cardio 2023.1.2__py3-none-any.whl → 2025.8.1__py3-none-any.whl

cardio/volume.py

@@ -1,116 +1,61 @@
 import logging
-import os
 
 import itk
 import numpy as np
-from vtkmodules.vtkCommonDataModel import vtkPiecewiseFunction
-from vtkmodules.vtkIOGeometry import vtkOBJReader
-from vtkmodules.vtkRenderingCore import (
-    vtkColorTransferFunction,
-    vtkRenderer,
-    vtkVolume,
-    vtkVolumeProperty,
-)
-from vtkmodules.vtkRenderingVolume import vtkGPUVolumeRayCastMapper
-from vtkmodules.vtkRenderingVolumeOpenGL2 import vtkOpenGLRayCastImageDisplayHelper
+import pydantic as pc
+import vtk
 
-from . import Object
-
-
-def reset_direction(image):
-    origin = np.asarray(itk.origin(image))
-    spacing = np.asarray(itk.spacing(image))
-    size = np.asarray(itk.size(image))
-    direction = np.asarray(image.GetDirection())
-
-    direction[direction == 1] = 0
-    origin += np.dot(size, np.dot(np.diag(spacing), direction))
-    direction = np.identity(3)
-
-    origin = itk.Point[itk.F, 3](origin)
-    spacing = itk.spacing(image)
-    size = itk.size(image)
-    direction = itk.matrix_from_array(direction)
-
-    interpolator = itk.LinearInterpolateImageFunction.New(image)
-    output = itk.resample_image_filter(
-        image,
-        size=size,
-        interpolator=interpolator,
-        output_spacing=spacing,
-        output_origin=origin,
-        output_direction=direction,
-    )
-
-    return output
+from .object import Object
+from .transfer_functions import load_preset
+from .utils import InterpolatorType, reset_direction
 
 
 class Volume(Object):
-    def __init__(self, cfg: str, renderer: vtkRenderer):
-        super().__init__(cfg, renderer)
-        self.actors: list[vtkVolume] = []
+    """Volume object with transfer functions and clipping support."""
 
-        self.ambient: float = cfg["ambient"]
-        self.diffuse: float = cfg["diffuse"]
-        self.specular: float = cfg["specular"]
+    pattern: str = pc.Field(
+        default="${frame}.nii.gz",
+        description="Filename pattern with $frame placeholder",
+    )
+    transfer_function_preset: str = pc.Field(description="Transfer function preset key")
+    _actors: list[vtk.vtkVolume] = pc.PrivateAttr(default_factory=list)
 
-        frame = 0
-        while os.path.exists(self.path_for_frame(frame)):
+    @pc.model_validator(mode="after")
+    def initialize_volume(self):
+        """Generate VTK volume actors for all frames."""
+        for frame, path in enumerate(self.path_list):
             logging.info(f"{self.label}: Loading frame {frame}.")
-            mapper = vtkGPUVolumeRayCastMapper()
-            actor = vtkVolume()
-            image = itk.imread(self.path_for_frame(frame))
-            image = reset_direction(image)
+
+            image = itk.imread(path)
+            image = reset_direction(image, InterpolatorType.LINEAR)
             image = itk.vtk_image_from_image(image)
-            mapper.SetInputData(image)
-            actor.SetMapper(mapper)
-            self.actors += [actor]
-            frame += 1
 
-        self.setup_property()
+            mapper = vtk.vtkGPUVolumeRayCastMapper()
+            mapper.SetInputData(image)
 
-    def setup_pipeline(self, frame: int):
-        for a in self.actors:
-            self.renderer.AddVolume(a)
-            a.SetVisibility(False)
-            a.SetProperty(self.property)
-        if self.visible:
-            self.actors[frame].SetVisibility(True)
-        self.renderer.ResetCamera()
+            actor = vtk.vtkVolume()
+            actor.SetMapper(mapper)
 
-    def setup_property(self):
+            self._actors.append(actor)
 
-        a = 0
-        b = 500
-        c = 1000
-        d = 1150
+        return self
 
-        # Create transfer mapping scalar value to opacity.
-        opacityTransferFunction = vtkPiecewiseFunction()
-        opacityTransferFunction.AddPoint(a, 0.00)
-        opacityTransferFunction.AddPoint(b, 0.15)
-        opacityTransferFunction.AddPoint(c, 0.15)
-        opacityTransferFunction.AddPoint(d, 0.85)
+    @property
+    def actors(self) -> list[vtk.vtkVolume]:
+        return self._actors
 
