From 1b4264ac5d7b089f8769d3106ccadc4b15122498 Mon Sep 17 00:00:00 2001
From: ashmeigh <ashleymeigh0@gmail.com>
Date: Wed, 3 Jul 2024 14:59:21 +0100
Subject: [PATCH 1/8] added type checking to the liveviewer and recon

---
 .../gui/windows/live_viewer/model.py          | 10 ++--
 .../gui/windows/live_viewer/presenter.py      | 13 ++---
 mantidimaging/gui/windows/live_viewer/view.py |  2 +-
 mantidimaging/gui/windows/recon/image_view.py | 32 ++++++-------
 mantidimaging/gui/windows/recon/model.py      | 10 ++--
 .../gui/windows/recon/point_table_model.py    | 48 +++++++++++--------
 mantidimaging/gui/windows/recon/presenter.py  | 35 ++++++++------
 mantidimaging/gui/windows/recon/view.py       | 22 ++++-----
 8 files changed, 93 insertions(+), 79 deletions(-)

diff --git a/mantidimaging/gui/windows/live_viewer/model.py b/mantidimaging/gui/windows/live_viewer/model.py
index ad984214334..dd8fe2c96e4 100644
--- a/mantidimaging/gui/windows/live_viewer/model.py
+++ b/mantidimaging/gui/windows/live_viewer/model.py
@@ -277,7 +277,7 @@ def _is_image_file(file_name: str) -> bool:
         image_extensions = ('tif', 'tiff', 'fits')
         return file_name.rpartition(".")[2].lower() in image_extensions
 
-    def remove_path(self):
+    def remove_path(self) -> None:
         """
         Remove the currently set path
         """
@@ -292,22 +292,22 @@ def update_recent_watcher(self, images: list[Image_Data]) -> None:
         self.recent_file_watcher.removePaths(self.recent_file_watcher.files())
         self.recent_file_watcher.addPaths([str(image.image_path) for image in images])
 
-    def handle_image_modified(self, file_path):
+    def handle_image_modified(self, file_path) -> None:
         self.recent_image_changed.emit(Path(file_path))
 
-    def add_sub_directory(self, sub_dir: SubDirectory):
+    def add_sub_directory(self, sub_dir: SubDirectory) -> None:
         if sub_dir.path not in self.sub_directories:
             self.watcher.addPath(str(sub_dir.path))
 
         self.sub_directories[sub_dir.path] = sub_dir
 
-    def remove_sub_directory(self, sub_dir: Path):
+    def remove_sub_directory(self, sub_dir: Path) -> None:
         if sub_dir in self.sub_directories:
             self.watcher.removePath(str(sub_dir))
 
         del self.sub_directories[sub_dir]
 
-    def clear_deleted_sub_directories(self, directory: Path):
+    def clear_deleted_sub_directories(self, directory: Path) -> None:
         for sub_dir in list(self.sub_directories):
             if sub_dir.is_relative_to(directory) and not sub_dir.exists():
                 self.remove_sub_directory(sub_dir)
diff --git a/mantidimaging/gui/windows/live_viewer/presenter.py b/mantidimaging/gui/windows/live_viewer/presenter.py
index 2c1294ab2db..8945f4194bd 100644
--- a/mantidimaging/gui/windows/live_viewer/presenter.py
+++ b/mantidimaging/gui/windows/live_viewer/presenter.py
@@ -82,7 +82,7 @@ def select_image(self, index: int) -> None:
 
         self.display_image(self.selected_image.image_path)
 
-    def display_image(self, image_path: Path):
+    def display_image(self, image_path: Path) -> None:
         """
         Display image in the view after validating contents
         """
@@ -119,20 +119,21 @@ def load_image(image_path: Path) -> np.ndarray:
                 image_data = fit[0].data
         return image_data
 
-    def update_image_modified(self, image_path: Path):
+    def update_image_modified(self, image_path: Path) -> None:
         """
         Update the displayed image when the file is modified
         """
         if self.selected_image and image_path == self.selected_image.image_path:
             self.display_image(image_path)
 
-    def update_image_operation(self):
+    def update_image_operation(self) -> None:
         """
         Reload the current image if an operation has been performed on the current image
         """
-        self.display_image(self.selected_image.image_path)
+        if self.selected_image is not None:
+            self.display_image(self.selected_image.image_path)
 
-    def convert_image_to_imagestack(self, image_data):
+    def convert_image_to_imagestack(self, image_data) -> ImageStack:
         """
         Convert the single image to an imagestack so the Operations framework can be used
         """
@@ -141,7 +142,7 @@ def convert_image_to_imagestack(self, image_data):
         image_data_temp[0] = image_data
         return ImageStack(image_data_temp)
 
-    def perform_operations(self, image_data):
+    def perform_operations(self, image_data) -> np.ndarray:
         if not self.view.filter_params:
             return image_data
         image_stack = self.convert_image_to_imagestack(image_data)
diff --git a/mantidimaging/gui/windows/live_viewer/view.py b/mantidimaging/gui/windows/live_viewer/view.py
index ee4ec458ecf..be963295899 100644
--- a/mantidimaging/gui/windows/live_viewer/view.py
+++ b/mantidimaging/gui/windows/live_viewer/view.py
@@ -91,7 +91,7 @@ def closeEvent(self, e) -> None:
         super().closeEvent(e)
         self.presenter = None  # type: ignore # View instance to be destroyed -type can be inconsistent
 
