def linear_nn(
experiment="one_month_forecast",
include_pred_month=True,
surrounding_pixels=None,
ignore_vars=None,
include_static=True,
):
# if the working directory is alread ml_drought don't need ../data
if Path(".").absolute().as_posix().split("/")[-1] == "ml_drought":
data_path = Path("data")
else:
data_path = Path("../data")
predictor = LinearNetwork(
layer_sizes=[100],
data_folder=data_path,
experiment=experiment,
include_pred_month=include_pred_month,
surrounding_pixels=surrounding_pixels,
ignore_vars=ignore_vars,
include_static=include_static,
)
predictor.train(num_epochs=50, early_stopping=5)
predictor.evaluate(save_preds=True)
predictor.save_model()
def linear_nn(
experiment="one_month_forecast",
include_pred_month=True,
surrounding_pixels=None,
explain=False,
static="features",
ignore_vars=None,
num_epochs=50,
early_stopping=5,
layer_sizes=[100],
predict_delta=False,
spatial_mask=None,
include_latlons=False,
):
predictor = LinearNetwork(
layer_sizes=layer_sizes,
data_folder=get_data_path(),
experiment=experiment,
include_pred_month=include_pred_month,
surrounding_pixels=surrounding_pixels,
static=static,
ignore_vars=ignore_vars,
predict_delta=predict_delta,
spatial_mask=spatial_mask,
include_latlons=include_latlons,
)
predictor.train(num_epochs=num_epochs, early_stopping=early_stopping)
predictor.evaluate(save_preds=True)
predictor.save_model()
if explain:
_ = predictor.explain(save_shap_values=True)
def test_save(self, tmp_path, monkeypatch):
layer_sizes = [10]
input_layer_sizes = copy(layer_sizes)
input_size = 10
dropout = 0.25
include_pred_month = True
include_latlons = True
include_monthly_aggs = True
surrounding_pixels = 1
ignore_vars = ['precip']
include_yearly_aggs = True
def mocktrain(self):
self.model = LinearModel(input_size,
layer_sizes,
dropout,
include_pred_month,
include_latlons,
include_yearly_aggs,
include_static=True)
self.input_size = input_size
monkeypatch.setattr(LinearNetwork, 'train', mocktrain)
model = LinearNetwork(data_folder=tmp_path,
layer_sizes=layer_sizes,
dropout=dropout,
experiment='one_month_forecast',
include_pred_month=include_pred_month,
include_latlons=include_latlons,
include_monthly_aggs=include_monthly_aggs,
include_yearly_aggs=include_yearly_aggs,
surrounding_pixels=surrounding_pixels,
ignore_vars=ignore_vars)
model.train()
model.save_model()
assert (tmp_path / 'models/one_month_forecast/linear_network/model.pt'
).exists(), f'Model not saved!'
model_dict = torch.load(model.model_dir / 'model.pt',
map_location='cpu')
for key, val in model_dict['model']['state_dict'].items():
assert (model.model.state_dict()[key] == val).all()
assert model_dict['dropout'] == dropout
assert model_dict['layer_sizes'] == input_layer_sizes
assert model_dict['model']['input_size'] == input_size
assert model_dict['include_pred_month'] == include_pred_month
assert model_dict['include_latlons'] == include_latlons
assert model_dict['include_monthly_aggs'] == include_monthly_aggs
assert model_dict['include_yearly_aggs'] == include_yearly_aggs
assert model_dict['surrounding_pixels'] == surrounding_pixels
assert model_dict['ignore_vars'] == ignore_vars
def run_models(data_path, experiment):
# NOTE: this model is the same for all experiments
print("Running persistence model")
predictor = Persistence(data_path, experiment=experiment)
predictor.evaluate(save_preds=True)
# linear regression
print(f"Running Linear Regression model: {experiment}")
predictor = LinearRegression(data_path,
experiment=experiment,
include_pred_month=True,
surrounding_pixels=1)
predictor.train(num_epochs=10, early_stopping=3)
# linear network
print(f"Running Linear Neural Network model: {experiment}")
predictor = LinearNetwork(
data_folder=data_path,
experiment=experiment,
layer_sizes=[100],
include_pred_month=True,
surrounding_pixels=1,
)
