Apply changes suggested and fix pre-commit

Author: unichronic

invesalius/data/mask.py

@@ -230,19 +230,19 @@ def __init__(self):
     @property
     def category(self):
         if self.name.lower().startswith("cortical"):
-            return "Cortical"
+            return "cortical"
         elif self.name.lower().startswith("subcortical"):
-            return "Subcortical"
+            return "subcortical"
         elif self.name.lower().startswith("ventricles"):
-            return "Ventricles"
+            return "ventricles"
         elif self.name.lower().startswith("white_matter"):
-            return "White_matter"
+            return "white_matter"
         elif self.name.lower().startswith("cerebellum"):
-            return "Cerebellum"
+            return "cerebellum"
         elif self.name.lower().startswith("brain_stem"):
-            return "Brain_stem"
+            return "brain_stem"
         elif self.name.lower().startswith("choroid_Plexus"):
-            return "Choroid_Plexus"
+            return "choroid_plexus"
         else:
             return "General"
 

invesalius/data/slice_.py

@@ -64,10 +64,10 @@ class SliceBuffer:
 
     def __init__(self):
         self.index: int = -1
-        self.image: Optional[np.ndarray] = None
-        self.mask: Optional[np.ndarray] = None
-        self.vtk_image: Optional[vtkImageData] = None
-        self.vtk_mask: Optional[vtkImageData] = None
+        self.image: np.ndarray | None = None
+        self.mask: np.ndarray | None = None
+        self.vtk_image: vtkImageData | None = None
+        self.vtk_mask: vtkImageData | None = None
 
     def discard_vtk_mask(self) -> None:
         self.vtk_mask = None
@@ -95,18 +95,16 @@ def discard_buffer(self) -> None:
 class Slice(metaclass=utils.Singleton):
     def __init__(self):
         self.selected_mask_indices = []
-        self._matrix = None
         self._matrix_filename = ""
-        self.current_mask: Optional[Mask] = None
+        self.current_mask: Mask | None = None
         self.blend_filter = None
-        self.histogram: Optional[np.ndarray] = None
+        self.histogram: np.ndarray | None = None
+        self._matrix: np.ndarray | None = None
         self._affine: np.ndarray = np.identity(4)
         self._n_tracts: int = 0
         self._tracker = None
         self.aux_matrices: dict[str, np.ndarray] = {}
-        self.aux_matrices_colours: dict[
-            str, dict[Union[int, float], Tuple[float, float, float]]
-        ] = {}
+        self.aux_matrices_colours: dict[str, dict[int | float, tuple[float, float, float]]] = {}
         self.state = const.STATE_DEFAULT
 
         self.to_show_aux = ""
@@ -143,7 +141,7 @@ def __init__(self):
         self.opacity: float = 0.8
 
     @property
-    def matrix(self) -> Optional[np.ndarray]:
+    def matrix(self) -> np.ndarray | None:
         return self._matrix
 
     @matrix.setter
@@ -155,11 +153,11 @@ def matrix(self, value: np.ndarray) -> None:
         self.center = [(s * d / 2.0) for (d, s) in zip(self.matrix.shape[::-1], self.spacing)]
 
     @property
-    def spacing(self) -> Tuple[float, float, float]:
+    def spacing(self) -> tuple[float, float, float]:
         return self._spacing
 
     @spacing.setter
-    def spacing(self, value: Tuple[float, float, float]) -> None:
+    def spacing(self, value: tuple[float, float, float]) -> None:
         self._spacing = value
         self.center = [(s * d / 2.0) for (d, s) in zip(self.matrix.shape[::-1], self.spacing)]
 
@@ -264,7 +262,7 @@ def __bind_events(self) -> None:
         Publisher.subscribe(self.do_threshold_to_all_slices, "Appy threshold all slices")
 
     def GetMaxSliceNumber(self, orientation: str) -> int:
-        shape: Tuple[int, int, int] = self.matrix.shape
+        shape: tuple[int, int, int] = self.matrix.shape
 
         # Because matrix indexing starts with 0 so the last slice is the shape
         # minu 1.
@@ -283,7 +281,7 @@ def discard_all_buffers(self) -> None:
 
     def get_world_to_invesalius_vtk_affine(
         self, inverse: bool = False
-    ) -> Tuple[np.ndarray, "vtkMatrix4x4", float]:
+    ) -> tuple[np.ndarray, "vtkMatrix4x4", float]:
         """
         Creates an affine matrix with img_shift adjustment and returns both the NumPy
         and VTK versions of the matrix, along with the img_shift value.
@@ -1247,46 +1245,30 @@ def CreateSurfaceFromIndex(self, surface_parameters):
         )
 
     def on_select_all_masks_changed(self, select_all_active):
-        """
-        Handle when select all masks checkbox is toggled
-        """
-        # Notify the UI to update the button text
         Publisher.sendMessage("Update create surface button", select_all_active=select_all_active)
 
-    def create_surfaces_for_all_masks(self, surface_parameters_template):
-        """
-        Create surfaces for all masks that have content (voxels > threshold)
-
-        Args:
-            surface_parameters_template: Template parameters to use for all surface creations
-        """
+    def create_surfaces_for_all_masks(self, surface_template):
         proj = Project()
         created_surfaces = []
-
-        # Get all masks from the project
         mask_dict = proj.mask_dict
 
         for mask_index in self.selected_mask_indices:
             if mask_index not in mask_dict:
                 continue
             mask = mask_dict[mask_index]
-            # Check if mask has content (similar to the check in AddNewActor)
             if mask.matrix.max() < 127:
-                print(f"Skipping mask '{mask.name}' (index {mask_index}) - no voxels selected")
+                print(f"Skipping mask '{mask.name}' (index {mask_index}) - no voxels available")
                 continue
 
-            # Create a copy of the template parameters for this specific mask
-            surface_parameters = surface_parameters_template.copy()
-            surface_parameters["options"] = surface_parameters_template["options"].copy()
+            surface_parameters = surface_template.copy()
+            surface_parameters["options"] = surface_template["options"].copy()
 
-            # Update the parameters for this specific mask
             surface_parameters["options"]["index"] = mask_index
             surface_parameters["options"]["name"] = f"{mask.name}"
-            surface_parameters["options"]["overwrite"] = False  # Always create new surfaces
+            surface_parameters["options"]["overwrite"] = False  # always create new surfaces
 
             print(f"Creating surface for mask '{mask.name}' (index {mask_index})")
 
-            # Create the surface for this mask
             try:
                 self.do_threshold_to_all_slices(mask)
                 Publisher.sendMessage(

invesalius/data/surface.py

@@ -66,7 +66,6 @@
 import invesalius.data.polydata_utils as pu
 import invesalius.data.slice_ as sl
 import invesalius.data.surface_process as surface_process
-import invesalius.data.vtk_utils as vtk_utils
 import invesalius.project as prj
 import invesalius.session as ses
 import invesalius.utils as utl
@@ -238,7 +237,6 @@ def __bind_events(self):
         Publisher.subscribe(self.export_all_surfaces_separately, "Export all surfaces separately")
 
         Publisher.subscribe(self.on_surfaces_creation_completed, "Surfaces creation completed")
-        Publisher.subscribe(self.on_no_surfaces_created, "No surfaces created")
 
     def on_surfaces_creation_completed(self, created_count):
         """

invesalius/gui/data_notebook.py

@@ -740,7 +740,7 @@ def on_selection_changed(self, evt):
         if hasattr(self, "category"):
             Publisher.sendMessage("Update mask select all checkbox", category=self.category)
         else:
-            print(f"[DEBUG] Selection changed but 'category' attribute not found on self.")
+            print(f"Selection changed but 'category' attribute not found on self.")
         if evt:
             evt.Skip()
 