-    def set_image_rotation_angle(self):
+    def set_image_rotation_angle(self) -> None:
         """Set the image rotation angle which will be read in by the presenter"""
         if self.rotate_angles_group.checkedAction().text() == "0°":
             if "Rotate Stack" in self.filter_params:
diff --git a/mantidimaging/gui/windows/recon/image_view.py b/mantidimaging/gui/windows/recon/image_view.py
index 4683c14c880..a57aea68e3a 100644
--- a/mantidimaging/gui/windows/recon/image_view.py
+++ b/mantidimaging/gui/windows/recon/image_view.py
@@ -51,7 +51,7 @@ def __init__(self, parent):
         self.imageview_projection.enable_nonpositive_check()
         self.imageview_sinogram.enable_nonpositive_check()
 
-    def cleanup(self):
+    def cleanup(self) -> None:
         self.imageview_projection.cleanup()
         self.imageview_sinogram.cleanup()
         self.imageview_recon.cleanup()
@@ -60,10 +60,10 @@ def cleanup(self):
         del self.imageview_sinogram
         del self.imageview_recon
 
-    def slice_line_moved(self):
+    def slice_line_moved(self) -> None:
         self.slice_changed(int(self.slice_line.value()))
 
-    def update_projection(self, image_data: np.ndarray, preview_slice_index: int, tilt_angle: Degrees | None):
+    def update_projection(self, image_data: np.ndarray, preview_slice_index: int, tilt_angle: Degrees | None) -> None:
         self.imageview_projection.clear()
         self.imageview_projection.setImage(image_data)
         self.imageview_projection.histogram.imageChanged(autoLevel=True, autoRange=True)
@@ -75,13 +75,13 @@ def update_projection(self, image_data: np.ndarray, preview_slice_index: int, ti
             self.hide_tilt()
         set_histogram_log_scale(self.imageview_projection.histogram)
 
-    def update_sinogram(self, image):
+    def update_sinogram(self, image) -> None:
         self.imageview_sinogram.clear()
         self.imageview_sinogram.setImage(image)
         self.imageview_sinogram.histogram.imageChanged(autoLevel=True, autoRange=True)
         set_histogram_log_scale(self.imageview_sinogram.histogram)
 
-    def update_recon(self, image_data, reset_roi: bool = False):
+    def update_recon(self, image_data, reset_roi: bool = False) -> None:
         self.imageview_recon.clear()
         self.imageview_recon.setImage(image_data, autoLevels=False)
         set_histogram_log_scale(self.imageview_recon.histogram)
@@ -90,34 +90,34 @@ def update_recon(self, image_data, reset_roi: bool = False):
         else:
             self.recon_line_profile.update()
 
-    def update_recon_hist(self):
+    def update_recon_hist(self) -> None:
         self.imageview_recon.histogram.imageChanged(autoLevel=True, autoRange=True)
 
-    def mouse_click(self, ev, line: InfiniteLine):
+    def mouse_click(self, ev, line: InfiniteLine) -> None:
         line.setPos(ev.pos())
         self.slice_changed(CloseEnoughPoint(ev.pos()).y)
 
-    def slice_changed(self, slice_index):
+    def slice_changed(self, slice_index) -> None:
         self.parent.presenter.do_preview_reconstruct_slice(slice_idx=slice_index)
         self.sigSliceIndexChanged.emit(slice_index)
 
-    def clear_recon(self):
+    def clear_recon(self) -> None:
         self.imageview_recon.clear()
 
-    def clear_recon_line_profile(self):
+    def clear_recon_line_profile(self) -> None:
         self.recon_line_profile.clear_plot()
 
-    def clear_sinogram(self):
+    def clear_sinogram(self) -> None:
         self.imageview_sinogram.clear()
 
-    def clear_projection(self):
+    def clear_projection(self) -> None:
         self.imageview_projection.clear()
 
-    def reset_slice_and_tilt(self, slice_index):
+    def reset_slice_and_tilt(self, slice_index) -> None:
         self.slice_line.setPos(slice_index)
         self.hide_tilt()
 
-    def hide_tilt(self):
+    def hide_tilt(self) -> None:
         """
         Hides the tilt line. This stops infinite zooming out loop that messes up the image view
         (the line likes to be unbound when the degree isn't a multiple o 90 - and the tilt never is)
@@ -126,7 +126,7 @@ def hide_tilt(self):
         if self.tilt_line.scene() is not None:
             self.imageview_projection.viewbox.removeItem(self.tilt_line)
 
-    def set_tilt(self, tilt: Degrees, pos: int | None = None):
+    def set_tilt(self, tilt: Degrees, pos: int | None = None) -> None:
         if not isnan(tilt.value):  # is isnan it means there is no tilt, i.e. the line is vertical
             if pos is not None:
                 self.tilt_line.setAngle(90)
@@ -134,5 +134,5 @@ def set_tilt(self, tilt: Degrees, pos: int | None = None):
             self.tilt_line.setAngle(90 + tilt.value)
         self.imageview_projection.viewbox.addItem(self.tilt_line)
 
-    def reset_recon_histogram(self):
+    def reset_recon_histogram(self) -> None:
         self.imageview_recon.histogram.autoHistogramRange()
diff --git a/mantidimaging/gui/windows/recon/model.py b/mantidimaging/gui/windows/recon/model.py
index 7fb7cdcf7fb..9cb2f5af815 100644
--- a/mantidimaging/gui/windows/recon/model.py
+++ b/mantidimaging/gui/windows/recon/model.py
@@ -82,7 +82,7 @@ def images(self):
     def num_points(self) -> int:
         return self.data_model.num_points
 
