numpy to cupy replacements

README.md

@@ -385,7 +385,7 @@ e.g., multiple XAI methods, multifaceted evaluation through several metrics, or
 You can then simply run a large-scale evaluation as follows (this aggregates the result by `np.mean` averaging):
 
 ```python
-import numpy as np
+import cupy as np
 results = quantus.evaluate(
       metrics=metrics,
       xai_methods=xai_methods,

docs/source/getting_started/getting_started_example.md

@@ -242,7 +242,7 @@ xai_methods = {
 You can then simply run a large-scale evaluation as follows (this aggregates the result by `np.mean` averaging):
 
 ```python
-import numpy as np
+import cupy as np
 results = quantus.evaluate(
       metrics=metrics,
       xai_methods=xai_methods,
@@ -275,7 +275,7 @@ For example, if you want to replace `similarity_func` in your evaluation, you ca
 
 ```python
 import scipy
-import numpy as np
+import cupy as np
 
 def my_similarity_func(a: np.array, b: np.array, **kwargs) -> float:
     """Calculate the similarity of a and b by subtraction."""

pyproject.toml

@@ -27,6 +27,8 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
 ]
 dependencies = [
+    "cupy>=13.0.0; python_version >= '3.9'",
+    "cupy<12.0.0; python_version == '3.7'",
     "numpy>=1.19.5",
     "pandas<=1.3.3; python_version == '3.7'",
     "pandas>=1.5.3; python_version > '3.7'",

quantus/evaluation.py

@@ -9,7 +9,7 @@
 import warnings
 from typing import Union, Callable, Dict, Optional, Any
 
-import numpy as np
+import cupy as np
 import pandas as pd
 
 from quantus.helpers import asserts

quantus/functions/complexity_func.py

@@ -7,7 +7,7 @@
 # Quantus project URL: <https://github.com/understandable-machine-intelligence-lab/Quantus>.
 
 import scipy
-import numpy as np
+import cupy as np
 
 
 def entropy(a: np.array, x: np.array, **kwargs) -> float:

quantus/functions/discretise_func.py

@@ -7,7 +7,7 @@
 # You should have received a copy of the GNU Lesser General Public License along with Quantus. If not, see <https://www.gnu.org/licenses/>.
 # Quantus project URL: <https://github.com/understandable-machine-intelligence-lab/Quantus>.
 
-import numpy as np
+import cupy as np
 
 
 def floating_points(a: np.array, **kwargs) -> float:

quantus/functions/explanation_func.py

@@ -10,7 +10,7 @@
 from importlib import util
 from typing import Optional, Union
 
-import numpy as np
+import cupy as np
 import quantus
 import scipy
 

quantus/functions/loss_func.py

@@ -6,7 +6,7 @@
 # You should have received a copy of the GNU Lesser General Public License along with Quantus. If not, see <https://www.gnu.org/licenses/>.
 # Quantus project URL: <https://github.com/understandable-machine-intelligence-lab/Quantus>.
 
-import numpy as np
+import cupy as np
 
 
 def mse(a: np.array, b: np.array, **kwargs) -> float:

quantus/functions/mosaic_func.py

@@ -10,7 +10,7 @@
 import random
 from typing import List, Tuple, Optional, Union, Any
 
-import numpy as np
+import cupy as np
 
 
 def build_single_mosaic(mosaic_images_list: List[np.ndarray]) -> np.ndarray:

quantus/functions/n_bins_func.py

@@ -7,7 +7,7 @@
 # Quantus project URL: <https://github.com/understandable-machine-intelligence-lab/Quantus>.
 
 import scipy
-import numpy as np
+import cupy as np
 
 
 def freedman_diaconis_rule(a_batch: np.ndarray) -> int:

quantus/functions/norm_func.py

@@ -6,7 +6,7 @@
 # You should have received a copy of the GNU Lesser General Public License along with Quantus. If not, see <https://www.gnu.org/licenses/>.
 # Quantus project URL: <https://github.com/understandable-machine-intelligence-lab/Quantus>.
 
-import numpy as np
+import cupy as np
 
 
 def fro_norm(a: np.array) -> float:

quantus/functions/normalise_func.py

@@ -9,7 +9,7 @@
 import warnings
 from typing import Optional, Sequence
 
-import numpy as np
+import cupy as np
 
 
 def normalise_by_max(

quantus/functions/perturb_func.py

@@ -12,7 +12,7 @@
 import warnings
 from typing import Any, Callable, Sequence, Tuple, Union, Optional
 import cv2
-import numpy as np
+import cupy as np
 from scipy.sparse import lil_matrix, csc_matrix
 from scipy.sparse.linalg import spsolve
 

quantus/functions/similarity_func.py

@@ -9,7 +9,7 @@
 
 from typing import Union
 
-import numpy as np
+import cupy as np
 import scipy
 import skimage
 

quantus/helpers/asserts.py

@@ -8,7 +8,7 @@
 
 
 from typing import Callable, Tuple, Sequence, Union
-import numpy as np
+import cupy as np
 
 
 def assert_features_in_step(

quantus/helpers/model/model_interface.py

@@ -10,7 +10,7 @@
 from abc import ABC, abstractmethod
 from typing import Any, Dict, Optional, Tuple, List, Union, Generator, TypeVar, Generic
 
-import numpy as np
+import cupy as np
 
 if util.find_spec("tensorflow"):
     import tensorflow as tf

quantus/helpers/model/pytorch_model.py

@@ -12,7 +12,7 @@
 import warnings
 import logging
 
-import numpy as np
+import cupy as np
 import torch
 from torch import nn
 from functools import lru_cache

