stouputils 1.14.0__py3-none-any.whl → 1.14.2__py3-none-any.whl

stouputils/data_science/data_processing/image/clahe.py

@@ -1,92 +1,92 @@
-
-# pyright: reportUnusedImport=false
-# ruff: noqa: F401
-
-# Imports
-from .common import Any, NDArray, check_image, cv2, np
-
-
-# Functions
-def clahe_image(
-	image: NDArray[Any],
-	clip_limit: float = 2.0,
-	tile_grid_size: int = 8,
-	ignore_dtype: bool = False,
-) -> NDArray[Any]:
-	""" Apply Contrast Limited Adaptive Histogram Equalization (CLAHE) to an image.
-
-	Args:
-		image           (NDArray[Any]):  Image to apply CLAHE to
-		clip_limit      (float):       Threshold for contrast limiting (1.0-4.0 recommended)
-		tile_grid_size  (int):         Size of grid for histogram equalization (2-16 recommended)
-		ignore_dtype    (bool):        Ignore the dtype check
-	Returns:
-		NDArray[Any]: Image with CLAHE applied
-
-	>>> ## Basic tests
-	>>> image = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
-	>>> clahed = clahe_image(image.astype(np.uint8), 2.0, 1)
-	>>> clahed.tolist()
-	[[28, 57, 85], [113, 142, 170], [198, 227, 255]]
-	>>> clahed.shape == image.shape
-	True
-
-	>>> img = np.full((10,10), 128, dtype=np.uint8)
-	>>> img[2:8, 2:8] = 200  # Create a bright region
-	>>> clahed = clahe_image(img, 2.0, 4)
-	>>> bool(np.mean(clahed) > np.mean(img))  # Should enhance contrast
-	True
-	>>> bool(np.std(clahed) > np.std(img))  # Should enhance contrast
-	True
-
-	>>> rgb = np.full((10,10,3), 128, dtype=np.uint8)
-	>>> rgb[2:8, 2:8, :] = 50  # Create a dark region
-	>>> clahed_rgb = clahe_image(rgb, 2.0, 4)
-	>>> bool(np.mean(clahed_rgb) > np.mean(rgb))  # Should enhance contrast
-	True
-	>>> bool(np.std(clahed_rgb) > np.std(rgb))  # Should enhance contrast
-	True
-	>>> clahed_rgb.shape == rgb.shape
-	True
-
-	>>> ## Test invalid inputs
-	>>> clahe_image("not an image", 2.0, 8)
-	Traceback (most recent call last):
-		...
-	AssertionError: Image must be a numpy array
-
-	>>> clahe_image(image.astype(np.uint8), "2.0", 8)
-	Traceback (most recent call last):
-		...
-	AssertionError: clip_limit must be a number, got <class 'str'>
-
-	>>> clahe_image(image.astype(np.uint8), 2.0, -1)
-	Traceback (most recent call last):
-		...
-	AssertionError: tile_grid_size must be positive, got -1
-	"""
-	# Check input data
-	check_image(image, ignore_dtype=ignore_dtype)
-	assert isinstance(clip_limit, float | int), f"clip_limit must be a number, got {type(clip_limit)}"
-	assert isinstance(tile_grid_size, int), f"tile_grid_size must be an integer, got {type(tile_grid_size)}"
-	assert tile_grid_size > 0, f"tile_grid_size must be positive, got {tile_grid_size}"
-
-	# Create CLAHE object
-	clahe: cv2.CLAHE = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(tile_grid_size, tile_grid_size))
-
-	# Handle different image types
-	if len(image.shape) == 2:
-		# Grayscale image
-		return clahe.apply(image)
-	else:
-		# Color image - convert to LAB color space
-		lab: NDArray[Any] = cv2.cvtColor(image, cv2.COLOR_BGR2LAB)
-		channel_l, channel_a, channel_b = cv2.split(lab)
-
-		# Apply CLAHE to L channel
-		cl: NDArray[Any] = clahe.apply(channel_l)
-
-		# Merge channels and convert back to BGR
-		limg: NDArray[Any] = cv2.merge((cl, channel_a, channel_b))
-		return cv2.cvtColor(limg, cv2.COLOR_LAB2BGR)
-
+
+# pyright: reportUnusedImport=false
+# ruff: noqa: F401
+
+# Imports
+from .common import Any, NDArray, check_image, cv2, np
+
+
+# Functions
+def clahe_image(
+	image: NDArray[Any],
+	clip_limit: float = 2.0,
+	tile_grid_size: int = 8,
+	ignore_dtype: bool = False,
+) -> NDArray[Any]:
+	""" Apply Contrast Limited Adaptive Histogram Equalization (CLAHE) to an image.
