diff --git a/configs/kriging.yaml b/configs/kriging.yaml index f90cd19c..f341fb45 100644 --- a/configs/kriging.yaml +++ b/configs/kriging.yaml @@ -1,25 +1,25 @@ # basic kriging setup features: - - name: my pickle files - type: pickle - files: - covariates: features.pk - targets: targets.pk +# - name: my pickle files +# type: pickle +# files: +# covariates: features.pk +# targets: targets.pk - name: my features 1 type: ordinal files: - - path: /path/to/GA_data/GA-cover2/LATITUDE_GRID1.tif - - path: /path/to/GA_data/GA-cover2/LONGITUDE_GRID1.tif + - path: configs/data/sirsam/LATITUDE_GRID1.tif + - path: configs/data/sirsam/LONGITUDE_GRID1.tif # transforms are performed in order transforms: - - centre - - standardise +# - centre +# - standardise imputation: nn # only used during prediction -mask: - file: /path/to/GA_data/mask/old_mask_test.tif - retain: 1 +#mask: +# file: /path/to/GA_data/mask/old_mask_test.tif +# retain: 1 # resample: choice (value, spatial) @@ -29,7 +29,7 @@ mask: # rows and cols: for spatial resampling, sample from rows X cols tiles # resampling is performed in sequence. The order of spatial/value is important. targets: - file: /path/to/GA_data/GA-cover2/geochem_sites.shp + file: configs/data/sirsam/out_resampled/geochem_sites.shp property: K_ppm_imp_ # resample: # - spatial: @@ -50,6 +50,7 @@ learning: arguments: method: ordinary # ordinary or universal variogram_model: spherical # linear, power, gaussian, spherical, exponential + variogram_parameters: [0, 1, 0.1] # [sill, range, nugget] for gaussian, spherical, exponential verbose: False @@ -74,4 +75,4 @@ validation: random_seed: 1 output: - directory: . + directory: krige diff --git a/setup.py b/setup.py index 3752bfee..0319db1b 100644 --- a/setup.py +++ b/setup.py @@ -99,7 +99,7 @@ def run(self): 'PyYAML >= 3.11', 'pandas >= 1.2.5', 'matplotlib >= 3.4.0', - 'PyKrige==1.3.0', + 'PyKrige==1.7.0', 'xgboost>=1.4.2', 'setuptools>=30.0.0', 'eli5>=0.8.2', diff --git a/uncoverml/krige.py b/uncoverml/krige.py index d46b390e..dfcfcd82 100644 --- a/uncoverml/krige.py +++ b/uncoverml/krige.py @@ -93,6 +93,7 @@ class Krige(TagsMixin, RegressorMixin, BaseEstimator, KrigePredictDistMixin): def __init__(self, method='ordinary', variogram_model='linear', + variogram_parameters=None, nlags=6, weight=False, n_closest_points=10, @@ -102,6 +103,7 @@ def __init__(self, raise ConfigException('Kirging method must be ' 'one of {}'.format(krige_methods.keys())) self.variogram_model = variogram_model + self.variogram_parameters = variogram_parameters self.verbose = verbose self.nlags = nlags self.weight = weight @@ -126,6 +128,7 @@ def fit(self, x, y, *args, **kwargs): y=x[:, 1], z=y, variogram_model=self.variogram_model, + variogram_parameters=self.variogram_parameters, verbose=self.verbose, nlags=self.nlags, weight=self.weight,