-    def initial_select_data(self, images: ImageStack | None):
+    def initial_select_data(self, images: ImageStack | None) -> None:
         self._images = images
         self.reset_cor_model()
 
@@ -137,7 +137,7 @@ def run_preview_recon(self,
         recon = self._apply_pixel_size(recon, recon_params)
         return recon
 
-    def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progress) -> ImageStack | None:
+    def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progress) -> ReconstructedObject:
         # Ensure we have some sample data
         images = self.images
         if images is None:
@@ -151,7 +151,7 @@ def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progr
         return recon
 
     @staticmethod
-    def _apply_pixel_size(recon, recon_params: ReconstructionParameters, progress=None):
+    def _apply_pixel_size(recon, recon_params: ReconstructionParameters, progress=None) -> ImageStack | None:
         if recon_params.pixel_size > 0.:
             recon = DivideFilter.filter_func(recon, value=recon_params.pixel_size, unit="micron", progress=progress)
             # update the reconstructed stack pixel size with the value actually used for division
@@ -255,7 +255,7 @@ def auto_find_correlation(self, progress: Progress) -> tuple[ScalarCoR, Degrees]
         return find_center(self.images, progress)
 
     @staticmethod
-    def proj_180_degree_shape_matches_images(images):
+    def proj_180_degree_shape_matches_images(images) -> None:
         return images.has_proj180deg() and images.height == images.proj180deg.height \
                and images.width == images.proj180deg.width
 
@@ -269,7 +269,7 @@ def stack_contains_negative_values(self) -> bool:
         return bool(np.any(self.images.data < 0))
 
     @property
-    def stack_id(self):
+    def stack_id(self) -> uuid.UUID | None:
         if self.images is not None:
             return self.images.id
         return None
diff --git a/mantidimaging/gui/windows/recon/point_table_model.py b/mantidimaging/gui/windows/recon/point_table_model.py
index e0578357199..2516681d6df 100644
--- a/mantidimaging/gui/windows/recon/point_table_model.py
+++ b/mantidimaging/gui/windows/recon/point_table_model.py
@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 from enum import Enum
+from typing import Any, Optional, Union
 
 from PyQt5.QtCore import QAbstractTableModel, QModelIndex, Qt
 
@@ -29,54 +30,59 @@ class CorTiltPointQtModel(QAbstractTableModel, CorTiltDataModel):
     def __init__(self, parent=None):
         super().__init__(parent)
 
-    def populate_slice_indices(self, begin, end, count, cor=0.0):
+    def populate_slice_indices(self, begin: int, end: int, count: int, cor: float = 0.0) -> None:
         self.beginResetModel()
         super().populate_slice_indices(begin, end, count, cor)
         self.endResetModel()
 
-    def sort_points(self):
+    def sort_points(self) -> None:
         self.layoutAboutToBeChanged.emit()
         super().sort_points()
         self.layoutChanged.emit()
 
-    def set_point(self, idx, slice_idx: int | None = None, cor: float | None = None, reset_results=True):
+    def set_point(self,
+                  idx: int,
+                  slice_idx: int | None = None,
+                  cor: float | None = None,
+                  reset_results: bool = True) -> None:
         super().set_point(idx, slice_idx, cor, reset_results)
         self.dataChanged.emit(self.index(idx, 0), self.index(idx, 1))
 
-    def columnCount(self, parent=None):
+    def columnCount(self, parent: QModelIndex | None = None) -> int:
         return 2
 
-    def rowCount(self, parent):
+    def rowCount(self, parent: QModelIndex) -> int:
         if parent.isValid():
             return 0
         return self.num_points
 
-    def flags(self, index):
+    def flags(self, index: QModelIndex) -> Qt.ItemFlags:
         flags = super().flags(index)
         flags |= Qt.ItemFlag.ItemIsEditable
         return flags
 
-    def data(self, index, role=Qt.ItemDataRole.DisplayRole):
-        if not index.isValid():
+    def data(self, index: QModelIndex, role: int = Qt.ItemDataRole.DisplayRole) -> int | str | float | None:
+        if not index.isValid() or index.row() >= len(self._points):
             return None
 
-        col = index.column()
-        col_field = Column(col)
+        point: Point = self._points[index.row()]
+        col_field: Column = Column(index.column())
 
         if role == Qt.ItemDataRole.DisplayRole:
             if col_field == Column.SLICE_INDEX:
-                return self._points[index.row()].slice_index
-            if col_field == Column.CENTRE_OF_ROTATION:
-                return self._points[index.row()].cor
+                return point.slice_index
+            elif col_field == Column.CENTRE_OF_ROTATION:
+                return point.cor
 
         elif role == Qt.ItemDataRole.ToolTipRole:
             if col_field == Column.SLICE_INDEX:
                 return 'Slice index (y coordinate of projection)'
             elif col_field == Column.CENTRE_OF_ROTATION:
                 return 'Centre of rotation for specific slice'
-            return ''
 
-    def getColumn(self, column_index) -> list[int]:
+        return None
+
+    def getColumn(self, column_index: int) -> list[int]:
         if column_index != 0 and column_index != 1:
             return []
         else:
@@ -85,7 +91,7 @@ def getColumn(self, column_index) -> list[int]:
                 column.append(point.slice_index)
             return column
 
-    def setData(self, index, val, role=Qt.ItemDataRole.EditRole):
+    def setData(self, index: QModelIndex, val: Any, role: Qt.ItemDataRole = Qt.ItemDataRole.EditRole) -> bool:
         if role != Qt.ItemDataRole.EditRole:
             return False
 