+
+	Args:
+		image           (NDArray[Any]):  Image to apply CLAHE to
+		clip_limit      (float):       Threshold for contrast limiting (1.0-4.0 recommended)
+		tile_grid_size  (int):         Size of grid for histogram equalization (2-16 recommended)
+		ignore_dtype    (bool):        Ignore the dtype check
+	Returns:
+		NDArray[Any]: Image with CLAHE applied
+
+	>>> ## Basic tests
+	>>> image = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+	>>> clahed = clahe_image(image.astype(np.uint8), 2.0, 1)
+	>>> clahed.tolist()
+	[[28, 57, 85], [113, 142, 170], [198, 227, 255]]
+	>>> clahed.shape == image.shape
+	True
+
+	>>> img = np.full((10,10), 128, dtype=np.uint8)
+	>>> img[2:8, 2:8] = 200  # Create a bright region
+	>>> clahed = clahe_image(img, 2.0, 4)
+	>>> bool(np.mean(clahed) > np.mean(img))  # Should enhance contrast
+	True
+	>>> bool(np.std(clahed) > np.std(img))  # Should enhance contrast
+	True
+
+	>>> rgb = np.full((10,10,3), 128, dtype=np.uint8)
+	>>> rgb[2:8, 2:8, :] = 50  # Create a dark region
+	>>> clahed_rgb = clahe_image(rgb, 2.0, 4)
+	>>> bool(np.mean(clahed_rgb) > np.mean(rgb))  # Should enhance contrast
+	True
+	>>> bool(np.std(clahed_rgb) > np.std(rgb))  # Should enhance contrast
+	True
+	>>> clahed_rgb.shape == rgb.shape
+	True
+
+	>>> ## Test invalid inputs
+	>>> clahe_image("not an image", 2.0, 8)
+	Traceback (most recent call last):
+		...
+	AssertionError: Image must be a numpy array
+
+	>>> clahe_image(image.astype(np.uint8), "2.0", 8)
+	Traceback (most recent call last):
+		...
+	AssertionError: clip_limit must be a number, got <class 'str'>
+
+	>>> clahe_image(image.astype(np.uint8), 2.0, -1)
+	Traceback (most recent call last):
+		...
