing step can produce a configuration file of local_expert_oi that will load the smoothed hyper parameters, skip optimisation and make predictions

Plot Results

Plot heat map of values from results tables by specifying plot template(s) in a configuration file and utilising plot functions from plot_utils.py

python -m examples.plot_from_results <input_config.json>

If <input_config.json> not supplied an example config (example_plot_from_results.json). In order the for example script to work the predictions made using the smoothed hyper parameters must be present.

Miscellaneous

Review Observation Data

To generate plots of observations, and generate statistics run: