Fix error 'ImageStack' object has no attribute 'shape'

CheckLicensesInFiles.py

@@ -11,14 +11,13 @@
 
 import json
 import sys
-from typing import List, Dict
 
 
-def load_copyright_header() -> Dict[str, str]:
+def load_copyright_header() -> dict[str, str]:
     return json.load(open(".licenserc.json"))
 
 
-def find_files_with_incorrect_license_headers(filepaths: List[str], copyright_text: str) -> List[str]:
+def find_files_with_incorrect_license_headers(filepaths: list[str], copyright_text: str) -> list[str]:
     copyright_lines = copyright_text.split("\n")
     incorrect_files = []
 
@@ -35,11 +34,11 @@ def find_files_with_incorrect_license_headers(filepaths: List[str], copyright_te
     return incorrect_files
 
 
-def has_shebang_line(file_lines: List[str]) -> bool:
+def has_shebang_line(file_lines: list[str]) -> bool:
     return file_lines[0].startswith("#!")
 
 
-def has_correct_copyright_lines(file_lines: List[str], copyright_lines: List[str]) -> bool:
+def has_correct_copyright_lines(file_lines: list[str], copyright_lines: list[str]) -> bool:
     if len(file_lines) < len(copyright_lines):
         return False
 

docs/ext/operations_user_doc.py

@@ -2,7 +2,6 @@
 # SPDX - License - Identifier: GPL-3.0-or-later
 from __future__ import annotations
 
-from typing import List
 import inspect
 
 from docutils import nodes
@@ -19,11 +18,11 @@
 """
 
 
-def make_heading(s: str, char: str) -> List[str]:
+def make_heading(s: str, char: str) -> list[str]:
     return [s, len(s) * char, ""]
 
 
-def split_lines(s: str) -> List[str]:
+def split_lines(s: str) -> list[str]:
     s = s.replace("\n\n", "DOUBLE_NEW_LINE")
     s = s.replace("\n", " ")
     s = s.replace("DOUBLE_NEW_LINE", "\n\n")
@@ -33,7 +32,7 @@ def split_lines(s: str) -> List[str]:
 PARAM_SKIP_LIST = ["images", "progress"]
 
 
-def get_params(s: str) -> List[str]:
+def get_params(s: str) -> list[str]:
     ret = []
     for line in s.split("\n"):
         if line.strip().startswith(":param"):
@@ -51,7 +50,7 @@ def get_params(s: str) -> List[str]:
 
 class OperationsUserDoc(Directive):
 
-    def run(self) -> List[Node]:
+    def run(self) -> list[Node]:
 
         try:
             from mantidimaging.core.operations.loader import load_filter_packages

docs/release_notes/next/fix-2129-median_cuda

@@ -0,0 +1 @@
+#2129 : fix: Pytest failure AttributeError: 'ImageStack' object has no attribute 'shape

mantidimaging/core/data/dataset.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 import uuid
 from dataclasses import dataclass
-from typing import Optional, List, Union
 
 import numpy as np
 
@@ -26,7 +25,7 @@ def __init__(self, name: str = ""):
         self._id: uuid.UUID = uuid.uuid4()
         self.recons = ReconList()
         self._name = name
-        self._sinograms: Optional[ImageStack] = None
+        self._sinograms: ImageStack | None = None
 
     @property
     def id(self) -> uuid.UUID:
@@ -41,11 +40,11 @@ def name(self, arg: str):
         self._name = arg
 
     @property
-    def sinograms(self) -> Optional[ImageStack]:
+    def sinograms(self) -> ImageStack | None:
         return self._sinograms
 
     @sinograms.setter
-    def sinograms(self, sino: Optional[ImageStack]):
+    def sinograms(self, sino: ImageStack | None):
         self._sinograms = sino
 
     @property
@@ -59,7 +58,7 @@ def __contains__(self, images_id: uuid.UUID) -> bool:
         return any(image.id == images_id for image in self.all)
 
     @property
-    def all_image_ids(self) -> List[uuid.UUID]:
+    def all_image_ids(self) -> list[uuid.UUID]:
         return [image_stack.id for image_stack in self.all if image_stack is not None]
 
     def add_recon(self, recon: ImageStack):
@@ -71,7 +70,7 @@ def delete_recons(self):
 
 class MixedDataset(BaseDataset):
 
-    def __init__(self, stacks: Optional[List[ImageStack]] = None, name: str = ""):
+    def __init__(self, stacks: list[ImageStack] | None = None, name: str = ""):
         super().__init__(name=name)
         stacks = [] if stacks is None else stacks
         self._stacks = stacks
@@ -80,7 +79,7 @@ def add_stack(self, stack: ImageStack):
         self._stacks.append(stack)
 
