cardio 2023.1.2__tar.gz → 2025.8.0__tar.gz

cardio-2025.8.0/PKG-INFO

@@ -0,0 +1,94 @@
+Metadata-Version: 2.3
+Name: cardio
+Version: 2025.8.0
+Summary: A simple web-based viewer for 3D and 4D ('cine') medical imaging data.
+Keywords: Medical,Imaging,3D,4D,Visualization
+Author: Davis Marc Vigneault
+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: isort ; extra == 'dev'
+Requires-Dist: pytest ; extra == 'dev'
+Requires-Dist: bumpver ; extra == 'dev'
+Requires-Dist: ruff>=0.12.10 ; 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 2025.8.0
+```
+
+### Developing
+
+Ensuring you have all required dependencies:
+
+```bash
+$ uv sync --all-extras
+```
+
+Pre-commit checklist:
+
+```bash
+$ isort .
+$ ruff format
+$ pytest -v
+```

cardio-2025.8.0/README.md

@@ -0,0 +1,40 @@
+# 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 2025.8.0
+```
+
+### Developing
+
+Ensuring you have all required dependencies:
+
+```bash
+$ uv sync --all-extras
+```
+
+Pre-commit checklist:
+
+```bash
+$ isort .
+$ ruff format
+$ pytest -v
+```

{cardio-2023.1.2 → cardio-2025.8.0}/pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["setuptools>61.0.0"]
-build-backend = "setuptools.build_meta"
+requires = ["uv_build>=0.8.13,<0.9.0"]
+build-backend = "uv_build"
 
 [project]
 name = "cardio"
-version = "2023.1.2"
+version = "2025.8.0"
 authors = [
     {name = "Davis Marc Vigneault", email = "davis.vigneault@gmail.com"}
 ]
@@ -23,14 +23,18 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Visualization",
 ]
 dependencies = [
-    "trame",
-    "vtk",
-    "itk",
-    "tomlkit",
-    "numpy",
+    "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",
 ]
-description = "A simple web-based viewer for 4D ('cine') medical imaging data."
-keywords = ["Medical", "Imaging", "4D", "Visualization"]
+description = "A simple web-based viewer for 3D and 4D ('cine') medical imaging data."
+keywords = ["Medical", "Imaging", "3D", "4D", "Visualization"]
 license = {file = "LICENSE"}
 maintainers = [
     {name = "Davis Marc Vigneault", email = "davis.vigneault@gmail.com"}
@@ -39,19 +43,24 @@ readme = "README.md"
 requires-python = ">=3.10"
 
 [project.optional-dependencies]
-dev = ["black", "isort", "pip-tools", "pytest", "bumpver", "build", "twine"]
+dev = [
+ "isort",
+ "pytest",
+ "bumpver",
+ "ruff>=0.12.10",
+]
 
 [project.gui-scripts]
 cardio = "cardio.app:main"
 
 [project.urls]
-repository = "https://github.com/dvigneault/cardio"
+repository = "https://github.com/sudomakeinstall/cardio"
 
 [tool.isort]
 profile = "black"
 
 [tool.bumpver]
-current_version = "2023.1.2"
+current_version = "2025.8.0"
 version_pattern = "YYYY.MM.INC0"
 commit_message = "ENH: Bump version from {old_version} => {new_version}"
 commit = true
@@ -66,3 +75,6 @@ push = false
 "src/cardio/__init__.py" = [
     '__version__ = "{version}"',
 ]
+"README.md" = [
+    'cardio {version}',
+]

{cardio-2023.1.2 → cardio-2025.8.0}/src/cardio/__init__.py

@@ -1,19 +1,27 @@
-from .object import Object
+from .logic import Logic
 from .mesh import Mesh
-from .volume import Volume
+from .object import Object
 from .scene import Scene
-from .logic import Logic
-from .ui import UI
 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
 
 __all__ = [
     "Object",
     "Mesh",
     "Volume",
+    "Segmentation",
     "Scene",
     "Screenshot",
     "UI",
     "Logic",
+    "load_preset",
+    "list_available_presets",
 ]
 
-__version__ = "2023.1.2"
+__version__ = "2025.8.0"

cardio-2025.8.0/src/cardio/app.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+
+# Third Party
+import pydantic_settings as ps
+import tomlkit as tk
+import trame as tm
+
+from . import __version__
+from .logic import Logic
+
+# Internal
+from .scene import Scene
+from .ui import UI
+
+
+class CardioApp(tm.app.TrameApp):
+    def __init__(self, name=None):
+        super().__init__(server=name, client_type="vue2")
+
+        # Add config file argument to Trame's parser
+        self.server.cli.add_argument(
+            "--config", help="TOML configuration file.", dest="cfg_file", required=False
+        )
+
+        # Add version argument
+        self.server.cli.add_argument(
+            "--version", action="version", version=f"cardio {__version__}"
+        )
+
+        # Create CLI settings source with Trame's parser - enable argument parsing
+        cli_settings = ps.CliSettingsSource(
+            Scene, root_parser=self.server.cli, cli_parse_args=True
+        )
+
+        # Parse arguments to get config file path (use parse_known_args to avoid conflicts)
+        args, unknown = self.server.cli.parse_known_args()
+        config_file = getattr(args, "cfg_file", None)
+
+        # Set the CLI source and config file on the Scene class temporarily
+        Scene._cli_source = cli_settings
+        Scene._config_file = config_file
+
+        try:
+            # Create Scene with CLI and config file support
+            scene = Scene()
+        finally:
+            # Clean up class attributes
+            if hasattr(Scene, "_cli_source"):
+                delattr(Scene, "_cli_source")
+            if hasattr(Scene, "_config_file"):
+                delattr(Scene, "_config_file")
+
+        Logic(self.server, scene)
+        UI(self.server, scene)
+
+
+def main():
+    app = CardioApp()
+    app.server.start(open_browser=False)
+
+
+if __name__ == "__main__":
+    main()