predictor.train(num_epochs=10, early_stopping=3)
predictor.evaluate(save_preds=True)
predictor.save_model()
# recurrent network
print(f"Running RNN (LSTM) model: {experiment}")
predictor = RecurrentNetwork(
data_folder=data_path,
hidden_size=128,
experiment=experiment,
include_pred_month=True,
surrounding_pixels=1,
)
predictor.train(num_epochs=10, early_stopping=3)
predictor.evaluate(save_preds=True)
predictor.save_model()
# EA LSTM
print(f"Running Entity Aware LSTM model: {experiment}")
predictor = EARecurrentNetwork(
data_folder=data_path,
hidden_size=128,
experiment=experiment,
include_pred_month=True,
surrounding_pixels=1,
)
predictor.train(num_epochs=10, early_stopping=3)
predictor.evaluate(save_preds=True)
predictor.save_model()
def linear_nn(experiment='one_month_forecast',
include_pred_month=True,
surrounding_pixels=1):
# if the working directory is alread ml_drought don't need ../data
if Path('.').absolute().as_posix().split('/')[-1] == 'ml_drought':
data_path = Path('data')
else:
data_path = Path('../data')
predictor = LinearNetwork(layer_sizes=[100],
data_folder=data_path,
experiment=experiment,
include_pred_month=include_pred_month,
surrounding_pixels=surrounding_pixels)
predictor.train(num_epochs=50, early_stopping=5)
predictor.evaluate(save_preds=True)
predictor.save_model()
_ = predictor.explain(save_shap_values=True)
def linear_nn(
experiment="one_month_forecast",
include_pred_month=True,
surrounding_pixels=None,
ignore_vars=None,
pretrained=False,
):
predictor = LinearNetwork(
layer_sizes=[100],
data_folder=get_data_path(),
experiment=experiment,
include_pred_month=include_pred_month,
surrounding_pixels=surrounding_pixels,
ignore_vars=ignore_vars,
)
predictor.train(num_epochs=50, early_stopping=5)
predictor.evaluate(save_preds=True)
predictor.save_model()
_ = predictor.explain(save_shap_values=True)
def test_get_background(self, tmp_path):
x, _, _ = _make_dataset(size=(5, 5), const=True)
y = x.isel(time=[-1])
train_features = tmp_path / "features/one_month_forecast/train/1980_1"
train_features.mkdir(parents=True)
x.to_netcdf(train_features / "x.nc")
y.to_netcdf(train_features / "y.nc")
norm_dict = {"VHI": {"mean": 0, "std": 1}}
with (tmp_path / "features/one_month_forecast/normalizing_dict.pkl"
).open("wb") as f:
pickle.dump(norm_dict, f)
# static
x_static, _, _ = _make_dataset(size=(5, 5), add_times=False)
static_features = tmp_path / f"features/static"
static_features.mkdir(parents=True)
x_static.to_netcdf(static_features / "data.nc")
static_norm_dict = {"VHI": {"mean": 0.0, "std": 1.0}}
with (tmp_path /
f"features/static/normalizing_dict.pkl").open("wb") as f:
pickle.dump(static_norm_dict, f)
model = LinearNetwork(
data_folder=tmp_path,
layer_sizes=[100],
dropout=0.25,
include_pred_month=True,
)
background = model._get_background(sample_size=3)
assert (background[0].shape[0] == 3
), f"Got {background[0].shape[0]} samples back, expected 3"
assert (background[1].shape[0] == 3
), f"Got {background[1].shape[0]} samples back, expected 3"
assert (len(background[1].shape) == 2
), f"Expected 2 dimensions, got {len(background[1].shape)}"
def test_get_background(self, tmp_path):
x, _, _ = _make_dataset(size=(5, 5), const=True)
y = x.isel(time=[-1])
train_features = tmp_path / 'features/one_month_forecast/train/hello'
train_features.mkdir(parents=True)
x.to_netcdf(train_features / 'x.nc')
y.to_netcdf(train_features / 'y.nc')
norm_dict = {'VHI': {'mean': 0, 'std': 1}}
with (tmp_path / 'features/one_month_forecast/normalizing_dict.pkl'
).open('wb') as f:
pickle.dump(norm_dict, f)
# static
x_static, _, _ = _make_dataset(size=(5, 5), add_times=False)
static_features = tmp_path / f'features/static'
static_features.mkdir(parents=True)
x_static.to_netcdf(static_features / 'data.nc')
static_norm_dict = {'VHI': {'mean': 0.0, 'std': 1.0}}
