cardio 2025.10.0__py3-none-any.whl → 2025.12.0__py3-none-any.whl

cardio/volume.py

@@ -20,7 +20,7 @@ class Volume(Object):
     """Volume object with transfer functions and clipping support."""
 
     pattern: str = pc.Field(
-        default="${frame}.nii.gz",
+        default="{frame}.nii.gz",
         description="Filename pattern with $frame placeholder",
     )
     transfer_function_preset: str = pc.Field(
@@ -30,6 +30,9 @@ class Volume(Object):
     _mpr_actors: dict[str, list[vtk.vtkImageActor]] = pc.PrivateAttr(
         default_factory=dict
     )
+    _crosshair_actors: dict[str, dict[str, vtk.vtkActor]] = pc.PrivateAttr(
+        default_factory=dict
+    )
 
     @pc.model_validator(mode="after")
     def initialize_volume(self):
@@ -134,6 +137,104 @@ class Volume(Object):
             return self.create_mpr_actors(frame)
         return self._mpr_actors[frame]
 
+    def create_crosshair_actors(self, colors: dict, line_width: float = 1.5) -> dict:
+        """Create 2D crosshair overlay actors for each MPR view.
+
+        Uses screen-space 2D actors that always appear centered in the view.
+
+        Args:
+            colors: Dict mapping view names to RGB tuples
+            line_width: Width of the crosshair lines
+
+        Returns:
+            Dict mapping view names to dicts with line actors
+        """
+        crosshairs = {}
+
+        for view_name in ["axial", "sagittal", "coronal"]:
+            view_crosshairs = {}
+
+            for line_name in ["line1", "line2"]:
+                # Create 2D line using normalized viewport coordinates
+                points = vtk.vtkPoints()
+                lines = vtk.vtkCellArray()
+
+                # Placeholder points - will set based on line orientation
+                if line_name == "line1":
+                    # Vertical line (one of the other planes)
+                    points.InsertNextPoint(0.5, 0.0, 0.0)
+                    points.InsertNextPoint(0.5, 1.0, 0.0)
+                else:
+                    # Horizontal line (other plane)
+                    points.InsertNextPoint(0.0, 0.5, 0.0)
+                    points.InsertNextPoint(1.0, 0.5, 0.0)
+
+                line = vtk.vtkLine()
+                line.GetPointIds().SetId(0, 0)
+                line.GetPointIds().SetId(1, 1)
+                lines.InsertNextCell(line)
+
+                polydata = vtk.vtkPolyData()
+                polydata.SetPoints(points)
+                polydata.SetLines(lines)
+
+                # Use coordinate transform to map normalized coords to viewport
+                coord = vtk.vtkCoordinate()
+                coord.SetCoordinateSystemToNormalizedViewport()
+
+                mapper = vtk.vtkPolyDataMapper2D()
+                mapper.SetInputData(polydata)
+                mapper.SetTransformCoordinate(coord)
+
+                actor = vtk.vtkActor2D()
+                actor.SetMapper(mapper)
+                actor.GetProperty().SetLineWidth(line_width)
+                actor.SetVisibility(False)
+
+                view_crosshairs[line_name] = {
+                    "polydata": polydata,
+                    "actor": actor,
+                }
+
+            # Set colors based on which planes the lines represent
+            if view_name == "axial":
+                view_crosshairs["line1"]["actor"].GetProperty().SetColor(
+                    *colors.get("sagittal", (1, 0, 0))
+                )
+                view_crosshairs["line2"]["actor"].GetProperty().SetColor(
+                    *colors.get("coronal", (0, 1, 0))
+                )
+            elif view_name == "sagittal":
+                view_crosshairs["line1"]["actor"].GetProperty().SetColor(
+                    *colors.get("axial", (0, 0, 1))
+                )
+                view_crosshairs["line2"]["actor"].GetProperty().SetColor(
+                    *colors.get("coronal", (0, 1, 0))
+                )
+            else:  # coronal
+                view_crosshairs["line1"]["actor"].GetProperty().SetColor(
+                    *colors.get("axial", (0, 0, 1))
+                )
+                view_crosshairs["line2"]["actor"].GetProperty().SetColor(
+                    *colors.get("sagittal", (1, 0, 0))
+                )
+
+            crosshairs[view_name] = view_crosshairs
+
+        self._crosshair_actors = crosshairs
+        return crosshairs
+
+    @property
+    def crosshair_actors(self) -> dict:
+        """Get crosshair actors."""
+        return self._crosshair_actors
+
+    def set_crosshairs_visible(self, visible: bool):
+        """Set visibility of all crosshair actors."""
+        for view_crosshairs in self._crosshair_actors.values():
+            for line_data in view_crosshairs.values():
+                line_data["actor"].SetVisibility(visible)
+
     def _get_mpr_coordinate_systems(self):
         """Get coordinate system transformation matrices for MPR views."""
         view_axcodes = {
@@ -197,12 +298,54 @@ class Volume(Object):
 