cardio-2025.8.0/src/cardio/assets/bone.toml

@@ -0,0 +1,42 @@
+name = "Bone"
+description = "Bone"
+
+ambient = 1.0
+diffuse = 1.0
+specular = 0.0
+
+[[transfer_functions]]
+
+[transfer_functions.opacity]
+[[transfer_functions.opacity.points]]
+x = -1024.0
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = 54.0
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = 536.0
+y = 0.1
+
+[[transfer_functions.opacity.points]]
+x = 3071.0
+y = 0.1
+
+[transfer_functions.color]
+[[transfer_functions.color.points]]
+x = -1024.0
+color = [0.0, 0.0, 0.0]
+
+[[transfer_functions.color.points]]
+x = 54.0
+color = [0.0, 0.0, 0.0]
+
+[[transfer_functions.color.points]]
+x = 536.0
+color = [1.0, 1.0, 1.0]
+
+[[transfer_functions.color.points]]
+x = 3071.0
+color = [1.0, 1.0, 1.0]

cardio-2025.8.0/src/cardio/assets/vascular_closed.toml

@@ -0,0 +1,78 @@
+name = "Vascular_Closed"
+description = "Vascular (Closed)"
+
+ambient = 0.7
+diffuse = 0.4
+specular = 1.0
+
+[[transfer_functions]]
+
+[transfer_functions.opacity]
+[[transfer_functions.opacity.points]]
+x = 150
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = 650
+y = 1.0
+
+[[transfer_functions.opacity.points]]
+x = 3071
+y = 1.0
+
+[transfer_functions.color]
+[[transfer_functions.color.points]]
+x = 150
+color = [1.0, 1.0, 1.0]
+
+[[transfer_functions.color.points]]
+x = 3071
+color = [1.0, 1.0, 1.0]
+
+[[transfer_functions]]
+
+[transfer_functions.opacity]
+[[transfer_functions.opacity.points]]
+x = -96.5
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = 269.0
+y = 0.05
+
+[[transfer_functions.opacity.points]]
+x = 474.5
+y = 0.0
+
+[transfer_functions.color]
+[[transfer_functions.color.points]]
+x = -96.5
+color = [1.0, 1.0, 1.0]
+
+[[transfer_functions.color.points]]
+x = 474.5
+color = [1.0, 1.0, 1.0]
+
+[[transfer_functions]]
+
+[transfer_functions.opacity]
+[[transfer_functions.opacity.points]]
+x = 120
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = 258.0
+y = 0.8
+
+[[transfer_functions.opacity.points]]
+x = 320
+y = 0.0
+
+[transfer_functions.color]
+[[transfer_functions.color.points]]
+x = 120
+color = [1.0, 0.0, 0.0]
+
+[[transfer_functions.color.points]]
+x = 320
+color = [1.0, 1.0, 0.0]

cardio-2025.8.0/src/cardio/assets/vascular_open.toml

@@ -0,0 +1,54 @@
+name = "Vascular_Open"
+description = "Vascular (Open)"
+
+ambient = 0.7
+diffuse = 0.4
+specular = 1.0
+
+[[transfer_functions]]
+
+[transfer_functions.opacity]
+[[transfer_functions.opacity.points]]
+x = -96.5
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = 269.0
+y = 0.05
+
+[[transfer_functions.opacity.points]]
+x = 474.5
+y = 0.0
+
+[transfer_functions.color]
+[[transfer_functions.color.points]]
+x = -96.5
+color = [1.0, 1.0, 1.0]
+
+[[transfer_functions.color.points]]
+x = 474.5
+color = [1.0, 1.0, 1.0]
+
+[[transfer_functions]]
+
+[transfer_functions.opacity]
+[[transfer_functions.opacity.points]]
+x = 117
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = 246.0
+y = 0.87
+
+[[transfer_functions.opacity.points]]
+x = 319
+y = 0.0
+
+[transfer_functions.color]
+[[transfer_functions.color.points]]
+x = 117
+color = [1.0, 0.0, 0.0]
+
+[[transfer_functions.color.points]]
+x = 319
+color = [1.0, 1.0, 0.0]

cardio-2025.8.0/src/cardio/assets/xray.toml

@@ -0,0 +1,42 @@
+name = "Radiograph"
+description = "Radiograph"
+
+ambient = 1.0
+diffuse = 1.0
+specular = 0.0
+
+[[transfer_functions]]
+
+[transfer_functions.opacity]
+[[transfer_functions.opacity.points]]
+x = -1024.0
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = -200.0
+y = 0.0
+
+[[transfer_functions.opacity.points]]
+x = 300.0
+y = 0.01
+
+[[transfer_functions.opacity.points]]
+x = 3071.0
+y = 0.01
+
+[transfer_functions.color]
+[[transfer_functions.color.points]]
+x = -1024.0
+color = [0.0, 0.0, 0.0]
+
+[[transfer_functions.color.points]]
+x = -200.0
+color = [0.0, 0.0, 0.0]
+
+[[transfer_functions.color.points]]
+x = 300.0
+color = [1.0, 1.0, 1.0]
+
+[[transfer_functions.color.points]]
+x = 3071.0
+color = [1.0, 1.0, 1.0]