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libzlib >=1.3.1,<2.0a0 - ucrt >=10.0.20348.0 - vc >=14.2,<15 - vc14_runtime >=14.29.30139 license: BSD-3-Clause license_family: BSD - purls: - - pkg:pypi/zstandard?source=hash-mapping - size: 444685 - timestamp: 1745870132644 + purls: [] + size: 354697 + timestamp: 1742433568506 From a13a4c1d5a288128701e117e4f7fe4a049c4e862 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Wed, 24 Sep 2025 10:59:40 -0400 Subject: [PATCH 2/6] refactor: allow list input for crop and resize image and mask --- src/readii/process/images/crop.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/readii/process/images/crop.py b/src/readii/process/images/crop.py index d69d574..e586681 100644 --- a/src/readii/process/images/crop.py +++ b/src/readii/process/images/crop.py @@ -3,6 +3,7 @@ import SimpleITK as sitk from imgtools.coretypes.box import RegionBox from imgtools.transforms.functional import resize +import numpy as np from readii.utils import logger @@ -13,7 +14,7 @@ def crop_and_resize_image_and_mask(image: sitk.Image, mask: sitk.Image, label: int = 1, crop_method: CropMethods = "cube", - resize_dimension: int | None = None + resize_dimension: int | list[int] | np.ndarray | None = None ) -> tuple[sitk.Image, sitk.Image]: """Crop an image and mask to an ROI in the mask and resize to a specified crop dimensions. @@ -69,7 +70,7 @@ def crop_and_resize_image_and_mask(image: sitk.Image, resize_dimension = 50 # Generate a cube bounding box with resize_dimensions around the centroid of a mask - crop_box = RegionBox.from_mask_centroid(mask, label).expand_to_cube(resize_dimension) + crop_box = RegionBox.from_mask_centroid(mask, label, resize_dimension) case "cube": # Generate a bounding box around the mask, then expand the dimensions to a cube with the maximum bounding box dimension From 25992ad7a01db8b6c6b274c090a27caefe6080d1 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Wed, 24 Sep 2025 11:12:02 -0400 Subject: [PATCH 3/6] feat: add resize dimension handling for centroid cropping --- src/readii/process/images/crop.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/readii/process/images/crop.py b/src/readii/process/images/crop.py index e586681..28e2144 100644 --- a/src/readii/process/images/crop.py +++ b/src/readii/process/images/crop.py @@ -1,9 +1,9 @@ from typing import Literal +import numpy as np import SimpleITK as sitk from imgtools.coretypes.box import RegionBox from imgtools.transforms.functional import resize -import numpy as np from readii.utils import logger @@ -68,6 +68,16 @@ def crop_and_resize_image_and_mask(image: sitk.Image, if resize_dimension is None: # Set resize_dimension to 50 if not provided -> default expected dimension for FMCIB resize_dimension = 50 + elif isinstance(resize_dimension, list): + # Convert to a set to get unique values - if longer than 1 then, raise error + match len(set(resize_dimension)): + case 1: # all values in resize dimension are the same, just use the first one + resize_dimension = resize_dimension[0] + case _: # values differ in resize dimension, raise error + message = "If using centroid crop method, resize dimension must be a single value, list of identical values, or None." \ + f"Current value: {resize_dimension}." + logger.error(message) + raise ValueError(message) # Generate a cube bounding box with resize_dimensions around the centroid of a mask crop_box = RegionBox.from_mask_centroid(mask, label, resize_dimension) From a7c5e639327e491029c66ad23029ee9e592a486d Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Wed, 24 Sep 2025 12:00:00 -0400 Subject: [PATCH 4/6] refactor: update resize dimension handling from coderabbit suggestion --- src/readii/process/images/crop.py | 44 ++++++++++++++++++++++--------- 1 file changed, 31 insertions(+), 13 deletions(-) diff --git a/src/readii/process/images/crop.py b/src/readii/process/images/crop.py index 28e2144..9e52b04 100644 --- a/src/readii/process/images/crop.py +++ b/src/readii/process/images/crop.py @@ -66,21 +66,39 @@ def crop_and_resize_image_and_mask(image: sitk.Image, case "centroid": if resize_dimension is None: - # Set