fix: add type hint for keys method and improve modality handling in ImageAutoInput

.github/workflows/main.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, macos-13, windows-latest] 
-        env: ["py310", "py311", "py312"]
+        env: ["py310", "py311", "py312", "py313"]
 
     steps:
       - uses: actions/checkout@v4
@@ -31,8 +31,9 @@ jobs:
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
           environments: ${{ matrix.env }}
-          pixi-version: v0.40.0
+          pixi-version: v0.41.1
           cache: true
+          locked: false
 
       - name: Run pytest
         env:
@@ -74,7 +75,7 @@ jobs:
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
           environments: ${{ matrix.env }}
-          pixi-version: v0.40.0
+          pixi-version: v0.41.1
           cache: true
           locked: false # wont be the same because of the tag
 
@@ -117,7 +118,7 @@ jobs:
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
           environments: ${{ matrix.env }}
-          pixi-version: v0.40.0
+          pixi-version: v0.41.1
           cache: true
           locked: false # wont be the same because of the tag
 
@@ -228,7 +229,6 @@ jobs:
 
       - name: Publish to PyPI
         # only push to pypi if on main
-        if: github.ref == 'refs/heads/main'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           verbose: true

pixi.toml

@@ -21,6 +21,7 @@ test = ["test", "quality"]
 py310 = { features = ["py310", "test"], no-default-feature = true }
 py311 = { features = ["py311", "test"], no-default-feature = true }
 py312 = { features = ["py312", "test"], no-default-feature = true }
+py313 = { features = ["py313", "test"], no-default-feature = true }
 
 ############################################## DEV ###############################################
 [feature.dev.pypi-dependencies]
@@ -49,6 +50,8 @@ python = "3.10.*"
 python = "3.11.*"
 [feature.py312.dependencies]
 python = "3.12.*"
+[feature.py313.dependencies]
+python = "3.13.*"
 
 ############################################## TEST ################################################
 [feature.test.pypi-dependencies]

src/imgtools/autopipeline.py

@@ -393,7 +393,10 @@ def process_one_subject(self, subject_id):
 
                 # Process image (CT/MR)
                 elif modality == "CT" or modality == 'MR':
-                    image = read_results[i].image
+                    try:
+                        image = read_results[i].image
+                    except AttributeError:
+                        image = read_results[i]
                     if len(image.GetSize()) == 4:
                         assert image.GetSize()[-1] == 1, f"There is more than one volume in this CT file for {subject_id}."
                         extractor = sitk.ExtractImageFilter()

src/imgtools/coretypes/box.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import math
 from dataclasses import dataclass, field
 from enum import Enum
 
@@ -108,7 +109,7 @@ def from_tuple(
         return cls(Coordinate3D(*coordmin), Coordinate3D(*coordmax))
 
     @classmethod
-    def from_mask_centroid(cls, mask: sitk.Image, label: int = 1) -> RegionBox:
+    def from_mask_centroid(cls, mask: sitk.Image, label: int = 1, desired_size: int | None = None) -> RegionBox:
         """Creates a RegionBox from the centroid of a mask image.
 
         Parameters
@@ -117,6 +118,8 @@ def from_mask_centroid(cls, mask: sitk.Image, label: int = 1) -> RegionBox:
             The input mask image.
         label : int, optional
             label in the mask image to calculate the centroid.
+        desired_size : int | None, optional
+            The desired size of the box. If None, the minimum size default from `expand_to_min_size` is used.
 
