Merge pull request #155 from siapy/fix

Add missing __all__ attributes

siapy/core/configs.py

@@ -1,5 +1,11 @@
 from pathlib import Path
 
+__all__ = [
+    "BASE_DIR",
+    "SIAPY_DIR",
+    "TEST_DATA_DIR",
+]
+
 BASE_DIR = Path(__file__).parent.parent.parent.absolute()
 SIAPY_DIR = Path(BASE_DIR, "siapy")
 TEST_DATA_DIR = Path(BASE_DIR, "tests", "data")

siapy/core/exceptions.py

@@ -1,5 +1,16 @@
 from typing import Any
 
+__all__ = [
+    "SiapyError",
+    "InvalidFilepathError",
+    "InvalidInputError",
+    "InvalidTypeError",
+    "ProcessingError",
+    "ConfigurationError",
+    "MethodNotImplementedError",
+    "DirectInitializationError",
+]
+
 
 class SiapyError(Exception):
     """Base exception for SiaPy library."""

siapy/core/logger.py

@@ -1,3 +1,5 @@
 import logging
 
+__all__ = ["logger"]
+
 logger = logging.getLogger("siapy")

siapy/core/types.py

@@ -1,11 +1,22 @@
+from typing import Any, Sequence
+
 import numpy as np
+import pandas as pd
 import spectral as sp
 from PIL.Image import Image
-import pandas as pd
-from typing import Sequence, Any
 
 from siapy.entities import SpectralImage, SpectralImageSet
 
+__all__ = [
+    "SpectralType",
+    "ImageType",
+    "ImageSizeType",
+    "ImageDataType",
+    "ImageContainerType",
+    "ArrayLike1dType",
+    "ArrayLike2dType",
+]
+
 SpectralType = sp.io.envi.BilFile | sp.io.envi.BipFile | sp.io.envi.BsqFile
 ImageType = SpectralImage | np.ndarray | Image
 ImageSizeType = int | tuple[int, int]

siapy/datasets/helpers.py

@@ -5,6 +5,12 @@
 if TYPE_CHECKING:
     from .schemas import ClassificationTarget, RegressionTarget, TabularDatasetData
 
+__all__ = [
+    "generate_classification_target",
+    "generate_regression_target",
+    "merge_signals_from_multiple_cameras",
+]
+
 
 def generate_classification_target(
     dataframe: pd.DataFrame,

siapy/datasets/schemas.py

@@ -8,6 +8,12 @@
 
 from .helpers import generate_classification_target, generate_regression_target
 
+__all__ = [
+    "ClassificationTarget",
+    "RegressionTarget",
+    "TabularDatasetData",
+]
+
 
 class Target(BaseModel, ABC):
     model_config = ConfigDict(arbitrary_types_allowed=True)

siapy/datasets/tabular.py

@@ -10,6 +10,10 @@
 from siapy.datasets.schemas import TabularDatasetData
 from siapy.entities import Signatures, SpectralImage, SpectralImageSet
 
+__all__ = [
+    "TabularDataset",
+]
+
 
 class MetaDataEntity(BaseModel):
     image_idx: int

siapy/entities/images.py

@@ -18,6 +18,12 @@
     from .pixels import Pixels
 
 
+__all__ = [
+    "GeometricShapes",
+    "SpectralImage",
+]
+
+
 @dataclass
 class GeometricShapes:
     def __init__(

siapy/entities/imagesets.py

@@ -10,6 +10,10 @@
 
 from .images import SpectralImage
 
+__all__ = [
+    "SpectralImageSet",
+]
+
 
 @dataclass
 class SpectralImageSet:

siapy/entities/pixels.py

@@ -5,6 +5,10 @@
 import numpy as np
 import pandas as pd
 
+__all__ = [
+    "Pixels",
+]
+
 
 class Coordinates(NamedTuple):
     U: Annotated[str, "u - x coordinate on the image"] = "u"

siapy/entities/shapes.py

@@ -9,6 +9,13 @@
 
 from .pixels import Pixels
 
+__all__ = [
+    "Shape",
+    "Rectangle",
+    "Point",
+    "FreeDraw",
+]
+
 SHAPE_TYPE_RECTANGLE = "rectangle"
 SHAPE_TYPE_POINT = "point"
 SHAPE_TYPE_FREEDRAW = "freedraw"

siapy/entities/signatures.py

@@ -9,6 +9,11 @@
 
 from .pixels import Pixels
 
+__all__ = [
+    "Signatures",
+    "Signals",
+]
+
 
 @dataclass
 class Signals:

siapy/features/features.py

@@ -10,6 +10,13 @@
 from siapy.features.spectral_indices import compute_spectral_indices
 from siapy.utils.general import set_random_seed
 