     @property
-    def all(self) -> List[ImageStack]:
+    def all(self) -> list[ImageStack]:
         all_images = self._stacks + self.recons.stacks
         if self.sinograms is None:
             return all_images
@@ -104,17 +103,17 @@ def delete_stack(self, images_id: uuid.UUID):
 @dataclass
 class StrictDataset(BaseDataset):
     sample: ImageStack
-    flat_before: Optional[ImageStack] = None
-    flat_after: Optional[ImageStack] = None
-    dark_before: Optional[ImageStack] = None
-    dark_after: Optional[ImageStack] = None
+    flat_before: ImageStack | None = None
+    flat_after: ImageStack | None = None
+    dark_before: ImageStack | None = None
+    dark_after: ImageStack | None = None
 
     def __init__(self,
                  sample: ImageStack,
-                 flat_before: Optional[ImageStack] = None,
-                 flat_after: Optional[ImageStack] = None,
-                 dark_before: Optional[ImageStack] = None,
-                 dark_after: Optional[ImageStack] = None,
+                 flat_before: ImageStack | None = None,
+                 flat_after: ImageStack | None = None,
+                 dark_before: ImageStack | None = None,
+                 dark_after: ImageStack | None = None,
                  name: str = ""):
         super().__init__(name=name)
         self.sample = sample
@@ -127,31 +126,31 @@ def __init__(self,
             self._name = sample.name
 
     @property
-    def all(self) -> List[ImageStack]:
+    def all(self) -> list[ImageStack]:
         image_stacks = [
             self.sample, self.proj180deg, self.flat_before, self.flat_after, self.dark_before, self.dark_after,
             self.sinograms
         ]
         return [image_stack for image_stack in image_stacks if image_stack is not None] + self.recons.stacks
 
     @property
-    def _nexus_stack_order(self) -> List[ImageStack]:
+    def _nexus_stack_order(self) -> list[ImageStack]:
         return list(filter(None, [self.dark_before, self.flat_before, self.sample, self.flat_after, self.dark_after]))
 
     @property
-    def nexus_arrays(self) -> List[np.ndarray]:
+    def nexus_arrays(self) -> list[np.ndarray]:
         return [image_stack.data for image_stack in self._nexus_stack_order]
 
     @property
-    def nexus_rotation_angles(self) -> List[np.ndarray]:
+    def nexus_rotation_angles(self) -> list[np.ndarray]:
         proj_angles = []
         for image_stack in self._nexus_stack_order:
             angles = image_stack.real_projection_angles()
             proj_angles.append(angles.value if angles else np.zeros(image_stack.num_images))
         return proj_angles
 
     @property
-    def image_keys(self) -> List[int]:
+    def image_keys(self) -> list[int]:
         image_keys = []
         if self.dark_before is not None:
             image_keys += _image_key_list(2, self.dark_before.data.shape[0])
@@ -220,7 +219,7 @@ def is_processed(self) -> bool:
         return False
 
 
-def _get_stack_data_type(stack_id: uuid.UUID, dataset: Union[MixedDataset, StrictDataset]) -> str:
+def _get_stack_data_type(stack_id: uuid.UUID, dataset: MixedDataset | StrictDataset) -> str:
     """
     Find the data type as a string of a stack.
     :param stack_id: The ID of the stack.

mantidimaging/core/data/imagestack.py

@@ -7,7 +7,7 @@
 import os.path
 import uuid
 from copy import deepcopy
-from typing import List, Optional, Any, Dict, Union, TextIO, TYPE_CHECKING, cast
+from typing import Any, TextIO, TYPE_CHECKING, cast
 
 import numpy as np
 
@@ -29,11 +29,11 @@ class ImageStack:
 
     def __init__(self,
                  data: np.ndarray | pu.SharedArray,
-                 filenames: Optional[List[str]] = None,
-                 indices: List[int] | Indices | None = None,
-                 metadata: Optional[Dict[str, Any]] = None,
+                 filenames: list[str] | None = None,
+                 indices: list[int] | Indices | None = None,
+                 metadata: dict[str, Any] | None = None,
                  sinograms: bool = False,
-                 name: Optional[str] = None):
+                 name: str | None = None):
         """
         :param data: a numpy array or SharedArray object containing the images of the Sample/Projection data
         :param filenames: All filenames that were matched for loading
@@ -53,12 +53,12 @@ def __init__(self,
 
         self._filenames = filenames
 
-        self.metadata: Dict[str, Any] = deepcopy(metadata) if metadata else {}
+        self.metadata: dict[str, Any] = deepcopy(metadata) if metadata else {}
         self._is_sinograms = sinograms
 