@@ -107,7 +113,7 @@ def setData(self, index, val, role=Qt.ItemDataRole.EditRole):
 
         return True
 
-    def insertRows(self, row, count, parent=None, slice_idx: int | None = None, cor: float | None = None):
+    def insertRows(self, row, count, parent=None, slice_idx: int | None = None, cor: float | None = None) -> None:
         self.beginInsertRows(parent if parent is not None else QModelIndex(), row, row + count - 1)
 
         for _ in range(count):
@@ -115,7 +121,7 @@ def insertRows(self, row, count, parent=None, slice_idx: int | None = None, cor:
 
         self.endInsertRows()
 
-    def removeRows(self, row, count, parent=None):
+    def removeRows(self, row, count, parent=None) -> None:
         if self.empty:
             return
 
@@ -126,7 +132,7 @@ def removeRows(self, row, count, parent=None):
 
         self.endRemoveRows()
 
-    def removeAllRows(self, parent=None):
+    def removeAllRows(self, parent: QModelIndex | None = None) -> None:
         if self.empty:
             return
 
@@ -134,12 +140,12 @@ def removeAllRows(self, parent=None):
         self.clear_points()
         self.endRemoveRows()
 
-    def appendNewRow(self, row: int, slice_idx: int, cor: float = 0.0):
+    def appendNewRow(self, row: int, slice_idx: int, cor: float = 0.0) -> None:
         self.insertRows(row, 1, slice_idx=slice_idx, cor=cor)
         self.set_point(row, slice_idx, cor)
         self.sort_points()
 
-    def headerData(self, section, orientation, role):
+    def headerData(self, section, orientation, role) -> str | None:
         if orientation != Qt.Orientation.Horizontal:
             return None
 
diff --git a/mantidimaging/gui/windows/recon/presenter.py b/mantidimaging/gui/windows/recon/presenter.py
index 2c524d2b42f..b2e0fb30c29 100644
--- a/mantidimaging/gui/windows/recon/presenter.py
+++ b/mantidimaging/gui/windows/recon/presenter.py
@@ -251,7 +251,7 @@ def do_preview_reconstruct_slice(self,
                                      cor=None,
                                      slice_idx: int | None = None,
                                      force_update: bool = False,
-                                     reset_roi: bool = False):
+                                     reset_roi: bool = False) -> None:
         if self.model.images is None:
             self.view.reset_recon_and_sino_previews()
             return
@@ -262,7 +262,7 @@ def do_preview_reconstruct_slice(self,
             on_preview_complete = partial(self._on_preview_reconstruct_slice_done, reset_roi=reset_roi)
             self._get_reconstruct_slice(cor, slice_idx, on_preview_complete)
 
-    def _on_preview_reconstruct_slice_done(self, task: TaskWorkerThread, reset_roi: bool = False):
+    def _on_preview_reconstruct_slice_done(self, task: TaskWorkerThread, reset_roi: bool = False) -> None:
         if task.error is not None:
             self.view.show_error_dialog(f"Encountered error while trying to reconstruct: {str(task.error)}")
             return
@@ -273,12 +273,12 @@ def _on_preview_reconstruct_slice_done(self, task: TaskWorkerThread, reset_roi:
             # will still be available after this function ends
             self.view.update_recon_preview(np.copy(images.data[0]), reset_roi)
 
-    def do_stack_reconstruct_slice(self, cor=None, slice_idx: int | None = None):
+    def do_stack_reconstruct_slice(self, cor=None, slice_idx: int | None = None) -> None:
         self.view.set_recon_buttons_enabled(False)
         slice_idx = self._get_slice_index(slice_idx)
         self._get_reconstruct_slice(cor, slice_idx, self._on_stack_reconstruct_slice_done)
 
-    def _on_stack_reconstruct_slice_done(self, task: TaskWorkerThread):
+    def _on_stack_reconstruct_slice_done(self, task: TaskWorkerThread) -> None:
         if task.error is not None:
             self.view.show_error_dialog(f"Encountered error while trying to reconstruct: {str(task.error)}")
             self.view.set_recon_buttons_enabled(True)
@@ -291,7 +291,14 @@ def _on_stack_reconstruct_slice_done(self, task: TaskWorkerThread):
                 assert self.model.images is not None
                 images.name = self.create_recon_output_filename("Recon_Slice")
                 self._replace_inf_nan(images)  # pyqtgraph workaround
-                self.view.show_recon_volume(images, self.model.stack_id)
+
+                stack_id = self.model.stack_id  # This might be a UUID or None
+                if stack_id is None:
+                    self.view.show_error_dialog("Stack ID is missing. Cannot display reconstruction.")
+                    return
+
+                self.view.show_recon_volume(images, stack_id)
+
                 images.record_operation('AstraRecon.single_sino',
                                         'Slice Reconstruction',
                                         slice_idx=slice_idx,
@@ -299,7 +306,7 @@ def _on_stack_reconstruct_slice_done(self, task: TaskWorkerThread):
         finally:
             self.view.set_recon_buttons_enabled(True)
 
-    def _do_refine_selected_cor(self):
+    def _do_refine_selected_cor(self) -> None:
         selected_rows = self.view.get_cor_table_selected_rows()
         if len(selected_rows):
             slice_idx = self.model.slices[selected_rows[0]]
@@ -339,7 +346,7 @@ def do_cor_fit(self) -> None:
         self.do_update_projection()
         self.do_preview_reconstruct_slice()
 
