cardio 2025.8.0__tar.gz → 2025.9.0__tar.gz

{cardio-2025.8.0 → cardio-2025.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: cardio
-Version: 2025.8.0
+Version: 2025.9.0
 Summary: A simple web-based viewer for 3D and 4D ('cine') medical imaging data.
 Keywords: Medical,Imaging,3D,4D,Visualization
 Author: Davis Marc Vigneault
@@ -34,17 +34,19 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Dist: trame-vuetify>=3.0.2
 Requires-Dist: trame-vtk>=2.9.1
-Requires-Dist: trame>=3.11.0
 Requires-Dist: itk>=5.4.4.post1
 Requires-Dist: vtk>=9.5.0
 Requires-Dist: tomlkit>=0.13.3
 Requires-Dist: numpy>=2.2.6
 Requires-Dist: pydantic>=2.11.7
 Requires-Dist: pydantic-settings>=2.0.0
-Requires-Dist: isort ; extra == 'dev'
-Requires-Dist: pytest ; extra == 'dev'
-Requires-Dist: bumpver ; extra == 'dev'
+Requires-Dist: trame>=3.12.0
+Requires-Dist: trame-client>=3.10.1
 Requires-Dist: ruff>=0.12.10 ; extra == 'dev'
+Requires-Dist: isort>=6.0.1 ; extra == 'dev'
+Requires-Dist: bumpver>=2025.1131 ; extra == 'dev'
+Requires-Dist: pytest>=8.4.1 ; extra == 'dev'
+Requires-Dist: coverage>=7.10.4 ; extra == 'dev'
 Maintainer: Davis Marc Vigneault
 Maintainer-email: Davis Marc Vigneault <davis.vigneault@gmail.com>
 Requires-Python: >=3.10
@@ -74,7 +76,7 @@ $ uv init
 $ uv add cardio
 $ . ./.venv/bin/activate
 (project) cardio --version
-cardio 2025.8.0
+cardio 2025.9.0
 ```
 
 ### Developing
@@ -92,3 +94,11 @@ $ isort .
 $ ruff format
 $ pytest -v
 ```
+
+Uploading:
+
+```bash
+$ bumpver update
+$ uv build --no-sources
+$ uv publish --token <pypi_api_key>
+```

{cardio-2025.8.0 → cardio-2025.9.0}/README.md

@@ -20,7 +20,7 @@ $ uv init
 $ uv add cardio
 $ . ./.venv/bin/activate
 (project) cardio --version
-cardio 2025.8.0
+cardio 2025.9.0
 ```
 
 ### Developing
@@ -38,3 +38,11 @@ $ isort .
 $ ruff format
 $ pytest -v
 ```
+
+Uploading:
+
+```bash
+$ bumpver update
+$ uv build --no-sources
+$ uv publish --token <pypi_api_key>
+```

{cardio-2025.8.0 → cardio-2025.9.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "cardio"
-version = "2025.8.0"
+version = "2025.9.0"
 authors = [
     {name = "Davis Marc Vigneault", email = "davis.vigneault@gmail.com"}
 ]
@@ -25,13 +25,14 @@ classifiers = [
 dependencies = [
     "trame-vuetify>=3.0.2",
     "trame-vtk>=2.9.1",
-    "trame>=3.11.0",
     "itk>=5.4.4.post1",
     "vtk>=9.5.0",
     "tomlkit>=0.13.3",
     "numpy>=2.2.6",
     "pydantic>=2.11.7",
     "pydantic-settings>=2.0.0",
+    "trame>=3.12.0",
+    "trame-client>=3.10.1",
 ]
 description = "A simple web-based viewer for 3D and 4D ('cine') medical imaging data."
 keywords = ["Medical", "Imaging", "3D", "4D", "Visualization"]
@@ -44,10 +45,11 @@ requires-python = ">=3.10"
 
 [project.optional-dependencies]
 dev = [
- "isort",
- "pytest",
- "bumpver",
  "ruff>=0.12.10",
+ "isort>=6.0.1",
+ "bumpver>=2025.1131",
+ "pytest>=8.4.1",
+ "coverage>=7.10.4",
 ]
 
 [project.gui-scripts]
@@ -60,7 +62,7 @@ repository = "https://github.com/sudomakeinstall/cardio"
 profile = "black"
 
 [tool.bumpver]
-current_version = "2025.8.0"
+current_version = "2025.9.0"
 version_pattern = "YYYY.MM.INC0"
 commit_message = "ENH: Bump version from {old_version} => {new_version}"
 commit = true

{cardio-2025.8.0 → cardio-2025.9.0}/src/cardio/__init__.py

@@ -1,15 +1,16 @@
+from . import window_level
 from .logic import Logic
 from .mesh import Mesh
 from .object import Object
 from .scene import Scene
 from .screenshot import Screenshot
 from .segmentation import Segmentation
-from .transfer_functions import (
-    list_available_presets,
-    load_preset,
-)
 from .ui import UI
 from .volume import Volume
+from .volume_property_presets import (
+    list_volume_property_presets,
+    load_volume_property_preset,
+)
 