         return bounds
 
+    def _build_cumulative_rotation(
+        self, rotation_sequence: list, rotation_angles: dict
+    ) -> np.ndarray:
+        """Build cumulative rotation matrix from sequence of rotations."""
+        cumulative_rotation = np.eye(3)
+        if rotation_sequence and rotation_angles:
+            for i, rotation in enumerate(rotation_sequence):
+                angle = rotation_angles.get(i, 0)
+                rotation_matrix = euler_angle_to_rotation_matrix(
+                    EulerAxis(rotation["axis"]), angle
+                )
+                cumulative_rotation = cumulative_rotation @ rotation_matrix
+        return cumulative_rotation
+
+    def get_scroll_vector(
+        self,
+        view_name: str,
+        rotation_sequence: list = None,
+        rotation_angles: dict = None,
+    ) -> np.ndarray:
+        """Get the current normal vector for a view after rotation.
+
+        Args:
+            view_name: One of "axial", "sagittal", "coronal"
+            rotation_sequence: List of rotation definitions
+            rotation_angles: Dict mapping rotation index to angle
+
+        Returns:
+            3D unit vector representing the scroll direction for this view
+        """
+        base_normals = {
+            "axial": np.array([0.0, 0.0, 1.0]),
+            "sagittal": np.array([1.0, 0.0, 0.0]),
+            "coronal": np.array([0.0, 1.0, 0.0]),
+        }
+
+        if view_name not in base_normals:
+            return np.array([0.0, 0.0, 1.0])
+
+        cumulative_rotation = self._build_cumulative_rotation(
+            rotation_sequence, rotation_angles
+        )
+        return cumulative_rotation @ base_normals[view_name]
+
     def update_slice_positions(
         self,
         frame: int,
-        axial_pos: float,
-        sagittal_pos: float,
-        coronal_pos: float,
+        origin: list,
         rotation_sequence: list = None,
         rotation_angles: dict = None,
     ):
@@ -210,62 +353,36 @@ class Volume(Object):
 
         Args:
             frame: Frame index
-            axial_pos: Physical position along Z axis (LAS Superior)
-            sagittal_pos: Physical position along X axis (LAS Left)
-            coronal_pos: Physical position along Y axis (LAS Anterior)
+            origin: [x, y, z] position in LPS coordinates (shared by all views)
+            rotation_sequence: List of rotation definitions
+            rotation_angles: Dict mapping rotation index to angle
         """
         if frame not in self._mpr_actors:
             return
 
-        volume_actor = self._actors[frame]
-        image_data = volume_actor.GetMapper().GetInput()
-        bounds = image_data.GetBounds()
-
         actors = self._mpr_actors[frame]
 
-        # Clamp positions to volume bounds
-        axial_pos = max(bounds[4], min(bounds[5], axial_pos))  # Z bounds
-        sagittal_pos = max(bounds[0], min(bounds[1], sagittal_pos))  # X bounds
-        coronal_pos = max(bounds[2], min(bounds[3], coronal_pos))  # Y bounds
-
         # Get coordinate system transformations for each MPR view
         transforms = self._get_mpr_coordinate_systems()
 
-        center = image_data.GetCenter()
-
-        # Step 1: Apply translation to determine slice origins in physical space
-        axial_origin = [center[0], center[1], axial_pos]
-        sagittal_origin = [sagittal_pos, center[1], center[2]]
-        coronal_origin = [center[0], coronal_pos, center[2]]
+        # Build cumulative rotation matrix
+        cumulative_rotation = self._build_cumulative_rotation(
+            rotation_sequence, rotation_angles
+        )
 