-    def _on_volume_recon_done(self, task) -> None:
+    def _on_volume_recon_done(self, task: TaskWorkerThread) -> None:
         self.recon_is_running = False
         if task.error is not None:
             self.view.show_error_dialog(f"Encountered error while trying to reconstruct: {str(task.error)}")
@@ -354,22 +361,22 @@ def _on_volume_recon_done(self, task) -> None:
         finally:
             self.view.set_recon_buttons_enabled(True)
 
-    def do_clear_all_cors(self):
+    def do_clear_all_cors(self) -> None:
         self.view.clear_cor_table()
         self.model.reset_selected_row()
 
-    def do_remove_selected_cor(self):
+    def do_remove_selected_cor(self) -> None:
         self.view.remove_selected_cor()
 
-    def set_last_cor(self, cor):
+    def set_last_cor(self, cor: ScalarCoR) -> None:
         self.model.last_cor = ScalarCoR(cor)
 
-    def do_calculate_cors_from_manual_tilt(self):
+    def do_calculate_cors_from_manual_tilt(self) -> None:
         cor = ScalarCoR(self.view.rotation_centre)
         tilt = Degrees(self.view.tilt)
         self._set_precalculated_cor_tilt(cor, tilt)
 
-    def _set_precalculated_cor_tilt(self, cor: ScalarCoR, tilt: Degrees):
+    def _set_precalculated_cor_tilt(self, cor: ScalarCoR, tilt: Degrees) -> None:
         self.model.set_precalculated(cor, tilt)
         self.view.set_results(*self.model.get_results())
         for idx, point in enumerate(self.model.data_model.iter_points()):
@@ -385,7 +392,7 @@ def _auto_find_correlation(self) -> None:
 
         self.recon_is_running = True
 
-        def completed(task: TaskWorkerThread):
+        def completed(task: TaskWorkerThread) -> None:
             if task.result is None and task.error is not None:
                 selected_stack = self.view.main_window.get_images_from_stack_uuid(self.view.stackSelector.current())
                 self.view.show_error_dialog(
@@ -439,7 +446,7 @@ def _completed_finding_cors(task: TaskWorkerThread) -> None:
                               },
                               tracker=self.async_tracker)
 
-    def proj_180_degree_shape_matches_images(self, images) -> bool:
+    def proj_180_degree_shape_matches_images(self, images) -> None:
         return self.model.proj_180_degree_shape_matches_images(images)
 
     def _do_nan_zero_negative_check(self) -> None:
diff --git a/mantidimaging/gui/windows/recon/view.py b/mantidimaging/gui/windows/recon/view.py
index df043a5756f..3a14b216882 100644
--- a/mantidimaging/gui/windows/recon/view.py
+++ b/mantidimaging/gui/windows/recon/view.py
@@ -208,7 +208,7 @@ def on_row_change(item, _):
             self.lbhc_enabled.toggled.connect(spinbox.setEnabled)
         self.lbhc_enabled.toggled.connect(lambda: self.presenter.notify(PresN.RECONSTRUCT_PREVIEW_SLICE))
 
-    def showEvent(self, e):
+    def showEvent(self, e) -> None:
         super().showEvent(e)
         if self.presenter.stack_selection_change_pending:
             self.presenter.set_stack_uuid(self.stackSelector.current())
@@ -219,13 +219,13 @@ def showEvent(self, e):
             self.presenter.stack_changed_pending = False
         self.activateWindow()
 
-    def closeEvent(self, e):
+    def closeEvent(self, e) -> None:
         if self.presenter.recon_is_running:
             e.ignore()
         else:
             self.hide()
 
-    def check_stack_for_invalid_180_deg_proj(self, uuid: UUID):
+    def check_stack_for_invalid_180_deg_proj(self, uuid: UUID) -> None:
         try:
             selected_images = self.main_window.get_images_from_stack_uuid(uuid)
         except KeyError:
@@ -275,7 +275,7 @@ def preview_image_on_button_press(self, event) -> None:
         if event.button == 1 and event.ydata is not None:
             self.presenter.set_preview_slice_idx(int(event.ydata))
 
-    def update_projection(self, image_data, preview_slice_index: int, tilt_angle: Degrees | None):
+    def update_projection(self, image_data, preview_slice_index: int, tilt_angle: Degrees | None) -> None:
         """
         Updates the preview projection image and associated annotations.
 
@@ -294,17 +294,17 @@ def update_projection(self, image_data, preview_slice_index: int, tilt_angle: De
 
         self.image_view.update_projection(image_data, preview_slice_index, tilt_angle)
 
-    def update_sinogram(self, image_data):
+    def update_sinogram(self, image_data) -> None:
         self.image_view.update_sinogram(image_data)
 
     def is_auto_update_preview(self) -> bool:
         return self.previewAutoUpdate.isChecked()
 
-    def handle_auto_update_preview_selection(self):
+    def handle_auto_update_preview_selection(self) -> None:
         if self.previewAutoUpdate.isChecked():
             self.presenter.notify(PresN.RECONSTRUCT_PREVIEW_SLICE)
 
-    def update_recon_preview(self, image_data: numpy.ndarray, reset_roi: bool = False):
+    def update_recon_preview(self, image_data: numpy.ndarray, reset_roi: bool = False) -> None:
         """
         Updates the reconstruction preview image with new data.
         """
@@ -314,7 +314,7 @@ def update_recon_preview(self, image_data: numpy.ndarray, reset_roi: bool = Fals
             self.image_view.update_recon_hist()
             self.update_recon_hist_needed = False
 
-    def reset_recon_and_sino_previews(self):
+    def reset_recon_and_sino_previews(self) -> None:
         """
         Resets the recon and sinogram preview images, forcing a complete redraw next time they
         are updated.
@@ -331,7 +331,7 @@ def reset_projection_preview(self) -> None:
     def reset_slice_and_tilt(self, slice_index: int) -> None:
         self.image_view.reset_slice_and_tilt(slice_index)
 
-    def on_table_row_count_change(self, _=None, __=None):
+    def on_table_row_count_change(self, _=None, __=None) -> None:
         """
         Called when rows have been added or removed from the point table.
 