with (tmp_path /
f'features/static/normalizing_dict.pkl').open('wb') as f:
pickle.dump(static_norm_dict, f)
model = LinearNetwork(data_folder=tmp_path,
layer_sizes=[100],
dropout=0.25,
include_pred_month=True)
background = model._get_background(sample_size=3)
assert background[0].shape[0] == 3, \
f'Got {background[0].shape[0]} samples back, expected 3'
assert background[1].shape[0] == 3, \
f'Got {background[1].shape[0]} samples back, expected 3'
assert len(background[1].shape) == 2, \
f'Expected 2 dimensions, got {len(background[1].shape)}'
def test_train(
self,
tmp_path,
capsys,
use_pred_months,
use_latlons,
experiment,
monthly_agg,
static,
predict_delta,
):
# make the x, y data (5*5 latlons, 36 timesteps, 3 features)
x, _, _ = _make_dataset(size=(5, 5), const=True)
y = x.isel(time=[-1])
x_add1, _, _ = _make_dataset(size=(5, 5),
const=True,
variable_name="precip")
x_add2, _, _ = _make_dataset(size=(5, 5),
const=True,
variable_name="temp")
x = xr.merge([x, x_add1, x_add2])
norm_dict = {
"VHI": {
"mean": 0,
"std": 1
},
"precip": {
"mean": 0,
"std": 1
},
"temp": {
"mean": 0,
"std": 1
},
}
test_features = tmp_path / f"features/{experiment}/train/1980_1"
test_features.mkdir(parents=True, exist_ok=True)
# make the normalising dictionary
with (tmp_path /
f"features/{experiment}/normalizing_dict.pkl").open("wb") as f:
pickle.dump(norm_dict, f)
x.to_netcdf(test_features / "x.nc")
y.to_netcdf(test_features / "y.nc")
if static:
x_static, _, _ = _make_dataset(size=(5, 5), add_times=False)
static_features = tmp_path / f"features/static"
static_features.mkdir(parents=True)
x_static.to_netcdf(static_features / "data.nc")
static_norm_dict = {"VHI": {"mean": 0.0, "std": 1.0}}
with (tmp_path /
f"features/static/normalizing_dict.pkl").open("wb") as f:
pickle.dump(static_norm_dict, f)
layer_sizes = [10]
dropout = 0.25
model = LinearNetwork(
data_folder=tmp_path,
layer_sizes=layer_sizes,
dropout=dropout,
experiment=experiment,
include_pred_month=use_pred_months,
include_latlons=use_latlons,
include_monthly_aggs=monthly_agg,
static="embeddings",
predict_delta=predict_delta,
)
model.train()
captured = capsys.readouterr()
expected_stdout = "Epoch 1, train smooth L1: "
assert expected_stdout in captured.out
assert (type(model.model) == LinearModel
), f"Model attribute not a linear regression!"
def test_predict(self, tmp_path, use_pred_months, use_latlons, experiment):
x, _, _ = _make_dataset(size=(5, 5), const=True)
y = x.isel(time=[-1])
train_features = tmp_path / f"features/{experiment}/train/1980_1"
train_features.mkdir(parents=True)
test_features = tmp_path / f"features/{experiment}/test/1980_1"
test_features.mkdir(parents=True)
# static
x_static, _, _ = _make_dataset(size=(5, 5), add_times=False)
static_features = tmp_path / f"features/static"
static_features.mkdir(parents=True)
x_static.to_netcdf(static_features / "data.nc")
static_norm_dict = {"VHI": {"mean": 0.0, "std": 1.0}}
with (tmp_path /
f"features/static/normalizing_dict.pkl").open("wb") as f:
pickle.dump(static_norm_dict, f)
# if nowcast we need another x feature
if experiment == "nowcast":
x_add1, _, _ = _make_dataset(size=(5, 5),
const=True,
variable_name="precip")
x_add2, _, _ = _make_dataset(size=(5, 5),
const=True,
variable_name="temp")
x = xr.merge([x, x_add1, x_add2])
norm_dict = {
"VHI": {
"mean": 0,
"std": 1
},
"precip": {
"mean": 0,
"std": 1
},
"temp": {
"mean": 0,
"std": 1
},
}
else:
norm_dict = {"VHI": {"mean": 0, "std": 1}}
with (tmp_path /
f"features/{experiment}/normalizing_dict.pkl").open("wb") as f:
pickle.dump(norm_dict, f)
x.to_netcdf(test_features / "x.nc")
y.to_netcdf(test_features / "y.nc")
x.to_netcdf(train_features / "x.nc")
y.to_netcdf(train_features / "y.nc")
layer_sizes = [10]
dropout = 0.25
model = LinearNetwork(
data_folder=tmp_path,
layer_sizes=layer_sizes,
dropout=dropout,