         Returns
         -------
@@ -131,8 +134,9 @@ def from_mask_centroid(cls, mask: sitk.Image, label: int = 1) -> RegionBox:
         centroid_idx = mask.TransformPhysicalPointToIndex(centroid)
 
         return RegionBox(
-            Coordinate3D(*centroid_idx), Coordinate3D(*centroid_idx)
-        )
+            Coordinate3D(*centroid_idx), 
+            Coordinate3D(*centroid_idx)
+        ).expand_to_cube(desired_size)
 
     @classmethod
     def from_mask_bbox(cls, mask: sitk.Image, label: int = 1) -> RegionBox:
@@ -275,15 +279,22 @@ def expand_to_min_size(self, size: int = 5) -> RegionBox:
         Notes
         -----
         Validation is done to ensure that any min coordinates that are negative are set to 0,
-        and the difference is added to the maximum coordinates
+        and the difference is added to the maximum coordinates.
+
+        If an extra dimension is not an integer (e.g. 1.5), the bounding box is shifted 1 voxel towards the minimum in that dimension.
         """
-        extra_x = max(0, size - self.size.width) // 2
-        extra_y = max(0, size - self.size.height) // 2
-        extra_z = max(0, size - self.size.depth) // 2
+        # Calculate extra dimensions to add to the existing coordinates
+        extra_x = max(0, size - self.size.width) / 2
+        extra_y = max(0, size - self.size.height) / 2
+        extra_z = max(0, size - self.size.depth) / 2
 
-        min_coord = self.min - (extra_x, extra_y, extra_z)
-        max_coord = self.max + (extra_x, extra_y, extra_z)
+        # Round extra dimension values UP to the nearest integer before adding to existing minimum coordinates
+        min_coord = self.min - tuple([math.ceil(extra) for extra in(extra_x, extra_y, extra_z)])
 
+        # Round extra dimensions DOWN to the nearest integer before adding to existing maximum coordinates
+        max_coord = self.max + tuple([math.floor(extra) for extra in(extra_x, extra_y, extra_z)])
+
+        # Adjust negative coordinates to ensure that the min values are not negative
         self._adjust_negative_coordinates(min_coord, max_coord)
 
         return RegionBox(min=min_coord, max=max_coord)
@@ -302,6 +313,21 @@ def _adjust_negative_coordinates(
                 setattr(min_coord, axis, 0)
                 setattr(max_coord, axis, getattr(max_coord, axis) + diff)
 
+
+    def check_out_of_bounds_coordinates(self, image: sitk.Image) -> None:
+        """Adjust the coordinates to ensure that the max values are not greater than the image size."""
+        # if any of the max values are greater than the image size, set them to the image size,
+        # and subtract the difference from the min values
+        for idx, axis in enumerate(["x", "y", "z"]):
+            max_value = getattr(self.max, axis)
+            image_size = image.GetSize()[idx]
+            if max_value > image_size:
+                logger.debug(f"Adjusting box {axis} coordinates to be within the image size.")
+                diff = max_value - image_size
+                setattr(self.min, axis, getattr(self.min, axis) - diff)
+                setattr(self.max, axis, image_size)
+
+
     def crop_image(self, image: sitk.Image) -> sitk.Image:
         """Crop an image to the coordinates defined by the box.
 
@@ -316,17 +342,12 @@ def crop_image(self, image: sitk.Image) -> sitk.Image:
             The cropped image.
         """
         try:
+            self.check_out_of_bounds_coordinates(image)
             cropped_image = sitk.RegionOfInterest(image, self.size, self.min)
-        except RuntimeError as e:
-            msg = (
-                f"The box {self} is outside"
-                f" the image size {calculate_image_boundaries(image)} "
-            )
-            # this is probably due to the box being outside the image
-            # try to crop the image to the largest possible region
-            # we could handle this in the future, for now let it raise the error
-            # and make user try again with an adjusted box
-            raise BoundingBoxOutsideImageError(msg) from e
+        except Exception as e:
+            msg = f"Error cropping image to the box: {e}"
+            logger.exception(msg)
+            raise e
         else:
             return cropped_image
 
@@ -369,6 +390,9 @@ def __repr__(self) -> str:
             f")"
         )
 
+    def copy(self) -> RegionBox:
+        """Create a copy of the RegionBox."""
+        return RegionBox(self.min, self.max)
 
 if __name__ == "__main__":  # pragma: no cover
     from rich import print  # noqa