@@ -343,7 +343,7 @@ def on_table_row_count_change(self, _=None, __=None):
         self.removeBtn.setEnabled(not empty)
         self.clearAllBtn.setEnabled(not empty)
 
-    def add_cor_table_row(self, row: int, slice_index: int, cor: float):
+    def add_cor_table_row(self, row: int, slice_index: int, cor: float) -> None:
         """
         Adds a row to the manual COR table with a specified slice index.
         """
@@ -464,7 +464,7 @@ def recon_params(self) -> ReconstructionParameters:
                                         regulariser=self.regulariser,
                                         beam_hardening_coefs=self.beam_hardening_coefs)
 
-    def set_table_point(self, idx, slice_idx, cor):
+    def set_table_point(self, idx, slice_idx, cor) -> None:
         # reset_results=False stops the resetting of the data model on
         # changing a point from here - otherwise calculating the CoR
         # for each slice from tilt ends up resetting the model afterwards

From 20c9645d591f298a27277a163b62b08259075e7b Mon Sep 17 00:00:00 2001
From: ashmeigh <ashleymeigh0@gmail.com>
Date: Mon, 8 Jul 2024 09:29:15 +0100
Subject: [PATCH 2/8] update

---
 mantidimaging/gui/windows/recon/model.py             | 3 +--
 mantidimaging/gui/windows/recon/point_table_model.py | 2 +-
 mantidimaging/gui/windows/recon/presenter.py         | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/mantidimaging/gui/windows/recon/model.py b/mantidimaging/gui/windows/recon/model.py
index 9cb2f5af815..9654bad8b1d 100644
--- a/mantidimaging/gui/windows/recon/model.py
+++ b/mantidimaging/gui/windows/recon/model.py
@@ -137,7 +137,7 @@ def run_preview_recon(self,
         recon = self._apply_pixel_size(recon, recon_params)
         return recon
 
-    def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progress) -> ReconstructedObject:
+    def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progress) -> ImageStack | None:
         # Ensure we have some sample data
         images = self.images
         if images is None:
@@ -146,7 +146,6 @@ def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progr
         # get the image height based on the current ROI
         recon = reconstructor.full(images, self.data_model.get_all_cors_from_regression(images.height), recon_params,
                                    progress)
-
         recon = self._apply_pixel_size(recon, recon_params, progress)
         return recon
 
diff --git a/mantidimaging/gui/windows/recon/point_table_model.py b/mantidimaging/gui/windows/recon/point_table_model.py
index 2516681d6df..ea48247e5c7 100644
--- a/mantidimaging/gui/windows/recon/point_table_model.py
+++ b/mantidimaging/gui/windows/recon/point_table_model.py
@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from enum import Enum
-from typing import Any, Optional, Union
+from typing import Any
 
 from PyQt5.QtCore import QAbstractTableModel, QModelIndex, Qt
 
diff --git a/mantidimaging/gui/windows/recon/presenter.py b/mantidimaging/gui/windows/recon/presenter.py
index b2e0fb30c29..a838b0f1987 100644
--- a/mantidimaging/gui/windows/recon/presenter.py
+++ b/mantidimaging/gui/windows/recon/presenter.py
@@ -368,7 +368,7 @@ def do_clear_all_cors(self) -> None:
     def do_remove_selected_cor(self) -> None:
         self.view.remove_selected_cor()
 
-    def set_last_cor(self, cor: ScalarCoR) -> None:
+    def set_last_cor(self, cor) -> None:
         self.model.last_cor = ScalarCoR(cor)
 
     def do_calculate_cors_from_manual_tilt(self) -> None:

From 2ca8fad7aeaa1eb0ef7afe265a021f54b3238714 Mon Sep 17 00:00:00 2001
From: ashmeigh <ashleymeigh0@gmail.com>
Date: Mon, 8 Jul 2024 11:58:33 +0100
Subject: [PATCH 3/8] fixed errors

---
 mantidimaging/gui/windows/recon/model.py     | 7 ++++++-
 mantidimaging/gui/windows/recon/presenter.py | 9 +++++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/mantidimaging/gui/windows/recon/model.py b/mantidimaging/gui/windows/recon/model.py
index 9654bad8b1d..a41ba4bc1bc 100644
--- a/mantidimaging/gui/windows/recon/model.py
+++ b/mantidimaging/gui/windows/recon/model.py
@@ -150,7 +150,12 @@ def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progr
         return recon
 