+	AssertionError: tile_grid_size must be positive, got -1
+	"""
+	# Check input data
+	check_image(image, ignore_dtype=ignore_dtype)
+	assert isinstance(clip_limit, float | int), f"clip_limit must be a number, got {type(clip_limit)}"
+	assert isinstance(tile_grid_size, int), f"tile_grid_size must be an integer, got {type(tile_grid_size)}"
+	assert tile_grid_size > 0, f"tile_grid_size must be positive, got {tile_grid_size}"
+
+	# Create CLAHE object
+	clahe: cv2.CLAHE = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(tile_grid_size, tile_grid_size))
+
+	# Handle different image types
+	if len(image.shape) == 2:
+		# Grayscale image
+		return clahe.apply(image)
+	else:
+		# Color image - convert to LAB color space
+		lab: NDArray[Any] = cv2.cvtColor(image, cv2.COLOR_BGR2LAB)
+		channel_l, channel_a, channel_b = cv2.split(lab)
+
+		# Apply CLAHE to L channel
+		cl: NDArray[Any] = clahe.apply(channel_l)
+
+		# Merge channels and convert back to BGR
+		limg: NDArray[Any] = cv2.merge((cl, channel_a, channel_b))
+		return cv2.cvtColor(limg, cv2.COLOR_LAB2BGR)
+

stouputils/data_science/data_processing/image/common.py

@@ -1,30 +1,30 @@
-
-
-# pyright: reportUnusedImport=false
-# ruff: noqa: F401
-
-# Imports
-from typing import Any
-
-import cv2
-import numpy as np
-from numpy.typing import NDArray
-
-
-# Functions
-def check_image(image: NDArray[Any], ignore_dtype: bool = False) -> None:
-	""" Check if the image is valid
-
-	Args:
-		image         (NDArray[Any]):  Image to check
-		ignore_dtype  (bool):        Ignore the dtype check
-	"""
-	# Check input data
-	assert isinstance(image, np.ndarray), "Image must be a numpy array"
-	assert len(image.shape) >= 2, "Image must have at least 2 dimensions"
-
-	# Check dtype
-	if not ignore_dtype:
-		dtypes: list[type] = [np.uint8, np.int16, np.float32, np.float64]
-		assert image.dtype in dtypes, f"Image must be of type {dtypes}"
-
+
+
+# pyright: reportUnusedImport=false
+# ruff: noqa: F401
+
+# Imports
+from typing import Any
+
+import cv2
+import numpy as np
+from numpy.typing import NDArray
+
+
+# Functions
+def check_image(image: NDArray[Any], ignore_dtype: bool = False) -> None:
+	""" Check if the image is valid
+
+	Args:
+		image         (NDArray[Any]):  Image to check
+		ignore_dtype  (bool):        Ignore the dtype check
+	"""
+	# Check input data
+	assert isinstance(image, np.ndarray), "Image must be a numpy array"
+	assert len(image.shape) >= 2, "Image must have at least 2 dimensions"
+
+	# Check dtype
+	if not ignore_dtype:
+		dtypes: list[type] = [np.uint8, np.int16, np.float32, np.float64]
+		assert image.dtype in dtypes, f"Image must be of type {dtypes}"
+

stouputils/data_science/data_processing/image/contrast.py

@@ -1,53 +1,53 @@
-
-# Imports
-from .common import Any, NDArray, check_image, cv2, np
-
-
-# Functions
-def contrast_image(image: NDArray[Any], factor: float, ignore_dtype: bool = False) -> NDArray[Any]:
-	""" Adjust the contrast of an image.
-
-	Args:
-		image         (NDArray[Any]):  Image to adjust contrast
-		factor        (float):       Contrast adjustment factor
-		ignore_dtype  (bool):        Ignore the dtype check
-	Returns:
-		NDArray[Any]: Image with adjusted contrast
-
-	>>> ## Basic tests
-	>>> image = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
-	>>> contrasted = contrast_image(image.astype(np.uint8), 1.5)
-	>>> contrasted.shape == image.shape
-	True
-
-	>>> img = np.array([[50, 100, 150]], dtype=np.uint8)
-	>>> high = contrast_image(img, 2.0)
-	>>> low = contrast_image(img, 0.5)
-	>>> bool(high.std() > img.std() > low.std())  # Higher contrast = higher std
-	True
-
-	>>> rgb = np.full((3,3,3), 128, dtype=np.uint8)
-	>>> rgb[1,1] = [50, 100, 150]
-	>>> cont_rgb = contrast_image(rgb, 1.5)
-	>>> cont_rgb.shape == (3,3,3)
-	True
-
-	>>> ## Test invalid inputs
-	>>> contrast_image("not an image", 1.5)
-	Traceback (most recent call last):
-		...
-	AssertionError: Image must be a numpy array
-
-	>>> contrast_image(image.astype(np.uint8), "1.5")
-	Traceback (most recent call last):
-		...