-        # Create transfer mapping scalar value to color.
-        colorTransferFunction = vtkColorTransferFunction()
-        colorTransferFunction.AddRGBPoint(a, 0.0, 0.0, 0.0)
-        colorTransferFunction.AddRGBPoint(b, 1.0, 0.5, 0.3)
-        colorTransferFunction.AddRGBPoint(c, 1.0, 0.5, 0.3)
-        colorTransferFunction.AddRGBPoint(d, 1.0, 1.0, 0.9)
+    @property
+    def preset(self):
+        """Load preset based on transfer_function_preset."""
+        return load_preset(self.transfer_function_preset)
 
-        volumeGradientOpacity = vtkPiecewiseFunction()
-        volumeGradientOpacity.AddPoint(0, 0.0)
-        volumeGradientOpacity.AddPoint(90, 0.5)
-        volumeGradientOpacity.AddPoint(100, 1.0)
+    def configure_actors(self):
+        """Configure volume properties without adding to renderer."""
+        for volume in self._actors:
+            volume.SetVisibility(False)
+            volume.SetProperty(self.preset.vtk_property)
 
-        # The property describes how the data will look.
-        self.property = vtkVolumeProperty()
-        self.property.SetColor(colorTransferFunction)
-        self.property.SetScalarOpacity(opacityTransferFunction)
-        self.property.SetGradientOpacity(volumeGradientOpacity)
-        self.property.ShadeOn()
-        self.property.SetInterpolationTypeToLinear()
-        self.property.SetAmbient(self.ambient)
-        self.property.SetDiffuse(self.diffuse)
-        self.property.SetSpecular(self.specular)
+    def apply_preset_to_actors(self):
+        """Apply the current preset to all actors."""
+        for actor in self._actors:
+            actor.SetProperty(self.preset.vtk_property)

cardio-2025.8.1.dist-info/METADATA

@@ -0,0 +1,102 @@
+Metadata-Version: 2.3
+Name: cardio
+Version: 2025.8.1
+Summary: A simple web-based viewer for 3D and 4D ('cine') medical imaging data.
+Keywords: Medical,Imaging,3D,4D,Visualization
+Author: Davis Marc Vigneault
+Author-email: Davis Marc Vigneault <davis.vigneault@gmail.com>
+License: Apache Software License 2.0
+         
+         Copyright (c) 2023, Davis Marc Vigneault
+         
+         Licensed under the Apache License, Version 2.0 (the "License");
+         you may not use this file except in compliance with the License.
+         You may obtain a copy of the License at
+         
+         http://www.apache.org/licenses/LICENSE-2.0
+         
+         Unless required by applicable law or agreed to in writing, software
+         distributed under the License is distributed on an "AS IS" BASIS,
+         WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+         See the License for the specific language governing permissions and
+         limitations under the License.
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Web Environment
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: JavaScript
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+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: 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'
+Maintainer: Davis Marc Vigneault
+Maintainer-email: Davis Marc Vigneault <davis.vigneault@gmail.com>
+Requires-Python: >=3.10
+Project-URL: repository, https://github.com/sudomakeinstall/cardio
+Provides-Extra: dev
+Description-Content-Type: text/markdown
+
+# cardio
+
+`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.
+
+## Quickstart
+
+### Installation
+
+```bash
+$ cd /path/to/your/project
+$ uv init
+$ uv add cardio
+$ . ./.venv/bin/activate
+(project) cardio --version
+cardio 2025.8.1
+```
+
+### Developing
+
+Ensuring you have all required dependencies:
+
+```bash
+$ uv sync --all-extras
+```
+
+Pre-commit checklist:
+
+```bash
+$ isort .
+$ ruff format
+$ pytest -v
+```
+
+Uploading:
+
+```bash
+$ bumpver update
+$ uv build --no-sources
+$ uv publish --token <pypi_api_key>
+```