     @staticmethod
-    def _apply_pixel_size(recon, recon_params: ReconstructionParameters, progress=None) -> ImageStack | None:
+    def _apply_pixel_size(recon: ImageStack | None,
+                          recon_params: ReconstructionParameters,
+                          progress: Progress | None = None) -> ImageStack | None:
+        if recon is None:
+            return None
+
         if recon_params.pixel_size > 0.:
             recon = DivideFilter.filter_func(recon, value=recon_params.pixel_size, unit="micron", progress=progress)
             # update the reconstructed stack pixel size with the value actually used for division
diff --git a/mantidimaging/gui/windows/recon/presenter.py b/mantidimaging/gui/windows/recon/presenter.py
index a838b0f1987..0ce699ec6e2 100644
--- a/mantidimaging/gui/windows/recon/presenter.py
+++ b/mantidimaging/gui/windows/recon/presenter.py
@@ -356,6 +356,7 @@ def _on_volume_recon_done(self, task: TaskWorkerThread) -> None:
         try:
             self._replace_inf_nan(task.result)  # pyqtgraph workaround
             assert self.model.images is not None
+            assert self.model.stack_id is not None
             task.result.name = self.create_recon_output_filename("Recon_Vol")
             self.view.show_recon_volume(task.result, self.model.stack_id)
         finally:
@@ -446,8 +447,12 @@ def _completed_finding_cors(task: TaskWorkerThread) -> None:
                               },
                               tracker=self.async_tracker)
 
-    def proj_180_degree_shape_matches_images(self, images) -> None:
-        return self.model.proj_180_degree_shape_matches_images(images)
+    def proj_180_degree_shape_matches_images(self, images: ImageStack) -> bool:
+        result = self.model.proj_180_degree_shape_matches_images(images)
+        if isinstance(result, bool):
+            return result
+        else:
+            raise ValueError("Expected a boolean from proj_180_degree_shape_matches_images")
 
     def _do_nan_zero_negative_check(self) -> None:
         """

From 91e564f0f51205c208f81f2c68be2c1837220833 Mon Sep 17 00:00:00 2001
From: ashmeigh <56345053+ashmeigh@users.noreply.github.com>
Date: Tue, 16 Jul 2024 14:07:20 +0100
Subject: [PATCH 4/8] Using # type: ignore to suppress mypy errors

Signed-off-by: ashmeigh <ashleymeigh0@gmail.com>
---
 mantidimaging/gui/windows/recon/model.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/mantidimaging/gui/windows/recon/model.py b/mantidimaging/gui/windows/recon/model.py
index a41ba4bc1bc..735829ecd48 100644
--- a/mantidimaging/gui/windows/recon/model.py
+++ b/mantidimaging/gui/windows/recon/model.py
@@ -134,7 +134,9 @@ def run_preview_recon(self,
                                                   images.projection_angles(recon_params.max_projection_angle),
                                                   recon_params,
                                                   progress=progress)
-        recon = self._apply_pixel_size(recon, recon_params)
+
+        recon = self._apply_pixel_size(recon, recon_params)  # type: ignore
+
         return recon
 
     def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progress) -> ImageStack | None:
@@ -146,7 +148,7 @@ def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progr
         # get the image height based on the current ROI
         recon = reconstructor.full(images, self.data_model.get_all_cors_from_regression(images.height), recon_params,
                                    progress)
-        recon = self._apply_pixel_size(recon, recon_params, progress)
+        recon = self._apply_pixel_size(recon, recon_params, progress)  # type: ignore
         return recon
 
     @staticmethod

From 353f90d7a673e2ff392bb0bd910db2d73a2ae26f Mon Sep 17 00:00:00 2001
From: ashmeigh <ashleymeigh0@gmail.com>
Date: Thu, 18 Jul 2024 08:15:09 +0100
Subject: [PATCH 5/8] made suggested changes

Signed-off-by: ashmeigh <ashleymeigh0@gmail.com>
---
 mantidimaging/gui/windows/recon/model.py     |  9 ++-------
 mantidimaging/gui/windows/recon/presenter.py | 12 ++----------
 2 files changed, 4 insertions(+), 17 deletions(-)

diff --git a/mantidimaging/gui/windows/recon/model.py b/mantidimaging/gui/windows/recon/model.py
index 735829ecd48..55c4a88ca6d 100644
--- a/mantidimaging/gui/windows/recon/model.py
+++ b/mantidimaging/gui/windows/recon/model.py
@@ -152,12 +152,7 @@ def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progr
         return recon
 
     @staticmethod
-    def _apply_pixel_size(recon: ImageStack | None,
-                          recon_params: ReconstructionParameters,
-                          progress: Progress | None = None) -> ImageStack | None:
-        if recon is None:
-            return None
-
+    def _apply_pixel_size(recon: ImageStack, recon_params: ReconstructionParameters, progress=None) -> ImageStack:
         if recon_params.pixel_size > 0.:
             recon = DivideFilter.filter_func(recon, value=recon_params.pixel_size, unit="micron", progress=progress)
             # update the reconstructed stack pixel size with the value actually used for division
@@ -261,7 +256,7 @@ def auto_find_correlation(self, progress: Progress) -> tuple[ScalarCoR, Degrees]
         return find_center(self.images, progress)
 
     @staticmethod
-    def proj_180_degree_shape_matches_images(images) -> None:
+    def proj_180_degree_shape_matches_images(images) -> bool:
         return images.has_proj180deg() and images.height == images.proj180deg.height \
                and images.width == images.proj180deg.width
 
diff --git a/mantidimaging/gui/windows/recon/presenter.py b/mantidimaging/gui/windows/recon/presenter.py
index 0ce699ec6e2..e9da077365d 100644
--- a/mantidimaging/gui/windows/recon/presenter.py
+++ b/mantidimaging/gui/windows/recon/presenter.py
@@ -278,12 +278,11 @@ def do_stack_reconstruct_slice(self, cor=None, slice_idx: int | None = None) ->
         slice_idx = self._get_slice_index(slice_idx)
         self._get_reconstruct_slice(cor, slice_idx, self._on_stack_reconstruct_slice_done)
 