+__all__ = [
+    "AutoFeatClassification",
+    "AutoFeatRegression",
+    "AutoSpectralIndicesClassification",
+    "AutoSpectralIndicesRegression",
+]
+
 
 class AutoFeatClassification(AutoFeatClassifier):
     def __init__(

siapy/features/helpers.py

@@ -8,6 +8,11 @@
 
 from siapy.core.exceptions import InvalidInputError
 
+__all__ = [
+    "FeatureSelectorConfig",
+    "feature_selector_factory",
+]
+
 
 class FeatureSelectorConfig(BaseModel):
     k_features: Annotated[

siapy/features/spectral_indices.py

@@ -14,6 +14,11 @@
     )
     import spyndex  # type: ignore
 
+__all__ = [
+    "get_spectral_indices",
+    "compute_spectral_indices",
+]
+
 
 def _convert_str_to_list(bands_acronym: Any) -> Any:
     if isinstance(bands_acronym, str):

siapy/models/metrics.py

@@ -16,6 +16,11 @@
 
 from siapy.core.exceptions import InvalidInputError
 
+__all__ = [
+    "calculate_classification_metrics",
+    "calculate_regression_metrics",
+]
+
 
 def normalized_RMSE(
     y_true: np.ndarray,

siapy/optimizers/configs.py

@@ -6,6 +6,12 @@
 from siapy.optimizers.parameters import TrialParameters
 from siapy.optimizers.scorers import Scorer
 
+__all__ = [
+    "CreateStudyConfig",
+    "OptimizeStudyConfig",
+    "TabularOptimizerConfig",
+]
+
 
 class CreateStudyConfig(BaseModel):
     model_config = ConfigDict(arbitrary_types_allowed=True)

siapy/optimizers/optimizers.py

@@ -14,6 +14,10 @@
     IntParameter,
 )
 
+__all__ = [
+    "TabularOptimizer",
+]
+
 
 class TabularOptimizer:
     def __init__(

siapy/optimizers/parameters.py

@@ -3,6 +3,13 @@
 
 from pydantic import BaseModel
 
+__all__ = [
+    "FloatParameter",
+    "IntParameter",
+    "CategoricalParameter",
+    "TrialParameters",
+]
+
 
 class FloatParameter(BaseModel):
     name: str

siapy/optimizers/scorers.py

@@ -9,6 +9,10 @@
 from siapy.utils.evaluators import ScorerFuncType, cross_validation, hold_out_validation
 from siapy.utils.general import initialize_object
 
+__all__ = [
+    "Scorer",
+]
+
 
 class Scorer:
     def __init__(self, scorer):

siapy/transformations/corregistrator.py

@@ -3,6 +3,13 @@
 
 from siapy.entities.pixels import Pixels
 
+__all__ = [
+    "map_affine_approx_2d",
+    "affine_matx_2d",
+    "align",
+    "transform",
+]
+
 
 def map_affine_approx_2d(points_ref: np.ndarray, points_mov: np.ndarray) -> np.ndarray:
     """Affine transformation"""

siapy/transformations/image.py

@@ -7,6 +7,15 @@
 from siapy.core.types import ImageSizeType, ImageType
 from siapy.utils.validators import validate_image_size, validate_image_to_numpy
 
+__all__ = [
+    "add_gaussian_noise",
+    "random_crop",
+    "random_mirror",
+    "random_rotation",
+    "rescale",
+    "area_normalization",
+]
+
 
 def add_gaussian_noise(
     image: ImageType,

siapy/utils/enums.py

@@ -1,5 +1,9 @@
 from enum import Enum, auto
 
+__all__ = [
+    "InteractiveButtonsEnum",
+]
+
 
 class InteractiveButtonsEnum(Enum):
     SAVE = auto()

siapy/utils/evaluators.py

@@ -15,6 +15,11 @@
 
 from .validators import check_model_prediction_methods
 
+__all__ = [
+    "cross_validation",
+    "hold_out_validation",
+]
+
 ScorerFuncType = Callable[[BaseEstimator, ArrayLike2dType, ArrayLike1dType], float]
 
 

siapy/utils/general.py

@@ -12,6 +12,18 @@
 from siapy.core import logger
 from siapy.core.exceptions import InvalidInputError
 
+__all__ = [
+    "initialize_object",
+    "initialize_function",
+    "ensure_dir",
+    "get_number_cpus",
+    "dict_zip",
+    "get_increasing_seq_indices",
+    "set_random_seed",
+    "get_classmethods",
+    "match_iterable_items_by_regex",
+]
+
 
 def initialize_object(
     module: types.ModuleType | Any,

siapy/utils/images.py

@@ -11,6 +11,16 @@
 from siapy.transformations.image import rescale
 from siapy.utils.validators import validate_image_to_numpy
 
+__all__ = [
+    "save_image",
+    "create_image",
+    "merge_images_by_specter",
+    "convert_radiance_image_to_reflectance",
+    "calculate_correction_factor_from_panel",
+    "blockfy_image",
+    "calculate_image_background_percentage",
+]
+
 
 def save_image(
     image: Annotated[np.ndarray, "The image to save."],

siapy/utils/plots.py

@@ -16,6 +16,14 @@
 from siapy.utils.enums import InteractiveButtonsEnum
 from siapy.utils.validators import validate_image_to_numpy_3channels
 
+__all__ = [
+    "pixels_select_click",
+    "pixels_select_lasso",
+    "display_image_with_areas",
+    "display_multiple_images_with_areas",
+    "display_signals",
+]
+
 
 def pixels_select_click(image: ImageType) -> Pixels:
     image_display = validate_image_to_numpy_3channels(image)

siapy/utils/validators.py

@@ -10,6 +10,13 @@
 from siapy.core.types import ImageSizeType, ImageType
 from siapy.entities import SpectralImage
 
+__all__ = [
+    "validate_image_to_numpy_3channels",
+    "validate_image_to_numpy",
+    "validate_image_size",
+    "check_model_prediction_methods",
+]
+
 
 def validate_image_to_numpy_3channels(image: ImageType) -> np.ndarray:
     if isinstance(image, SpectralImage):