cardio-2025.8.1.dist-info/RECORD

@@ -0,0 +1,22 @@
+cardio/__init__.py,sha256=MsdbwMMtvuZbIS_niBq_ZXvds_jH4oPgkyCPO5heLLU,505
+cardio/app.py,sha256=sJ2IbOrV2X-5XTkORUbxuvqvg3-Iaotkq_ofIjVzJCA,1791
+cardio/assets/bone.toml,sha256=vv8uVYSHIoKuHkNCoBOkGe2_qoEbXMvQO6ypm3mMOtA,675
+cardio/assets/vascular_closed.toml,sha256=XtaZS_Zd6NSAtY3ZlUfiog3T86u9Ii0oSutU2wBQy78,1267
+cardio/assets/vascular_open.toml,sha256=1M3sV1IGt3zh_3vviysKEk9quKfjF9xUBcIq3kxVHFM,879
+cardio/assets/xray.toml,sha256=siPem0OZ2OkWH0e5pizftpItJKGJgxKJ_S2K0316ubQ,693
+cardio/logic.py,sha256=Ir4W1pz_hNlQA3QgzIrh701LJY7qBF4O05qkNKfszJw,15126
+cardio/mesh.py,sha256=DUsjzYsTuUDsICqRK3pj49FtXjQ79CJ0HaEYupEE9R4,9392
+cardio/object.py,sha256=6YnEwXL5CUWoG-RAI8ETZG_DWmWi1URjVMiimCxD1zk,6448
+cardio/property_config.py,sha256=XJYcKeRcq8s9W9jqxzVer75r5jBLuvebv780FYdPV8U,1723
+cardio/scene.py,sha256=u9j2ZDobTvO8snTnNk-n3NmO7ZQ2cSC6maRCfkcMQaM,7401
+cardio/screenshot.py,sha256=l8bLgxnU5O0FlnmsyVAzKwM9Y0401IzcdnDP0WqFSTY,640
+cardio/segmentation.py,sha256=enj1V5Rw42dxjqSRUiylEQcdgvj8A-Do9Z638tf7nc8,6706
+cardio/transfer_functions.py,sha256=oOKShXBOBpDt8VTEZyc4IT9mCMxuYkWCKHE9kzGrs3o,9183
+cardio/types.py,sha256=DYDgA5QmYdU3QQrEgZMouEbMEIf40DJCeXo4V7cDXtg,356
+cardio/ui.py,sha256=ifbXHRSDY2Sm-zcriIk4wVySuF0NwHrZu8NCN098gIY,23180
+cardio/utils.py,sha256=zgyJ2PWTAWIaU8SVA9KF_XFB4251QxYAT6w3cqaIerA,3051
+cardio/volume.py,sha256=vCOUWKeN99Whdv0b9IEalFGUpKuNe4DILKWBL02nUUM,1892
+cardio-2025.8.1.dist-info/WHEEL,sha256=4n27za1eEkOnA7dNjN6C5-O2rUiw6iapszm14Uj-Qmk,79
+cardio-2025.8.1.dist-info/entry_points.txt,sha256=xRd1otqKtW9xmidJ4CFRX1V9KWmsBbtxrgMtDColq3w,40
+cardio-2025.8.1.dist-info/METADATA,sha256=xAxvU4IGTLBcLRuoJ-6rRphuAxz4NQv3g0KTJg5WjXw,3453
+cardio-2025.8.1.dist-info/RECORD,,

cardio-2025.8.1.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: uv 0.8.13
+Root-Is-Purelib: true
+Tag: py3-none-any

{cardio-2023.1.2.dist-info → cardio-2025.8.1.dist-info}/entry_points.txt

@@ -1,2 +1,3 @@
 [gui_scripts]
 cardio = cardio.app:main
+

cardio-2023.1.2.dist-info/LICENSE

@@ -1,15 +0,0 @@
-Apache Software License 2.0
-
-Copyright (c) 2023, Davis Marc Vigneault
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.