-	AssertionError: factor must be a number, got <class 'str'>
-	"""
-	# Check input data
-	check_image(image, ignore_dtype=ignore_dtype)
-	assert isinstance(factor, float | int), f"factor must be a number, got {type(factor)}"
-
-	# Apply contrast adjustment
-	mean: float = float(np.mean(image))
-	return cv2.addWeighted(image, factor, image, 0, mean * (1 - factor))
-
+
+# Imports
+from .common import Any, NDArray, check_image, cv2, np
+
+
+# Functions
+def contrast_image(image: NDArray[Any], factor: float, ignore_dtype: bool = False) -> NDArray[Any]:
+	""" Adjust the contrast of an image.
+
+	Args:
+		image         (NDArray[Any]):  Image to adjust contrast
+		factor        (float):       Contrast adjustment factor
+		ignore_dtype  (bool):        Ignore the dtype check
+	Returns:
+		NDArray[Any]: Image with adjusted contrast
+
+	>>> ## Basic tests
+	>>> image = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+	>>> contrasted = contrast_image(image.astype(np.uint8), 1.5)
+	>>> contrasted.shape == image.shape
+	True
+
+	>>> img = np.array([[50, 100, 150]], dtype=np.uint8)
+	>>> high = contrast_image(img, 2.0)
+	>>> low = contrast_image(img, 0.5)
+	>>> bool(high.std() > img.std() > low.std())  # Higher contrast = higher std
+	True
+
+	>>> rgb = np.full((3,3,3), 128, dtype=np.uint8)
+	>>> rgb[1,1] = [50, 100, 150]
+	>>> cont_rgb = contrast_image(rgb, 1.5)
+	>>> cont_rgb.shape == (3,3,3)
+	True
+
+	>>> ## Test invalid inputs
+	>>> contrast_image("not an image", 1.5)
+	Traceback (most recent call last):
+		...
+	AssertionError: Image must be a numpy array
+
+	>>> contrast_image(image.astype(np.uint8), "1.5")
+	Traceback (most recent call last):
+		...
+	AssertionError: factor must be a number, got <class 'str'>
+	"""
+	# Check input data
+	check_image(image, ignore_dtype=ignore_dtype)
+	assert isinstance(factor, float | int), f"factor must be a number, got {type(factor)}"
+
+	# Apply contrast adjustment
+	mean: float = float(np.mean(image))
+	return cv2.addWeighted(image, factor, image, 0, mean * (1 - factor))
+

stouputils/data_science/data_processing/image/curvature_flow_filter.py

@@ -1,74 +1,74 @@
-
-# pyright: reportUnknownMemberType=false
-# pyright: reportUnknownArgumentType=false
-# pyright: reportUnknownVariableType=false
-# pyright: reportUnusedImport=false
-# ruff: noqa: F401
-
-# Imports
-import SimpleITK as Sitk
-
-from .common import Any, NDArray, check_image, np
-
-
-# Functions
-def curvature_flow_filter_image(
-	image: NDArray[Any],
-	time_step: float = 0.05,
-	number_of_iterations: int = 5,
-	ignore_dtype: bool = False,
-) -> NDArray[Any]:
-	""" Apply a curvature flow filter to an image.
-
-	Args:
-		image                (NDArray[Any]):  Image to apply the curvature flow filter
-		time_step            (float):       Time step for the curvature flow filter
-		number_of_iterations (int):         Number of iterations for the curvature flow filter
-		ignore_dtype         (bool):        Ignore the dtype check
-	Returns:
-		NDArray[Any]: Image with the curvature flow filter applied
-
-	>>> ## Basic tests
-	>>> image = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], dtype=np.uint8)
-	>>> filtered = curvature_flow_filter_image(image, 0.05, 5)
-	>>> filtered.tolist()[0][0]
-	1.2910538407309702
-	>>> filtered.shape == image.shape
-	True
-	>>> filtered.dtype == image.dtype
-	False
-
-	>>> rgb = np.full((3,3,3), 128, dtype=np.uint8)
-	>>> rgb[1,1] = [50, 100, 150]
-	>>> filtered_rgb = curvature_flow_filter_image(rgb, 0.05, 5)
-	>>> filtered_rgb.shape == (3,3,3)
-	True
-
-	>>> ## Test invalid inputs
-	>>> curvature_flow_filter_image("not an image")
-	Traceback (most recent call last):
-		...