-        self._proj180deg: Optional[ImageStack] = None
+        self._proj180deg: ImageStack | None = None
         self._log_file: InstrumentLog | None = None
-        self._projection_angles: Optional[ProjectionAngles] = None
+        self._projection_angles: ProjectionAngles | None = None
 
         if name is None:
             if filenames is not None:
@@ -93,11 +93,11 @@ def count(self) -> int:
         return len(self._filenames) if self._filenames else 0
 
     @property
-    def filenames(self) -> Optional[List[str]]:
+    def filenames(self) -> list[str] | None:
         return self._filenames
 
     @filenames.setter
-    def filenames(self, new_ones: List[str]) -> None:
+    def filenames(self, new_ones: list[str]) -> None:
         assert len(new_ones) == self.data.shape[0], "Number of filenames and number of images must match."
         self._filenames = new_ones
 
@@ -112,7 +112,7 @@ def load_metadata(self, f: TextIO) -> None:
         self.metadata = json.load(f) | self.metadata
         self._is_sinograms = self.metadata.get(const.SINOGRAMS, False)
 
-    def save_metadata(self, f: TextIO, rescale_params: Optional[Dict[str, Union[str, float]]] = None) -> None:
+    def save_metadata(self, f: TextIO, rescale_params: dict[str, str | float] | None = None) -> None:
         self.metadata[const.SINOGRAMS] = self.is_sinograms
 
         if rescale_params is not None:
@@ -238,7 +238,7 @@ def has_proj180deg(self) -> bool:
         return self._proj180deg is not None
 
     @property
-    def proj180deg(self) -> Optional['ImageStack']:
+    def proj180deg(self) -> "ImageStack" | None:
         return self._proj180deg
 
     @proj180deg.setter
@@ -306,7 +306,7 @@ def set_projection_angles(self, angles: ProjectionAngles) -> None:
 
         self._projection_angles = angles
 
-    def real_projection_angles(self) -> Optional[ProjectionAngles]:
+    def real_projection_angles(self) -> ProjectionAngles | None:
         """
         Return only the projection angles that are from a log file or have been manually loaded.
         :return: Real projection angles if they were found, None otherwise.
@@ -334,7 +334,7 @@ def projection_angles(self, max_angle: float = 360.0) -> ProjectionAngles:
         else:
             return ProjectionAngles(np.linspace(0, np.deg2rad(max_angle), self.num_projections))
 
-    def counts(self) -> Optional[Counts]:
+    def counts(self) -> Counts | None:
         if self._log_file is not None:
             return self._log_file.counts()
         else:
@@ -352,7 +352,7 @@ def pixel_size(self, value: float) -> None:
     def clear_proj180deg(self) -> None:
         self._proj180deg = None
 
-    def make_name_unique(self, existing_names: List[str]) -> None:
+    def make_name_unique(self, existing_names: list[str]) -> None:
         name = self.name
         num = 1
         while self.name in existing_names:

mantidimaging/core/data/reconlist.py

@@ -4,15 +4,15 @@
 
 import uuid
 from collections import UserList
-from typing import List, Optional, TYPE_CHECKING
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from mantidimaging.core.data import ImageStack
 
 
 class ReconList(UserList):
 
-    def __init__(self, data: Optional[List[ImageStack]] = None):
+    def __init__(self, data: list[ImageStack] | None = None):
         data = [] if data is None else data
         super().__init__(data)
         self._id: uuid.UUID = uuid.uuid4()
@@ -22,9 +22,9 @@ def id(self) -> uuid.UUID:
         return self._id
 
     @property
-    def ids(self) -> List[uuid.UUID]:
+    def ids(self) -> list[uuid.UUID]:
         return [recon.id for recon in self.data]
 
     @property
-    def stacks(self) -> List[ImageStack]:
+    def stacks(self) -> list[ImageStack]:
         return self.data

mantidimaging/core/io/csv_output.py

@@ -1,7 +1,7 @@
 # Copyright (C) 2024 ISIS Rutherford Appleton Laboratory UKRI
 # SPDX - License - Identifier: GPL-3.0-or-later
 from __future__ import annotations
-from typing import IO, Optional
+from typing import IO
 
 import numpy as np
 
@@ -10,7 +10,7 @@ class CSVOutput:
 
     def __init__(self) -> None:
         self.columns: dict[str, np.ndarray] = {}
-        self.num_rows: Optional[int] = None
+        self.num_rows: int | None = None
 
     def add_column(self, name: str, values: np.ndarray) -> None:
         as_column = values.reshape((-1, 1))