experiment=experiment,
include_pred_month=use_pred_months,
include_latlons=use_latlons,
)
model.train()
test_arrays_dict, pred_dict = model.predict()
# the foldername "1980_1" is the only one which should be in the dictionaries
assert ("1980_1" in test_arrays_dict.keys()) and (len(test_arrays_dict)
== 1)
assert ("1980_1" in pred_dict.keys()) and (len(pred_dict) == 1)
# _make_dataset with const=True returns all ones
assert (test_arrays_dict["1980_1"]["y"] == 1).all()
def test_save(self, tmp_path, monkeypatch):
layer_sizes = [10]
input_layer_sizes = copy(layer_sizes)
input_size = 10
dropout = 0.25
include_pred_month = True
include_latlons = True
include_monthly_aggs = True
surrounding_pixels = 1
ignore_vars = ["precip"]
include_yearly_aggs = True
normalize_y = False
def mocktrain(self):
self.model = LinearModel(
input_size,
layer_sizes,
dropout,
include_pred_month,
include_latlons,
include_yearly_aggs,
include_static=True,
include_prev_y=True,
)
self.input_size = input_size
monkeypatch.setattr(LinearNetwork, "train", mocktrain)
model = LinearNetwork(
data_folder=tmp_path,
layer_sizes=layer_sizes,
dropout=dropout,
experiment="one_month_forecast",
include_pred_month=include_pred_month,
include_latlons=include_latlons,
include_monthly_aggs=include_monthly_aggs,
include_yearly_aggs=include_yearly_aggs,
surrounding_pixels=surrounding_pixels,
ignore_vars=ignore_vars,
include_prev_y=True,
normalize_y=normalize_y,
)
model.train()
model.save_model()
assert (tmp_path / "models/one_month_forecast/linear_network/model.pt"
).exists(), f"Model not saved!"
model_dict = torch.load(model.model_dir / "model.pt",
map_location="cpu")
for key, val in model_dict["model"]["state_dict"].items():
assert (model.model.state_dict()[key] == val).all()
assert model_dict["dropout"] == dropout
assert model_dict["layer_sizes"] == input_layer_sizes
assert model_dict["model"]["input_size"] == input_size
assert model_dict["include_pred_month"] == include_pred_month
assert model_dict["include_latlons"] == include_latlons
assert model_dict["include_monthly_aggs"] == include_monthly_aggs
assert model_dict["include_yearly_aggs"] == include_yearly_aggs
assert model_dict["surrounding_pixels"] == surrounding_pixels
assert model_dict["ignore_vars"] == ignore_vars
assert model_dict["include_prev_y"] is True
assert model_dict["normalize_y"] == normalize_y
# train models
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from src.models import LinearRegression, LinearNetwork, Persistence
from src.models.data import DataLoader
data_path = Path("data")
l = LinearRegression(data_path)
l.train()
ln = LinearNetwork(layer_sizes=[100], data_folder=data_path)
ln.train(num_epochs=10)
# ------------------------------------------------------------------------------
# try and explain the LinearRegression model
# ------------------------------------------------------------------------------
test_arrays_loader = DataLoader(
data_path=data_path, batch_file_size=1, shuffle_data=False, mode="test"
)
key, val = list(next(iter(test_arrays_loader)).items())[0]
explanations = l.explain(val.x)
# plot the SHAP explanations
# 1. mean spatial and temporal response
mean_expl = explanations.mean(axis=0).mean(axis=0)
x_vars = val.x_vars
def test_train(self, tmp_path, capsys, use_pred_months, use_latlons,
experiment, monthly_agg, static):
# make the x, y data (5*5 latlons, 36 timesteps, 3 features)
x, _, _ = _make_dataset(size=(5, 5), const=True)
y = x.isel(time=[-1])
x_add1, _, _ = _make_dataset(size=(5, 5),
const=True,
variable_name='precip')
x_add2, _, _ = _make_dataset(size=(5, 5),
const=True,
variable_name='temp')
x = xr.merge([x, x_add1, x_add2])
norm_dict = {
'VHI': {
'mean': 0,
'std': 1
},
'precip': {
'mean': 0,
'std': 1
},
'temp': {
'mean': 0,
'std': 1
}
}
test_features = tmp_path / f'features/{experiment}/train/hello'