@@ -894,7 +894,7 @@ def OnEditLabel(self, evt):
         evt.Skip()
 
     def OnCheckItem(self, index, flag):
-        print(f"[DEBUG] OnCheckItem called with index: {index}, flag: {flag}")
+        print(f" OnCheckItem called with index: {index}, flag: {flag}")
 
         global_idx = -1
         for g_id, l_id in self.mask_list_index.items():
@@ -903,10 +903,10 @@ def OnCheckItem(self, index, flag):
                 break
 
         if global_idx == -1:
-            print(f"[DEBUG] OnCheckItem: global_idx not found for local index {index}")
+            print(f" OnCheckItem: global_idx not found for local index {index}")
             return
 
-        print(f"[DEBUG] OnCheckItem: global_idx = {global_idx}")
+        print(f" OnCheckItem: global_idx = {global_idx}")
 
         if flag:
             Publisher.sendMessage("Change mask selected", index=global_idx)
@@ -915,7 +915,7 @@ def OnCheckItem(self, index, flag):
         Publisher.sendMessage("Show mask", index=global_idx, value=flag)
 
         # Also trigger selection update since this affects the overall selection state
-        print(f"[DEBUG] OnCheckItem: triggering selection update")
+        print(f" OnCheckItem: triggering selection update")
         self.on_selection_changed(None)
 
     def InsertNewItem(self, index=0, label=_("Mask"), threshold="(1000, 4500)", colour=None):

invesalius/gui/deep_learning_seg_dialog.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding: UTF-8 -*-
 
-import importlib
 import multiprocessing
 import time
 from typing import Dict
@@ -439,13 +438,13 @@ def __init__(self, parent, auto_segment=False):
 class SubpartSegmenterDialog(DeepLearningSegmenterDialog):
     def __init__(self, parent, auto_segment=False):
         self.mask_types = {
-            "Cortical": _("Cortical"),
-            "Subcortical": _("Subcortical"),
-            "White_matter": _("White Matter"),
-            "Cerebellum": _("Cerebellum"),
-            "Ventricles": _("Ventricles"),
-            "Brain_stem": _("Brain Stem"),
-            "Choroid_Plexus": _("Choroid Plexus"),
+            "cortical": _("Cortical"),
+            "subcortical": _("Subcortical"),
+            "white_matter": _("White Matter"),
+            "cerebellum": _("Cerebellum"),
+            "ventricles": _("Ventricles"),
+            "brain_stem": _("Brain Stem"),
+            "choroid_plexus": _("Choroid Plexus"),
         }
 
         self.selected_mask_types = []
@@ -455,7 +454,7 @@ def __init__(self, parent, auto_segment=False):
             title=_("Subpart Segmentation"),
             has_torch=True,
             has_tinygrad=True,
-            segmenter=segment.SubpartSegementProcess,
+            segmenter=segment.SubpartSegmentProcess,
             auto_segment=auto_segment,
         )
 
@@ -477,28 +476,6 @@ def _init_gui(self):
             self.mask_checkboxes[mask_id] = wx.CheckBox(self, wx.ID_ANY, mask_label)
             self.mask_checkboxes[mask_id].SetValue(False)
 
-        self._check_model_availability()
-
-    def _check_model_availability(self):
-        """Check if required models and dependencies are available"""
-        try:
-            # Try to create a dummy process to check model availability
-            # This is safer than calling slc.Slice().matrix which might not be ready
-            self.models_missing = False
-            self.missing_reason = ""
-
-            # We could add specific checks here, but for now we'll do it lazily
-            # during segmentation start to avoid initialization issues
-
-        except Exception as e:
-            self.models_missing = True
-            self.missing_reason = str(e)
-
-        if self.models_missing:
-            self.lbl_models_missing = wx.StaticText(
-                self, -1, _("FastSurfer models not found. Please check installation.")
-            )
-
     def _do_layout(self):
         """Override _do_layout to arrange FastSurferCNN specific UI elements"""
         super()._do_layout()
@@ -545,15 +522,6 @@ def _do_layout(self):
                 # Fallback - just add to the main sizer
                 self.main_sizer.Add(self.mask_types_sizer, 0, wx.ALL | wx.EXPAND, 5)
 