quantus/helpers/model/tf_model.py

@@ -13,7 +13,7 @@
 from keras import activations
 from keras import Model
 from keras.models import clone_model
-import numpy as np
+import cupy as np
 import tensorflow as tf
 from warnings import warn
 from cachetools import cachedmethod, LRUCache

quantus/helpers/perturbation_utils.py

@@ -2,7 +2,7 @@
 
 import sys
 from typing import List, TYPE_CHECKING, Callable, Mapping
-import numpy as np
+import cupy as np
 import functools
 
 if sys.version_info >= (3, 8):

quantus/helpers/plotting.py

@@ -9,7 +9,7 @@
 from typing import List, Union, Dict, Any
 
 import matplotlib.pyplot as plt
-import numpy as np
+import cupy as np
 
 from quantus.helpers import warn
 

quantus/helpers/utils.py

@@ -11,7 +11,7 @@
 from importlib import util
 from typing import Any, Dict, Optional, Sequence, Tuple, Union, List, TypeVar
 
-import numpy as np
+import cupy as np
 from skimage.segmentation import slic, felzenszwalb
 
 from quantus.helpers import asserts

quantus/helpers/warn.py

@@ -9,7 +9,7 @@
 import time
 import warnings
 
-import numpy as np
+import cupy as np
 
 from quantus.helpers.utils import get_name
 

quantus/metrics/axiomatic/completeness.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.helpers import warn

quantus/metrics/axiomatic/input_invariance.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional, Union
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_shift, perturb_batch
 from quantus.helpers import asserts, warn

quantus/metrics/axiomatic/non_sensitivity.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.helpers import asserts, warn

quantus/metrics/base.py

@@ -29,7 +29,7 @@
 )
 
 import matplotlib.pyplot as plt
-import numpy as np
+import cupy as np
 from sklearn.utils import gen_batches
 from tqdm.auto import tqdm
 

quantus/metrics/complexity/complexity.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 import scipy
 
 from quantus.helpers import warn

quantus/metrics/complexity/effective_complexity.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.helpers import warn
 from quantus.helpers.enums import (

quantus/metrics/complexity/sparseness.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.helpers import warn
 from quantus.helpers.enums import (

quantus/metrics/faithfulness/faithfulness_correlation.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.functions.similarity_func import correlation_pearson

quantus/metrics/faithfulness/faithfulness_estimate.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.functions.similarity_func import correlation_pearson

quantus/metrics/faithfulness/infidelity.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional, Union
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.loss_func import mse
 from quantus.functions.perturb_func import baseline_replacement_by_indices

quantus/metrics/faithfulness/irof.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.helpers import asserts, utils, warn

quantus/metrics/faithfulness/monotonicity.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.helpers import asserts, utils, warn

quantus/metrics/faithfulness/monotonicity_correlation.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.functions.similarity_func import correlation_spearman

quantus/metrics/faithfulness/pixel_flipping.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional, Union
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.helpers import asserts, plotting, utils, warn

quantus/metrics/faithfulness/region_perturbation.py

@@ -10,7 +10,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.helpers import asserts, plotting, utils, warn

quantus/metrics/faithfulness/road.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import noisy_linear_imputation
 from quantus.helpers import warn

quantus/metrics/faithfulness/selectivity.py

@@ -10,7 +10,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.perturb_func import baseline_replacement_by_indices
 from quantus.helpers import plotting, utils, warn

quantus/metrics/faithfulness/sensitivity_n.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.functions.normalise_func import normalise_by_max
 from quantus.functions.perturb_func import baseline_replacement_by_indices

quantus/metrics/faithfulness/sufficiency.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional, no_type_check
 
-import numpy as np
+import cupy as np
 from scipy.spatial.distance import cdist
 
 from quantus.helpers.model.model_interface import ModelInterface

quantus/metrics/localisation/attribution_localisation.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 
 from quantus.helpers import asserts, warn
 from quantus.helpers.enums import (

quantus/metrics/localisation/auc.py

@@ -9,7 +9,7 @@
 import sys
 from typing import Any, Callable, Dict, List, Optional
 
-import numpy as np
+import cupy as np
 from sklearn.metrics import auc, roc_curve
 
 from quantus.helpers import asserts, warn