 __all__ = [
     "Object",
@@ -20,8 +21,8 @@ __all__ = [
     "Screenshot",
     "UI",
     "Logic",
-    "load_preset",
-    "list_available_presets",
+    "load_volume_property_preset",
+    "list_volume_property_presets",
 ]
 
-__version__ = "2025.8.0"
+__version__ = "2025.9.0"

{cardio-2025.8.0 → cardio-2025.9.0}/src/cardio/app.py

@@ -15,7 +15,7 @@ from .ui import UI
 
 class CardioApp(tm.app.TrameApp):
     def __init__(self, name=None):
-        super().__init__(server=name, client_type="vue2")
+        super().__init__(server=name, client_type="vue3")
 
         # Add config file argument to Trame's parser
         self.server.cli.add_argument(

cardio-2025.9.0/src/cardio/blend_transfer_functions.py

@@ -0,0 +1,84 @@
+# System
+import numpy as np
+
+# Third Party
+import vtk
+
+
+def blend_transfer_functions(tfs, scalar_range=(-2000, 2000), num_samples=512):
+    """
+    Blend multiple transfer functions using volume rendering emission-absorption model.
+
+    Based on the volume rendering equation from:
+    - Levoy, M. "Display of Surfaces from Volume Data" IEEE Computer Graphics and Applications, 1988
+    - Kajiya, J.T. & Von Herzen, B.P. "Ray tracing volume densities" ACM SIGGRAPH Computer Graphics, 1984
+    - Engel, K. et al. "Real-time Volume Graphics" A K Peters, 2006, Chapter 2
+
+    The volume rendering integral: I = ∫ C(s) * μ(s) * T(s) ds
+    where C(s) = emission color, μ(s) = opacity, T(s) = transmission
+
+    For discrete transfer functions, this becomes:
+    - Total emission = Σ(color_i * opacity_i)
+    - Total absorption = Σ(opacity_i)
+    - Final color = total_emission / total_absorption
+    """
+    if len(tfs) == 1:
+        return tfs[0]
+
+    sample_points = np.linspace(
+        start=scalar_range[0],
+        stop=scalar_range[1],
+        num=num_samples,
+    )
+
+    # Initialize arrays to store blended values
+    blended_opacity = []
+    blended_color = []
+
+    for scalar_val in sample_points:
+        # Accumulate emission and absorption for volume rendering
+        total_emission = [0.0, 0.0, 0.0]
+        total_absorption = 0.0
+
+        for otf, ctf in tfs:
+            # Get opacity and color for this scalar value
+            layer_opacity = otf.GetValue(scalar_val)
+            layer_color = [0.0, 0.0, 0.0]
+            ctf.GetColor(scalar_val, layer_color)
+
+            # Volume rendering accumulation:
+            # Emission = color * opacity (additive)
+            # Absorption = opacity (multiplicative through transmission)
+            for i in range(3):
+                total_emission[i] += layer_color[i] * layer_opacity
+
+            total_absorption += layer_opacity
+
+        # Clamp values to reasonable ranges
+        total_absorption = min(total_absorption, 1.0)
+        for i in range(3):
+            total_emission[i] = min(total_emission[i], 1.0)
+
+        # For the final color, normalize emission by absorption if absorption > 0
+        if total_absorption > 0.001:  # Avoid division by zero
+            final_color = [total_emission[i] / total_absorption for i in range(3)]
+        else:
+            final_color = [0.0, 0.0, 0.0]
+
+        # Clamp final colors
+        final_color = [min(c, 1.0) for c in final_color]
+
+        blended_opacity.append(total_absorption)
+        blended_color.append(final_color)
+
+    # Create new VTK transfer functions with blended values
+    blended_otf = vtk.vtkPiecewiseFunction()
+    blended_ctf = vtk.vtkColorTransferFunction()
+
+    for i, scalar_val in enumerate(sample_points):
+        blended_otf.AddPoint(scalar_val, blended_opacity[i])
+        blended_ctf.AddRGBPoint(
+            scalar_val, blended_color[i][0], blended_color[i][1], blended_color[i][2]
+        )
+
+    return blended_otf, blended_ctf

cardio-2025.9.0/src/cardio/color_transfer_function.py

@@ -0,0 +1,29 @@
+# Third Party
+import pydantic as pc
+import vtk
+
+# Internal
+from .types import RGBColor
+
+
+class ColorTransferFunctionPoint(pc.BaseModel):
+    """A single point in a color transfer function."""
+
+    x: float = pc.Field(description="Scalar value")
+    color: RGBColor
+
+
+class ColorTransferFunctionConfig(pc.BaseModel):
+    """Configuration for a VTK color transfer function."""
+
+    points: list[ColorTransferFunctionPoint] = pc.Field(
+        min_length=1, description="Points defining the color transfer function"
+    )
+
+    @property
+    def vtk_function(self) -> vtk.vtkColorTransferFunction:
+        """Create VTK color transfer function from this configuration."""
+        ctf = vtk.vtkColorTransferFunction()
+        for point in self.points:
+            ctf.AddRGBPoint(point.x, *point.color)
+        return ctf