cardio-2023.1.2.dist-info/METADATA

@@ -1,69 +0,0 @@
-Metadata-Version: 2.1
-Name: cardio
-Version: 2023.1.2
-Summary: A simple web-based viewer for 4D ('cine') medical imaging data.
-Author-email: Davis Marc Vigneault <davis.vigneault@gmail.com>
-Maintainer-email: Davis Marc Vigneault <davis.vigneault@gmail.com>
-License: Apache Software License 2.0
-        
-        Copyright (c) 2023, Davis Marc Vigneault
-        
-        Licensed under the Apache License, Version 2.0 (the "License");
-        you may not use this file except in compliance with the License.
-        You may obtain a copy of the License at
-        
-        http://www.apache.org/licenses/LICENSE-2.0
-        
-        Unless required by applicable law or agreed to in writing, software
-        distributed under the License is distributed on an "AS IS" BASIS,
-        WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-        See the License for the specific language governing permissions and
-        limitations under the License.
-        
-Project-URL: repository, https://github.com/dvigneault/cardio
-Keywords: Medical,Imaging,4D,Visualization
-Classifier: Development Status :: 3 - Alpha
-Classifier: Environment :: Web Environment
-Classifier: Intended Audience :: Healthcare Industry
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Natural Language :: English
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: JavaScript
-Classifier: Topic :: Scientific/Engineering :: Image Processing
-Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Classifier: Topic :: Scientific/Engineering :: Visualization
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: trame
-Requires-Dist: vtk
-Requires-Dist: itk
-Requires-Dist: tomlkit
-Requires-Dist: numpy
-Provides-Extra: dev
-Requires-Dist: black ; extra == 'dev'
-Requires-Dist: isort ; extra == 'dev'
-Requires-Dist: pip-tools ; extra == 'dev'
-Requires-Dist: pytest ; extra == 'dev'
-Requires-Dist: bumpver ; extra == 'dev'
-Requires-Dist: build ; extra == 'dev'
-Requires-Dist: twine ; extra == 'dev'
-
-# Cardio
-
-`cardio` is a simple web-based viewer for 4D ('cine') medical imaging data.  `cardio` is able to render sequences of mesh files (e.g., `\*.obj` files) and volume renderings of image files (e.g. \*.nii.gz files).  `cardio` is launched from the commandline and configured using a TOML file.
-
-## Quickstart
-
-```bash
-$ python -m venv .venv
-$ . ./.venv/bin/activate
-(.venv) pip install cardio
-(.venv) cardio --config ./examples/cfg-example.toml
-
-App running at:
- - Local:   http://localhost:8080/
- - Network: http://127.0.0.1:8080/
-```

cardio-2023.1.2.dist-info/RECORD

@@ -1,16 +0,0 @@
-__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cardio/__init__.py,sha256=urw8Xx4cNfgYfH4mqVXe6udtdluu-Pz-9XN2irQUHIg,316
-cardio/app.py,sha256=nFMzMtLobvopWMwPKsb_Qw9gQBAw4aiUNuq8WAkAqQg,607
-cardio/logic.py,sha256=te1MTzJTPPP3coe9ntvLBK19irFI0e49tjH2fwmQ_54,4183
-cardio/mesh.py,sha256=Jk2LMYx1XdV8RUU83oEJJ5k5BUS39i1tglEXgdmD3nY,1306
-cardio/object.py,sha256=sur65ZkkLd6aThnL0DBNo69XkPQ4Ek_Og60Wcp6f8bI,436
-cardio/scene.py,sha256=wltKTRAn-RVw9-FzJYonfNxUc6hL4UeAf7wxt3t5BZQ,3182
-cardio/screenshot.py,sha256=VRBf9jZtkGzJ1-Gq4rFsazgTuwF9Y-qpq9LsYy2gcX0,744
-cardio/ui.py,sha256=oUh_K-SgbZ6cxDK40a7Wm6XCkOxvcXKHVbdRZthAi5o,7024
-cardio/volume.py,sha256=7sC6h9dUvZFDONFhUs2D9Cwwvsqyav7N_Z_l1rYgiWY,3882
-cardio-2023.1.2.dist-info/LICENSE,sha256=Bt7BKWq-r2ZQvNet9olLms6u19TxM9eU02hAxFnsBbQ,591
-cardio-2023.1.2.dist-info/METADATA,sha256=1hC2ucBt8fFmQ6SSg68bTYdtAhTUEB89gMCHhTHHR80,2743
-cardio-2023.1.2.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-cardio-2023.1.2.dist-info/entry_points.txt,sha256=sTB22uP2O9JPpPxExkCveTODevrcoIIMvmnx_gmp8AM,39
-cardio-2023.1.2.dist-info/top_level.txt,sha256=a10HKI2DqoBdJWkvEOeWgO7cPYy9XHVY2VOGso-7rxI,16
-cardio-2023.1.2.dist-info/RECORD,,

cardio-2023.1.2.dist-info/WHEEL

@@ -1,5 +0,0 @@
-Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
-Root-Is-Purelib: true
-Tag: py3-none-any
-

cardio-2023.1.2.dist-info/top_level.txt

@@ -1,2 +0,0 @@
-__init__
-cardio