resize_dimension to 50 if not provided -> default expected dimension for FMCIB - resize_dimension = 50 - elif isinstance(resize_dimension, list): - # Convert to a set to get unique values - if longer than 1 then, raise error - match len(set(resize_dimension)): - case 1: # all values in resize dimension are the same, just use the first one - resize_dimension = resize_dimension[0] - case _: # values differ in resize dimension, raise error - message = "If using centroid crop method, resize dimension must be a single value, list of identical values, or None." \ - f"Current value: {resize_dimension}." + # Set to 50 if not provided -> default expected dimension for FMCIB + centroid_dimension = 50 + elif isinstance(resize_dimension, (list, tuple, np.ndarray)): + # Ensure all values are identical to form a cube; collapse to a single int + if isinstance(resize_dimension, np.ndarray): + uniques = np.unique(resize_dimension) + if uniques.size == 1: + centroid_dimension = int(uniques[0]) + else: + message = ( + "If using centroid crop method, resize_dimension must be a single value, " + "or a list/tuple/array of identical values, or None. " + f"Current value: {resize_dimension}." + ) logger.error(message) raise ValueError(message) - - # Generate a cube bounding box with resize_dimensions around the centroid of a mask - crop_box = RegionBox.from_mask_centroid(mask, label, resize_dimension) + else: + unique_vals = set(int(v) for v in resize_dimension) + if len(unique_vals) == 1: + centroid_dimension = int(next(iter(unique_vals))) + else: + message = ( + "If using centroid crop method, resize_dimension must be a single value, " + "or a list/tuple/array of identical values, or None. " + f"Current value: {resize_dimension}." + ) + logger.error(message) + raise ValueError(message) + else: + # Single scalar provided + centroid_dimension = int(resize_dimension) + # Generate a cube bounding box with resize dimension around the centroid of a mask + crop_box = RegionBox.from_mask_centroid(mask, label, centroid_dimension) case "cube": # Generate a bounding box around the mask, then expand the dimensions to a cube with the maximum bounding box dimension From 58671440086efa560f4f1b5e9140e950c3eab360 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Wed, 24 Sep 2025 12:43:22 -0400 Subject: [PATCH 5/6] refactor: removed different handling for list vs tuple/array for centroid dimension This list should never be longer than 3 values, so using set is fine --- src/readii/process/images/crop.py | 33 ++++++++++--------------------- 1 file changed, 10 insertions(+), 23 deletions(-) diff --git a/src/readii/process/images/crop.py b/src/readii/process/images/crop.py index 9e52b04..f3c65b9 100644 --- a/src/readii/process/images/crop.py +++ b/src/readii/process/images/crop.py @@ -70,30 +70,17 @@ def crop_and_resize_image_and_mask(image: sitk.Image, centroid_dimension = 50 elif isinstance(resize_dimension, (list, tuple, np.ndarray)): # Ensure all values are identical to form a cube; collapse to a single int - if isinstance(resize_dimension, np.ndarray): - uniques = np.unique(resize_dimension) - if uniques.size == 1: - centroid_dimension = int(uniques[0]) - else: - message = ( - "If using centroid crop method, resize_dimension must be a single value, " - "or a list/tuple/array of identical values, or None. " - f"Current value: {resize_dimension}." - ) - logger.error(message) - raise ValueError(message) + unique_vals = {int(v) for v in resize_dimension} + if len(unique_vals) == 1: + centroid_dimension = int(next(iter(unique_vals))) else: - unique_vals = set(int(v) for v in resize_dimension) - if len(unique_vals) == 1: - centroid_dimension = int(next(iter(unique_vals))) - else: - message = ( - "If using centroid crop method, resize_dimension must be a single value, " - "or a list/tuple/array of identical values, or None. " - f"Current value: {resize_dimension}." - ) - logger.error(message) - raise ValueError(message) + message = ( + "If using centroid crop method, resize_dimension must be a single value, " + "or a list/tuple/array of identical values, or None. 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