-        # Step 2: Apply cumulative rotation around the translated origins
-        if rotation_sequence and rotation_angles:
-            cumulative_rotation = np.eye(3)
-            for i, rotation in enumerate(rotation_sequence):
-                angle = rotation_angles.get(i, 0)
-                rotation_matrix = euler_angle_to_rotation_matrix(
-                    EulerAxis(rotation["axis"]), angle
-                )
-                cumulative_rotation = cumulative_rotation @ rotation_matrix
+        # Apply rotation to base transforms
+        axial_transform = cumulative_rotation @ transforms["axial"]
+        sagittal_transform = cumulative_rotation @ transforms["sagittal"]
+        coronal_transform = cumulative_rotation @ transforms["coronal"]
 
-            # Apply rotation to base transforms
-            axial_transform = cumulative_rotation @ transforms["axial"]
-            sagittal_transform = cumulative_rotation @ transforms["sagittal"]
-            coronal_transform = cumulative_rotation @ transforms["coronal"]
-        else:
-            # Use base transforms without rotation
-            axial_transform = transforms["axial"]
-            sagittal_transform = transforms["sagittal"]
-            coronal_transform = transforms["coronal"]
-
-        # Update slices with translated origins and rotated transforms
-        axial_matrix = create_vtk_reslice_matrix(axial_transform, axial_origin)
+        # All views share the same origin
+        axial_matrix = create_vtk_reslice_matrix(axial_transform, origin)
         actors["axial"]["reslice"].SetResliceAxes(axial_matrix)
 
-        sagittal_matrix = create_vtk_reslice_matrix(sagittal_transform, sagittal_origin)
+        sagittal_matrix = create_vtk_reslice_matrix(sagittal_transform, origin)
         actors["sagittal"]["reslice"].SetResliceAxes(sagittal_matrix)
 
-        coronal_matrix = create_vtk_reslice_matrix(coronal_transform, coronal_origin)
+        coronal_matrix = create_vtk_reslice_matrix(coronal_transform, origin)
         actors["coronal"]["reslice"].SetResliceAxes(coronal_matrix)
 
     def update_mpr_window_level(self, frame: int, window: float, level: float):

cardio/volume_property.py

@@ -1,8 +1,6 @@
-# Third Party
 import pydantic as pc
 import vtk
 
-# Internal
 from .blend_transfer_functions import blend_transfer_functions
 from .transfer_function_pair import TransferFunctionPairConfig
 from .types import ScalarComponent

cardio/volume_property_presets.py

@@ -1,11 +1,8 @@
-# System
 import pathlib as pl
 
-# Third Party
 import pydantic as pc
 import tomlkit as tk
 
-# Internal
 from .volume_property import VolumePropertyConfig
 
 

cardio/window_level.py

@@ -1,7 +1,5 @@
-# System
 import functools as ft
 
-# Third Party
 import pydantic as pc
 
 

{cardio-2025.10.0.dist-info → cardio-2025.12.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: cardio
-Version: 2025.10.0
+Version: 2025.12.0
 Summary: A simple web-based viewer for 3D and 4D ('cine') medical imaging data.
 Keywords: Medical,Imaging,3D,4D,Visualization
 Author: Davis Marc Vigneault
@@ -59,12 +59,11 @@ Description-Content-Type: text/markdown
 `cardio` is a simple web-based viewer for 3D and 4D ('cine') medical imaging data,
 built primarily on [trame](https://github.com/kitware/trame),
 [vtk](https://github.com/kitware/vtk), and
-[itk](https://github.com/insightsoftwareconsortium/itk).  `cardio` is able to
-render sequences of mesh files (e.g., `\*.obj` files), segmentation files (e.g.
-`\*nii.gz` files with discrete labels) and volume renderings of grayscale images
-(e.g. \*.nii.gz files with continuous values).  `cardio` is launched from the
-commandline and may be configured either directly from the commandline, via a static
-TOML configuration file, or a combination of the two.
+[itk](https://github.com/insightsoftwareconsortium/itk).  `cardio` can render sequences
+of mesh files (e.g., `\*.obj` files), segmentation files (e.g., `\*nii.gz` files with
+discrete labels) and volume renderings of grayscale images (e.g., `\*.nii.gz` files with
+continuous values).  `cardio` is launched from the commandline and may be configured via
+commandline arguments, a static TOML configuration file, or a combination of the two.
 
 ## Quickstart
 
@@ -76,7 +75,7 @@ $ uv init
 $ uv add cardio
 $ . ./.venv/bin/activate
 (project) cardio --version
-cardio 2025.10.0
+cardio 2025.12.0
 ```
 
 ### Developing

cardio-2025.12.0.dist-info/RECORD

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cardio-2025.10.0.dist-info/RECORD

@@ -1,29 +0,0 @@
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