-    def _on_stack_reconstruct_slice_done(self, task: TaskWorkerThread) -> None:
+    def _on_stack_reconstruct_slice_done(self, task: TaskWorkerThread):
         if task.error is not None:
             self.view.show_error_dialog(f"Encountered error while trying to reconstruct: {str(task.error)}")
             self.view.set_recon_buttons_enabled(True)
             return
-
         try:
             images: ImageStack = task.result
             slice_idx = self._get_slice_index(None)
@@ -291,14 +290,7 @@ def _on_stack_reconstruct_slice_done(self, task: TaskWorkerThread) -> None:
                 assert self.model.images is not None
                 images.name = self.create_recon_output_filename("Recon_Slice")
                 self._replace_inf_nan(images)  # pyqtgraph workaround
-
-                stack_id = self.model.stack_id  # This might be a UUID or None
-                if stack_id is None:
-                    self.view.show_error_dialog("Stack ID is missing. Cannot display reconstruction.")
-                    return
-
-                self.view.show_recon_volume(images, stack_id)
-
+                self.view.show_recon_volume(images, self.model.stack_id)
                 images.record_operation('AstraRecon.single_sino',
                                         'Slice Reconstruction',
                                         slice_idx=slice_idx,

From d8d2fb1c3f1cc227855221d7a086904719d4772c Mon Sep 17 00:00:00 2001
From: ashmeigh <ashleymeigh0@gmail.com>
Date: Fri, 19 Jul 2024 12:09:27 +0100
Subject: [PATCH 6/8] fixed error on _on_stack_reconstruct_slice_done

---
 mantidimaging/gui/windows/recon/presenter.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/mantidimaging/gui/windows/recon/presenter.py b/mantidimaging/gui/windows/recon/presenter.py
index e9da077365d..c55dd236219 100644
--- a/mantidimaging/gui/windows/recon/presenter.py
+++ b/mantidimaging/gui/windows/recon/presenter.py
@@ -287,10 +287,11 @@ def _on_stack_reconstruct_slice_done(self, task: TaskWorkerThread):
             images: ImageStack = task.result
             slice_idx = self._get_slice_index(None)
             if images is not None:
-                assert self.model.images is not None
+                source_id = self.model.stack_id
+                assert source_id is not None
                 images.name = self.create_recon_output_filename("Recon_Slice")
                 self._replace_inf_nan(images)  # pyqtgraph workaround
-                self.view.show_recon_volume(images, self.model.stack_id)
+                self.view.show_recon_volume(images, source_id)
                 images.record_operation('AstraRecon.single_sino',
                                         'Slice Reconstruction',
                                         slice_idx=slice_idx,

From 986fc84386fb5c46b9dc48c93de9e8d7f115b7c4 Mon Sep 17 00:00:00 2001
From: ashmeigh <ashleymeigh0@gmail.com>
Date: Tue, 23 Jul 2024 08:24:40 +0100
Subject: [PATCH 7/8] chnage 180 back to orgin and added # type: ignore in the
 apply pixel size

---
 mantidimaging/gui/windows/recon/presenter.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/mantidimaging/gui/windows/recon/presenter.py b/mantidimaging/gui/windows/recon/presenter.py
index c55dd236219..44804a4b83a 100644
--- a/mantidimaging/gui/windows/recon/presenter.py
+++ b/mantidimaging/gui/windows/recon/presenter.py
@@ -440,12 +440,8 @@ def _completed_finding_cors(task: TaskWorkerThread) -> None:
                               },
                               tracker=self.async_tracker)
 
-    def proj_180_degree_shape_matches_images(self, images: ImageStack) -> bool:
-        result = self.model.proj_180_degree_shape_matches_images(images)
-        if isinstance(result, bool):
-            return result
-        else:
-            raise ValueError("Expected a boolean from proj_180_degree_shape_matches_images")
+    def proj_180_degree_shape_matches_images(self, images) -> bool:
+        return self.model.proj_180_degree_shape_matches_images(images)
 
     def _do_nan_zero_negative_check(self) -> None:
         """

From 9b7232c32f1c2dbe40a405b48bb89efb80d7f310 Mon Sep 17 00:00:00 2001
From: Sam Tygier <sam.tygier@stfc.ac.uk>
Date: Wed, 24 Jul 2024 16:11:10 +0100
Subject: [PATCH 8/8] Remove unnecessary ignores

---
 mantidimaging/gui/windows/recon/model.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mantidimaging/gui/windows/recon/model.py b/mantidimaging/gui/windows/recon/model.py
index 55c4a88ca6d..b7dbb648b9b 100644
--- a/mantidimaging/gui/windows/recon/model.py
+++ b/mantidimaging/gui/windows/recon/model.py
@@ -135,7 +135,7 @@ def run_preview_recon(self,
                                                   recon_params,
                                                   progress=progress)
 
-        recon = self._apply_pixel_size(recon, recon_params)  # type: ignore
+        recon = self._apply_pixel_size(recon, recon_params)
 
         return recon
 
@@ -148,7 +148,7 @@ def run_full_recon(self, recon_params: ReconstructionParameters, progress: Progr
         # get the image height based on the current ROI
         recon = reconstructor.full(images, self.data_model.get_all_cors_from_regression(images.height), recon_params,
                                    progress)
-        recon = self._apply_pixel_size(recon, recon_params, progress)  # type: ignore
+        recon = self._apply_pixel_size(recon, recon_params, progress)
         return recon
 
     @staticmethod