-        if self.models_missing:
-            error_sizer = wx.BoxSizer(wx.VERTICAL)
-            error_sizer.Add(self.lbl_models_missing, 0, wx.ALL, 5)
-
-            index = self.main_sizer.GetItemCount() - 1
-            self.main_sizer.Insert(index, error_sizer, 0, wx.EXPAND | wx.ALL, 5)
-
-            self.btn_segment.Enable(False)
-
         self.main_sizer.Fit(self)
         self.Layout()
 
@@ -575,7 +543,7 @@ def OnSegment(self, evt):
                 device_id = self.torch_devices[self.cb_devices.GetValue()]
             except (KeyError, AttributeError):
                 device_id = "cpu"
-            use_gpu = True if not "cpu" in device_id.lower() else False
+            use_gpu = True if "cpu" not in device_id.lower() else False
         elif backend.lower() == "tinygrad":
             try:
                 device_id = self.tinygrad_devices[self.cb_devices.GetValue()]
@@ -637,18 +605,10 @@ def AfterSegment(self):
             checkbox.Enable()
 
     def apply_segment_threshold(self):
-        print("apply_segment_threshold: Starting...")
         threshold = self.sld_threshold.GetValue() / 100.0
-        print(f"apply_segment_threshold: Threshold value: {threshold}")
-
-        print("apply_segment_threshold: Calling apply_segment_threshold...")
         self.ps.apply_segment_threshold(threshold)
-        print("apply_segment_threshold: apply_segment_threshold completed")
-
-        print("apply_segment_threshold: Discarding buffers and reloading slice...")
         slc.Slice().discard_all_buffers()
         Publisher.sendMessage("Reload actual slice")
-        print("apply_segment_threshold: Completed successfully")
 
     def OnStop(self, evt):
         super().OnStop(evt)
@@ -811,6 +771,10 @@ def _init_gui(self):
 
         self.patch_cmb = wx.ComboBox(self, choices=patch_size, value="480")
 
+        self.path_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        self.path_sizer.Add(self.patch_txt, 0, wx.EXPAND | wx.ALL, 5)
+        self.path_sizer.Add(self.patch_cmb, 2, wx.EXPAND | wx.ALL, 5)
+
         self.method = wx.RadioBox(
             self,
             -1,
@@ -849,7 +813,7 @@ def OnSegment(self, evt):
         apply_wwwl = self.chk_apply_wwwl.GetValue()
         create_new_mask = self.chk_new_mask.GetValue()
         use_gpu = self.chk_use_gpu.GetValue()
-        prob_threshold = self.sld_threshold.GetValue() / 100.0
+        # prob_threshold = self.sld_threshold.GetValue() / 100.0
         method = self.method.GetSelection()
 
         self.btn_close.Disable()

invesalius/segmentation/deep_learning/__init__.py

@@ -1 +1 @@
-__all__ = ["fastsurfer", "segment.py"]
+__all__ = ["fastsurfer_subpart", "segment"]

invesalius/segmentation/deep_learning/fastsurfer_subpart/__init__.py

@@ -13,8 +13,10 @@
 # limitations under the License.
 
 __all__ = [
-    "misc" "models",
-    "data_process" "inference",
+    "misc",
+    "models",
+    "data_process",
+    "inference",
     "quick_qc",
     "reduce_to_aseg",
     "pipeline",

invesalius/segmentation/deep_learning/fastsurfer_subpart/data_process.py

@@ -148,7 +148,6 @@ def read_classes_from_lut(lut_file: str | Path):
         dtype=names,
         **kwargs,
     )
-    return lut
 
 
 def aparc_aseg_to_label(

invesalius/segmentation/deep_learning/fastsurfer_subpart/misc.py

@@ -831,9 +831,7 @@ def make_subjects_dir(self):
         Try to create the subject directory.
         """
         if self.config.out_dir is None:
-            LOGGER.info(
-                "No Subjects directory found, absolute paths for filenames are " "required."
-            )
+            LOGGER.info("No Subjects directory found, absolute paths for filenames are required.")
             return
 
         LOGGER.info(f"Output will be stored in Subjects Directory: {self.config.out_dir}")