-	AssertionError: Image must be a numpy array
-
-	>>> curvature_flow_filter_image(image, time_step="not a float")
-	Traceback (most recent call last):
-		...
-	AssertionError: time_step must be a float
-
-	>>> curvature_flow_filter_image(image, number_of_iterations="not an integer")
-	Traceback (most recent call last):
-		...
-	AssertionError: number_of_iterations must be an integer
-	"""
-	# Check input data
-	check_image(image, ignore_dtype=ignore_dtype)
-	assert isinstance(time_step, float), "time_step must be a float"
-	assert isinstance(number_of_iterations, int), "number_of_iterations must be an integer"
-	assert time_step > 0, "time_step must be greater than 0"
-	assert number_of_iterations > 0, "number_of_iterations must be greater than 0"
-
-	# Apply the curvature flow filter
-	image_Sitk: Sitk.Image = Sitk.GetImageFromArray(image)
-	image_Sitk = Sitk.CurvatureFlow(image_Sitk, timeStep=time_step, numberOfIterations=number_of_iterations)
-	return Sitk.GetArrayFromImage(image_Sitk)
-
+
+# pyright: reportUnknownMemberType=false
+# pyright: reportUnknownArgumentType=false
+# pyright: reportUnknownVariableType=false
+# pyright: reportUnusedImport=false
+# ruff: noqa: F401
+
+# Imports
+import SimpleITK as Sitk
+
+from .common import Any, NDArray, check_image, np
+
+
+# Functions
+def curvature_flow_filter_image(
+	image: NDArray[Any],
+	time_step: float = 0.05,
+	number_of_iterations: int = 5,
+	ignore_dtype: bool = False,
+) -> NDArray[Any]:
+	""" Apply a curvature flow filter to an image.
+
+	Args:
+		image                (NDArray[Any]):  Image to apply the curvature flow filter
+		time_step            (float):       Time step for the curvature flow filter
+		number_of_iterations (int):         Number of iterations for the curvature flow filter
+		ignore_dtype         (bool):        Ignore the dtype check
+	Returns:
+		NDArray[Any]: Image with the curvature flow filter applied
+
+	>>> ## Basic tests
+	>>> image = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], dtype=np.uint8)
+	>>> filtered = curvature_flow_filter_image(image, 0.05, 5)
+	>>> filtered.tolist()[0][0]
+	1.2910538407309702
+	>>> filtered.shape == image.shape
+	True
+	>>> filtered.dtype == image.dtype
+	False
+
+	>>> rgb = np.full((3,3,3), 128, dtype=np.uint8)
+	>>> rgb[1,1] = [50, 100, 150]
+	>>> filtered_rgb = curvature_flow_filter_image(rgb, 0.05, 5)
+	>>> filtered_rgb.shape == (3,3,3)
+	True
+
+	>>> ## Test invalid inputs
+	>>> curvature_flow_filter_image("not an image")
+	Traceback (most recent call last):
+		...
+	AssertionError: Image must be a numpy array
+
+	>>> curvature_flow_filter_image(image, time_step="not a float")
+	Traceback (most recent call last):
+		...
+	AssertionError: time_step must be a float
+
+	>>> curvature_flow_filter_image(image, number_of_iterations="not an integer")
+	Traceback (most recent call last):
+		...
+	AssertionError: number_of_iterations must be an integer
+	"""
+	# Check input data
+	check_image(image, ignore_dtype=ignore_dtype)
+	assert isinstance(time_step, float), "time_step must be a float"
+	assert isinstance(number_of_iterations, int), "number_of_iterations must be an integer"
+	assert time_step > 0, "time_step must be greater than 0"
+	assert number_of_iterations > 0, "number_of_iterations must be greater than 0"
+
+	# Apply the curvature flow filter
+	image_Sitk: Sitk.Image = Sitk.GetImageFromArray(image)
+	image_Sitk = Sitk.CurvatureFlow(image_Sitk, timeStep=time_step, numberOfIterations=number_of_iterations)
+	return Sitk.GetArrayFromImage(image_Sitk)
+