test_features.mkdir(parents=True, exist_ok=True)
# make the normalising dictionary
with (tmp_path /
f'features/{experiment}/normalizing_dict.pkl').open('wb') as f:
pickle.dump(norm_dict, f)
x.to_netcdf(test_features / 'x.nc')
y.to_netcdf(test_features / 'y.nc')
if static:
x_static, _, _ = _make_dataset(size=(5, 5), add_times=False)
static_features = tmp_path / f'features/static'
static_features.mkdir(parents=True)
x_static.to_netcdf(static_features / 'data.nc')
static_norm_dict = {'VHI': {'mean': 0.0, 'std': 1.0}}
with (tmp_path /
f'features/static/normalizing_dict.pkl').open('wb') as f:
pickle.dump(static_norm_dict, f)
layer_sizes = [10]
dropout = 0.25
model = LinearNetwork(data_folder=tmp_path,
layer_sizes=layer_sizes,
dropout=dropout,
experiment=experiment,
include_pred_month=use_pred_months,
include_latlons=use_latlons,
include_monthly_aggs=monthly_agg,
include_static=static)
model.train()
# check the number of input features is properly initialised
n_input_features = [p for p in model.model.dense_layers.parameters()
][0].shape[-1]
# Expect to have 12 more features if use_pred_months
if experiment == 'nowcast':
n_expected = 107
else:
# NOTE: data hasn't been through `src.Engineer` therefore including
# current data (hence why more features than `nowcast`)
n_expected = 108
if monthly_agg:
n_expected *= 2
if use_pred_months:
n_expected += 12
if use_latlons:
n_expected += 2
n_expected += 3 # +3 for the yearly means
if static:
n_expected += 1 # for the static variable
assert n_input_features == n_expected, "Expected the number" \
f"of input features to be: {n_expected}" \
f"Got: {n_input_features}"
captured = capsys.readouterr()
expected_stdout = 'Epoch 1, train smooth L1: '
assert expected_stdout in captured.out
assert type(model.model) == LinearModel, \
f'Model attribute not a linear regression!'
def test_predict(self, tmp_path, use_pred_months, use_latlons, experiment):
x, _, _ = _make_dataset(size=(5, 5), const=True)
y = x.isel(time=[-1])
train_features = tmp_path / f'features/{experiment}/train/hello'
train_features.mkdir(parents=True)
test_features = tmp_path / f'features/{experiment}/test/hello'
test_features.mkdir(parents=True)
# static
x_static, _, _ = _make_dataset(size=(5, 5), add_times=False)
static_features = tmp_path / f'features/static'
static_features.mkdir(parents=True)
x_static.to_netcdf(static_features / 'data.nc')
static_norm_dict = {'VHI': {'mean': 0.0, 'std': 1.0}}
with (tmp_path /
f'features/static/normalizing_dict.pkl').open('wb') as f:
pickle.dump(static_norm_dict, f)
# if nowcast we need another x feature
if experiment == 'nowcast':
x_add1, _, _ = _make_dataset(size=(5, 5),
const=True,
variable_name='precip')
x_add2, _, _ = _make_dataset(size=(5, 5),
const=True,
variable_name='temp')
x = xr.merge([x, x_add1, x_add2])
norm_dict = {
'VHI': {
'mean': 0,
'std': 1
},
'precip': {
'mean': 0,
'std': 1
},
'temp': {
'mean': 0,
'std': 1
}
}
else:
norm_dict = {'VHI': {'mean': 0, 'std': 1}}
with (tmp_path /
f'features/{experiment}/normalizing_dict.pkl').open('wb') as f:
pickle.dump(norm_dict, f)
x.to_netcdf(test_features / 'x.nc')
y.to_netcdf(test_features / 'y.nc')
x.to_netcdf(train_features / 'x.nc')
y.to_netcdf(train_features / 'y.nc')
layer_sizes = [10]
dropout = 0.25
model = LinearNetwork(data_folder=tmp_path,
layer_sizes=layer_sizes,
dropout=dropout,
experiment=experiment,
include_pred_month=use_pred_months,
include_latlons=use_latlons)
model.train()
test_arrays_dict, pred_dict = model.predict()
# the foldername "hello" is the only one which should be in the dictionaries
assert ('hello' in test_arrays_dict.keys()) and (len(test_arrays_dict)
== 1)
assert ('hello' in pred_dict.keys()) and (len(pred_dict) == 1)
# _make_dataset with const=True returns all ones
assert (test_arrays_dict['hello']['y'] == 1).all()